Update post repository name from "EMC_post" to "UPP" #433

KateFriedman-NOAA · 2021-08-26T20:03:24Z

The name of the EMC_post repository on GitHub will be changing to UPP the week of September 6th. Email from @HuiyaChuang-NOAA :

In an effort to unify naming conventions for UPP across the board, we are planning to change the name of UPP repository
on Github from "EMC_post" to "UPP" in the week of September 6.

If you currently have a UPP fork, you will need to manually change the name yourself.  If you have a script that checks
out UPP code from Github, please update your script to use the new name "UPP". More information on the impacts of
repository name change can be found in the Github documentation. 

Updates will be posted to the UPP Github Discussions board; questions may also be posted to the board and will be
answered by code managers.  

Please feel free to contact me or the other two UPP code managers with any questions:
Wen.Meng@noaa.gov
fossell@ucar.edu

Will need to update repo name for EMC_post in both Externals.cfg and checkout.sh. Will need to update the develop, operations, and GEFS branches. Most other branches can be updated via a sync merge from develop or operations. Thankfully GitHub will forward branches/tags that still point to "EMC_post" to the newly renamed "UPP" repo so no tags/branches should break from this change.

Tasks:

change repo name in develop branch
change repo name in operations branch
change repo name in release/gefs_v12 branch

The text was updated successfully, but these errors were encountered:

KateFriedman-NOAA · 2021-08-26T20:38:20Z

ON HOLD pending actual name change.

HuiyaChuang-NOAA · 2021-08-26T21:21:11Z

@KateFriedman-NOAA
Thank you for responding to this. @WenMeng-NOAA and I will send out an announcement when the change is made.

KateFriedman-NOAA · 2021-09-07T19:37:37Z

Change to rename the EMC_post repo to UPP has occurred. Quickly testing checkout, build, and single free-forecast cycle on Hera to confirm no issues.

WenMeng-NOAA · 2021-09-07T19:39:51Z

@KateFriedman-NOAA Thanks for verifying.

- the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: NOAA-EMC#433

…anch - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: NOAA-EMC#433

KateFriedman-NOAA · 2021-09-09T15:13:34Z

Initiated PRs to update the EMC_post/UPP checkout in both the develop (#441) and operations (#442) branches. Added @WenMeng-NOAA as reviewer in both PRs to sign off on repo name change in checkout.

…anch (#442) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433

- the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433

KateFriedman-NOAA · 2021-09-21T18:46:17Z

@WalterKolczynski-NOAA Last item for this issue is to update the repo name in the GEFS branch. Can close once complete.

KateFriedman-NOAA · 2021-10-12T14:36:31Z

@XianwuXue-NOAA updated the repo name in his fork branch which will come back to the auth repo later. See change here:

https://github.com/XianwuXue-NOAA/global-workflow/blob/feature/gefs_v12_github_port2acorn/sorc/checkout.sh

All done, closing issue.

Squashed commit of the following: commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb70 e5cd6369 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11e 0740b5b6 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74b fc48af56 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013dec ce66c74b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea5 7a166da9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2 5c042e08 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4 cfca8bb2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f5558 fba8cef5 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d1 e08f5558 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb3 e08f5558 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f b2879fe9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature branch for testing Refs: #178 commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:41:32 2021 +0000 Correct if-statement syntax in config.init Refs: #178 commit 005d33d7b100b279e0db5290824c3e7acabfa4ba Merge: 5ec376ba e09a398f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 15:23:05 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e09a398f1cedc7252219e75bf0b319d2601bc8df Merge: e3fcfebc 6bad810b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri May 21 09:58:49 2021 -0400 Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade EMC_verif-global v2.0.0 major release updates commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a Author: Mallory Row <mallory.row@noaa.gov> Date: Fri May 21 13:55:13 2021 +0000 Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit 9cf615d11b096ea4843f4e5938a6a65f3500df49 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 20 20:10:18 2021 +0000 Modulefile updates for testing with waves on - updated ww3 and base modulefiles to add modules and update some - added new: pio/2.5.2i, fms/2020.04.03 - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6 Refs: #164 commit b155ff37040658703168268d4e58fe4e6b45a50d Author: Mallory Row <mallory.row@noaa.gov> Date: Thu May 20 15:00:04 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit cae62e3f47e245e70fcf3721fb4c022ea11c059f Merge: 8def77af e3fcfebc Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 19 19:45:05 2021 +0000 Sync merge with develop and WW3 build updates - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack - WW3 build updates: revert back to separate module files for build; address modulefile reorganization in separate issue - remove CCPP option with system build, doing CCPP by default now Refs: #164 commit 5ec376bababd935e4f3b15c4754105f5bd750657 Merge: 6b6b9ed3 e3fcfebc Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed May 19 18:24:31 2021 +0000 Merge remote-tracking branch 'origin/develop' into issue178 * origin/develop: change fv3gfs checkout head fixed a compilation error, NEMs/exe existing, in hera build_fv3.sh with ATM fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 bugfix for not removing last point from list in wave post pnt jobs changes added in link_fv3gfs for fix_aer changed fix dir for link_fv3gfs changes on build_fv3.sh and symlinks to optical data files instead of cp Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination updated config.fcst testing merra2 workflow in hera update merra2 before a new pull request Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions udate config.base.emc.dyn high resolution MERRA2 data used fixed a bug related to orion added merra2 input and update diag_table merra2 workflow for orion Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) commit 4641c5d206a95e0e66276fa86d46ecd580213fd5 Merge: eff8a125 e3fcfebc Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 19 14:51:19 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit e3fcfebc1ff9c9f9ceda7b775de0c34117de6459 Merge: 95e0dffe fa5d1e2b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 19 10:02:19 2021 -0400 Merge pull request #254 from AnningCheng-NOAA/merra2 Addition of support for MERRA2 commit fa5d1e2ba242a08e26cb7bac8c68b700a83d1d60 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue May 18 10:41:16 2021 -0400 change fv3gfs checkout head commit 283c4a044847bbadd0cef46e14dde4de97abe986 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 17 15:56:56 2021 -0400 fixed a compilation error, NEMs/exe existing, in hera commit 6b574160f94329754677e7f4541ab07c44185bb0 Author: anning.cheng <anning.cheng@noaa.gov> Date: Fri May 14 13:44:18 2021 +0000 build_fv3.sh with ATM commit dfc8aa9a2cf5370fff38520d2a28f3960be3b583 Merge: bf5d1106 95e0dffe Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed May 12 20:11:44 2021 +0000 Merge remote-tracking branch 'upstream/develop' into merra2 commit eff8a1258aa70c061fe69697388f8914935726ee Merge: b1ad0b96 95e0dffe Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 12 19:15:17 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit 95e0dffea435af17be9150fcd0c842763768b45f Merge: fc727f40 dd4d1879 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 12 14:51:10 2021 -0400 Merge pull request #323 from NOAA-EMC/sync/operations_v16.0.9 Bring operations branch v16.0.9 changes into develop commit dd4d1879093516a7950c9e0e59f6e44e462199f6 Merge: fc727f40 68b9157b Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 10 16:40:13 2021 +0000 Merge remote-tracking branch 'origin/operations' into sync/operations_v16.0.9 * origin/operations: bugfix for not removing last point from list in wave post pnt jobs Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) Refs: #309 commit 8def77afd4a9f1cd6cdca42c956bc7ebf675a58d Merge: c6e2a96e d46e8cf4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 10 11:45:02 2021 -0400 Merge pull request #322 from JessicaMeixner-NOAA/hpcstackww3 Updates for ww3 pre and post exec builds for hpc-stack commit d46e8cf49aff0dbf72e457f1177e10e6f50252a6 Author: Jessica Meixner <Jessica.Meixner@noaa.gov> Date: Mon May 10 15:31:56 2021 +0000 update for ww3_pre/post build: -- remove ww3 specific module files -- updated module base files to be in sync with ufs-weather-model except that jasper is a more recent version which is needed for ww3_grib -- added extra ww3 execs needed for this branch -- added ww3prepost build to build_all and partial build commit c6e2a96e86611cce00455609d9be803d580e7bc0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:30:13 2021 +0000 Change fix file linking to scan for possible subfolders in set - instead of providing subfolder names, scan for subfolders in FIX_DIR path and then create symlinks based on existing subfolders in set - will not have to keep updating list of subfolders now Refs: #164 commit aa1d1e9ca1d8521ef22e1bdb654d4a70e7b1e29e Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:27:13 2021 +0000 Change CCPP_SUITE from FV3_GFS_v16beta to FV3_GFS_v16 - newer ufs-weather-model hash supports FV3_GFS_v16 suite Refs: #164 commit 1aea3ee393c99d4f76556fbbdbebc43f629558c2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:30:06 2021 +0000 Add build script and modulefiles for WW3 build - WW3 execs no longer built by FV3 build, need separate build now - add new build_ww3prepost.sh script for building WW3 execs in ufs-weather-model checkout - add modulefiles for WCOSS-Dell, Hera, and Orion Refs: #164 commit 214431a2c04f6e685e966810621fc2fae771d2f5 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:26:00 2021 +0000 Update WAFS execs to include .x - update WAFS exec names in link_fv3gfs.sh to include ".x" extension that was added with new version Refs: #164 commit eb1613764794a35d165e55423682ed592b2aaacb Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:22:06 2021 +0000 ufs-weather-model hash update for WW3 support with hpc-stack - update ufs-weather-model hash to 554aedcd63e4a7c5012570406132eaf76e249ca9 - update build_fv3.sh for new compile arguments for CCPP/WW3 build Refs: #164 commit b1ad0b96328a54112ecc13ff4b71dcc08556a8c1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 5 14:13:58 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.1 Refs: #315 commit c206e8d2606f14ee6188740f881673ff512b866b Author: Mallory Row <mallory.row@noaa.gov> Date: Mon May 3 19:16:42 2021 +0000 Fix typo in config.metp There was a typo in the grid-to-obs METviewer related config variables. The variables started with "g2g1" instead of "g2o1". Refs: #315 commit f9013decd5af75f66eda619175bacc7549f4746a Author: Brian Curtis <Brian.Curtis@noaa.gov> Date: Mon May 3 14:37:13 2021 -0400 Files to test for python3 compatibility commit 858f216330d7ab71137afe6331f6576fec413aee Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:19:56 2021 +0000 Update EMC_post, UFS_UTILS, EMC_gfs_wafs versions in Externals.cfg Refs: #164 commit 6ce83363726ece6dbd34719430dd44f5e63bbc3c Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:14:54 2021 +0000 Component updates for UPP, WAFS, UFS_UTILS - new tag in checkout for UFS_UTILS to use hpc/1.1.0 - new hash in checkout for UPP/EMC_post to support GTG and GTG code copy fix - new hash in checkout for WAFS/EMC_gfs_wafs to support hpc-stack - build script update for WAFS (cmake/stack) - WAFS GCIP config update to fix runtime error Refs: #164 commit 709095709ca60498d05ea0f519b494501e1ecdf2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:11:51 2021 +0000 Update util_shared to 1.3.0 on WCOSS-Dell - version changed in production for v16.0.9 footer fix Refs: #164 commit bf5d110632fc67653441e6830bfdcdddda906706 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 3 10:53:37 2021 -0400 fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 commit fb47a5a0f7391f670461b00eaf324c3b0102ef1f Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Apr 28 17:50:15 2021 +0000 Update TC_tracker version in config.vrfy - new TC_tracker.v1.1.15.4 was made available by Jiayi Peng - new version supports hpc-stack on supported platforms - installed locally on WCOSS-Dells, Hera, and Orion Refs: #164 commit 587ac0c914430d5b887327d7c566c452d2eace62 Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed Apr 28 10:36:49 2021 -0400 changes added in link_fv3gfs for fix_aer commit 48690cd07ceeb90c6808346a04a31a6166505c86 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed Apr 28 14:00:46 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.0 commit 1d0e0c29979101b451f1fda265af3f9a716bb9de Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Apr 27 19:33:09 2021 +0000 Reverting resource related changes - will commit resource adjustments separately Refs: #164 commit 101905ce4d92a544d353700b0acdc137aa61b088 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue Apr 27 14:15:59 2021 -0400 changed fix dir for link_fv3gfs commit 7cd6e0e3000a47b39fa0c7e75ad66150e96385d8 Author: Mallory Row <mallory.row@noaa.gov> Date: Fri Apr 23 14:44:03 2021 +0000 Fix setting of 'SDATE_GFS' for free forecast XML In the workflow XML for free forecasts there is no SDATE_GFS variable. The 'SDATE_GFS' variable was changed to be set to the value of 'SDATE'. Refs: #315 commit d34b99d4e3d369b784fd9d2c639a0bddd1bbfc0c Author: Mallory Row <mallory.row@noaa.gov> Date: Fri Apr 23 12:59:51 2021 +0000 Clean up and add new settings in metp.sh SDATE_GFS was added into the script preamble following the addition of the variable being added as a rocoto exported environment variable for metp tasks. Config.vrfy was removed from the list of relevant configs to source. Variables CDATEm1 and PDYm1 were removed and replaced with VDATE. VDATE is the verification date to be done by the metp tasks based on VRFYBACK_HRS set in config.metp. Lines were added to catch the exit status of VERIFGLOBAL_SH and to exit if not succesfully run so it can be caught by rocoto. Refs: #315 commit 998f1a454427dedd46bb20b36e381bedbdf3e349 Author: Mallory Row <mallory.row@noaa.gov> Date: Fri Apr 23 12:49:38 2021 +0000 Revamp of config.metp Following the EMC_verif-global configuration remake, config.metp has been revamped to support the new configuration settings. Refs: #315 commit 6a01ae405202b8984fe8efa73573d7fdba2b74d2 Author: Mallory Row <mallory.row@noaa.gov> Date: Thu Apr 22 17:17:14 2021 +0000 Add 'SDATE_GFS' rocoto env var for metp tasks The connector script between EMC_verif-global and global-workflow run_verif_global_in_global_workflow.sh (housed in EMC_verif-global) contains a new feature that checks the maximum forecast hour for verification is the hour's initialization date is equal to or after the first GFS cycle initialization. If the date is before, the maximum forecast hour is adjusted to the maximum hour relative to the forecast verification date and the first GFS cycle initialization. This feature was added to cut down on METplus calls being done on data that don't exist. Refs: #315 commit dfec5816add3c56721360a418ec9f3459cfd4d8c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 15:27:56 2021 +0000 Update UFS_UTILS hash to 9d9dd23e37a51fcc5ff6b7499b834c85ab32e5f3 Refs: #164 commit be564bb85eeefbb1699992e0ed4f0705e4e2ee24 Author: anning.cheng <anning.cheng@noaa.gov> Date: Thu Apr 22 11:22:02 2021 -0400 changes on build_fv3.sh and symlinks to optical data files instead of cp commit 15c6619c6e211eb67ca6aa5c995e4a3bf4cf586f Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 14:03:46 2021 +0000 Adjust C768 fcst thread value for reduced node usage - change C768 nth_fv3_gfs value from 7 to 2 Refs: #164 commit ece41632a76e697184a46bb2a428c35ccdf08305 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Apr 22 13:58:22 2021 +0000 Add separate gfs resource variables to fcst in config.resources Refs: #164 commit 00c18b5e341d601fd83da2f9df2ac928e8dcf7c8 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 13:44:13 2021 +0000 Update FIX_DIR paths in link_fv3gfs.sh - change platform FIX_DIR paths from fix_nco_gfsv16 set to developmental fix set for v17+ Refs: #164 commit b6c392c7569ed909d6b0b27c0f6a4f828b7acdfd Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 13:40:25 2021 +0000 Set DO_WAVE=NO in config.base - set default DO_WAVE setting to NO in config.base.emc.dyn - turn off waves until hpc-stack for WW3 execs build is ready Refs: #164 commit 2b703d335b8e3e97c9764bd60d87188ed11938fd Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 13:17:28 2021 +0000 Set WAFS checkout to be optional with -o flag - add checkout_wafs to -o flag settings Refs: #164 commit 305bf5e0fb3c665cf71f10023feed1a121be329b Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 13:01:04 2021 +0000 Update Externals.cfg to match checkout.sh versions Refs: #164 commit 3cc02d507df48e2b9f99163d737123e5b5c716c0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 12:52:46 2021 +0000 Update GLDAS and UFS_UTILS checkouts - update GLDAS checkout to gldas_gfsv16_release.v1.15.0 tag; corrects build on Orion - update UFS_UTILS checkout to 4f44bf89 hash of develop (supports stack) Refs: #164 commit 9d733f87203ebd2298d22c0ac9491520bae60983 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Apr 22 12:15:13 2021 +0000 Add support for separate gfs thread values - nth_fv3_gfs was added to configs, add support to setup scripts for resource calculations Refs: #164 commit 4c64dce093fb3925b40b2a3f0b57fd196b14d92c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Apr 22 12:14:21 2021 +0000 Reduce npe_wav_gfs from 440 to 140 to dev users Refs: #164 commit 35c16e3aafc3addd3d24225880b5319332cca97a Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Apr 22 12:12:16 2021 +0000 Add wgrib2 module load to module_base.wcoss_dell_p3 - add wgrib2/2.0.8 module load - add setting of WGRIB2 to equal wgrib2 Refs: #164 commit 6b6b9ed3949c2e3ca3d697ffd3bb3a65ec728744 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon Apr 12 17:13:06 2021 +0000 getic and init job updates for v16 in ops - update GFSv16 implementation cycle in config if-blocks to be 2021032100 - add note about missing ops data on HPSS for 2021032106 cycle - add run_v16.chgres.sh as default RUNICSH script Refs: #178 commit 48ea7abd9fe4cfd0e774c92383948c9bb477a905 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon Apr 12 17:10:59 2021 +0000 Low resolution resource adjustments - C96, C192, and C384 config.fv3 resource updates for successful jobs - provided by Jun Wang and Fanglin Yang - tested on Hera Refs: #178 commit b55ecf8e5ae761ddc8e3897411aceb4e0529e106 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Apr 6 15:34:05 2021 +0000 Remove Tide/Gyre reference from machine-setup.sh Refs: #164 commit ab488f1aeb383d84a67b37e47a888d58662cf82f Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Apr 6 15:33:11 2021 +0000 Update OznMonBuild, RadMonBuild and module_base for hpc-stack on WCOSS-Dell Refs: #164 commit 384440ced59c18af777f7f9bb30016f3e71a1c31 Merge: 2f6d7ab0 fc727f40 Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon Mar 22 17:15:27 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack * origin/develop: Add two WAFS sorc folders to .gitignore Remove unneeded builds from build_all and partial build Delete unneeded files after workflow utils build was converted to cmake Remove global_chgres exec symlink from link_fv3gfs.sh Refs: #164 commit f35e6090bcf097355e691266bbc12ace6591c150 Merge: 5c77500b fc727f40 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon Mar 22 15:48:55 2021 +0000 Merge remote-tracking branch 'upstream/develop' into issue178 * upstream/develop: Add two WAFS sorc folders to .gitignore Remove unneeded builds from build_all and partial build Delete unneeded files after workflow utils build was converted to cmake Refs: #178 commit 5c77500bc4742a840a26f05aedffe2aca3e15ec7 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon Mar 22 15:44:40 2021 +0000 Add exit in init.sh when C768 v16 warm starts detected Exit init.sh and init job when high res C768 v16 warm starts are detected and running chgres_cube is not needed. Refs: #178 commit fc727f405afd4948ee99be1c13c9f2541405cc8b Merge: 258b342d 7582541c Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Mar 10 16:40:18 2021 -0500 Merge pull request #288 from NOAA-EMC/feature/issue272 Post-cmake cleanup and decommissioning commit 7582541c3b4ec182756ad1fa9164c21e0345f058 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Mar 10 20:08:43 2021 +0000 Add two WAFS sorc folders to .gitignore - two missing WAFS symlinks were added to link_fv3gfs.sh in prior commit; include them in gitignore file now Refs: #272 commit 4f7243bc68164faf0008893467c5a2ea53d216ae Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Mar 9 18:07:23 2021 +0000 Remove global_chgres exec from link_fv3gfs.sh; no longer exists from UFS_UTILS Refs: #178 commit fcd720edef1fe242c27d543f445bb3b4ee4fe9ec Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Mar 9 17:54:51 2021 +0000 Remove unneeded UFS_UTILS symlinks in link_fv3gfs.sh Refs: #178 commit 2f6d7ab06b3be6eaedb3406efca77ded61ef7aca Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Mar 9 17:41:14 2021 +0000 Module base updates for WCOSS-Dell, Hera, and Orion - add zlib module load - reorder wgrib2, hdf5, and netcdf module loads to accommodate module dependencies Refs: #164 commit 1285d803fd402945ebc03eb42eb8bfa3d2aa10da Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Mar 9 10:59:09 2021 -0600 Update GSI checkout to clone GSI-master @ 9c1fc15 Refs: #164 commit 14736c8320bec43651208950c16ea85ae2372985 Merge: e6a9e576 bea02f8a Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Mar 9 16:56:42 2021 +0000 Merge branch 'feature/hpc-stack' of https://github.com/NOAA-EMC/global-workflow into feature/hpc-stack * 'feature/hpc-stack' of https://github.com/NOAA-EMC/global-workflow: Correct if-block syntax in config.postsnd and config.wavepostbndpnt after testing setup scripts FHMAX_WAV_IBP variable check for wavepostbndpnt job Bufr sounding job update Add config.resources.nco.static ecflow forecast job resource updates from NCO v16.0.7 install Update EMC_verif-global tag to verif_global_v1.13.5 Add missing symlinks for WAFS source code folders Update EMC_gfs_wafs tag to gfs_wafs.v6.0.19 Remove KEEPDATA from config.base.nco.static Pull in config changes from NCO v16.0.7 install Pull in workflow changes from NCO v16.0.7 install Update EMC_verif-global tag to verif_global_v1.13.4 ecFlow resource adjustments from NCO for forecast and post jobs issue #257 shorten run time on Mars Dell1 file system commit e6a9e576744a1c245148bdc4b967a5674c9416b5 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Mar 9 16:55:41 2021 +0000 Remove UFS_UTILS symlinks no longer needed in link_fv3gfs.sh Refs: #164 commit 370e81474ce8f4076b0853b37de7da9c65d65c88 Merge: 364e46ff 258b342d Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Mar 9 16:14:40 2021 +0000 Merge remote-tracking branch 'upstream/develop' into issue178 * upstream/develop: Correct if-block syntax in config.postsnd and config.wavepostbndpnt after testing setup scripts FHMAX_WAV_IBP variable check for wavepostbndpnt job Bufr sounding job update Add config.resources.nco.static ecflow forecast job resource updates from NCO v16.0.7 install Update EMC_verif-global tag to verif_global_v1.13.5 Add missing symlinks for WAFS source code folders Update EMC_gfs_wafs tag to gfs_wafs.v6.0.19 Remove KEEPDATA from config.base.nco.static Pull in config changes from NCO v16.0.7 install Pull in workflow changes from NCO v16.0.7 install remove flags that were not present in Makefiles update jasper to 2.x.25. remove compiler flag in fv3nc2nemsio Update EMC_verif-global tag to verif_global_v1.13.4 another use of _d where an _4 is needed Adjust how target is set for build_workflow_utils Add workflow_utils to build_all and link scripts copy/paste error from enkf_chgres_recenter.fd to enkf_chgres_recenter_nc.fd. When going from nemsio to netcdf, the linking of ip, sp and w3nco changed from _d to _4. update .gitignore to exclude build and install directories as well as compiled files. bugfix in build_workflow_utils.sh hack. nceplibs-ncio now creates the module ncio and not fv3gfs_ncio. Update EMC_verif-global tag to verif_global_v1.13.4 add cmake build capability for workflow utilities ecFlow resource adjustments from NCO for forecast and post jobs issue #257 shorten run time on Mars Dell1 file system Refs: #178 commit 364e46ff2acabed7bd9f6cb07ca10aa19033a980 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Mar 9 16:08:57 2021 +0000 Add pull of gdas wave restart files in getic.sh if DO_WAVE=YES Refs: #178 commit bea02f8a6fc496794471e57aa75e030092027bd5 Merge: fd50508f 258b342d Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon Mar 8 14:02:51 2021 -0600 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack * origin/develop: Correct if-block syntax in config.postsnd and config.wavepostbndpnt after testing setup scripts FHMAX_WAV_IBP variable check for wavepostbndpnt job Bufr sounding job update Add config.resources.nco.static ecflow forecast job resource updates from NCO v16.0.7 install Update EMC_verif-global tag to verif_global_v1.13.5 Add missing symlinks for WAFS source code folders Update EMC_gfs_wafs tag to gfs_wafs.v6.0.19 Remove KEEPDATA from config.base.nco.static Pull in config changes from NCO v16.0.7 install Pull in workflow changes from NCO v16.0.7 install Update EMC_verif-global tag to verif_global_v1.13.4 ecFlow resource adjustments from NCO for forecast and post jobs issue #257 shorten run time on Mars Dell1 file system Refs: #164 commit e9e1f3ba976f053c6738d95d6de673a065d293c1 Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon Mar 8 19:54:24 2021 +0000 Remove unneeded builds from build_all and partial build - remove build sections in build_all.sh that ran builds that are now consolidated into build_workflow_utils.sh - remove build options in partial build script and config that are now consolidated into workflow_utils build Refs: #272 commit 26fa8c355c241a64d19097da3caa54cba0e46b77 Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon Mar 8 19:38:45 2021 +0000 Delete unneeded files after workflow utils build was converted to cmake - remove modulefiles that are no longer needed; consolidated into new workflow_utils.* modulefiles - remove build scripts that are no longer needed; consolidated into new build_workflow_utils.sh script Refs: #272 commit 258b342d5b6535cf87973105d770a63f4245d44a Merge: f6aa6939 729631d6 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Mar 8 12:59:46 2021 -0500 Merge pull request #282 from NOAA-EMC/feature/issue238 GFSv16.0.7 changes from NCO commit 729631d66f72ba8a3929e4927129d000879c9a1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon Mar 8 17:40:17 2021 +0000 Correct if-block syntax in config.postsnd and config.wavepostbndpnt after testing setup scripts Refs: #238 commit a1edf0de4deaccbf7f77f2fb4d24d1ca96c26171 Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon Mar 8 17:21:05 2021 +0000 FHMAX_WAV_IBP variable check for wavepostbndpnt job - add variable override in exgfs_wave_post_bndpnt.sh for FHMAX_WAV_IBP - add check to config.wavepostbndpnt for when FHMAX_GFS is less than FHMAX_WAV_IBP; set FHMAX_WAV_IBP to equal FHMAX_GFS when shorter gfs forecast than 180hrs; resolves runtime error with wavepostbndpnt job waiting for forecast output that will never arrive Refs: #238 commit ac76613f33f7d196a1d04972bc7c975d579da571 Merge: 0f97ccda f6aa6939 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon Mar 8 10:09:47 2021 -0600 Merge remote-tracking branch 'upstream/develop' into merra2 * upstream/develop: remove flags that were not present in Makefiles update jasper to 2.x.25. remove compiler flag in fv3nc2nemsio Update EMC_verif-global tag to verif_global_v1.13.4 another use of _d where an _4 is needed Adjust how target is set for build_workflow_utils Add workflow_utils to build_all and link scripts copy/paste error from enkf_chgres_recenter.fd to enkf_chgres_recenter_nc.fd. When going from nemsio to netcdf, the linking of ip, sp and w3nco changed from _d to _4. update .gitignore to exclude build and install directories as well as compiled files. bugfix in build_workflow_utils.sh hack. nceplibs-ncio now creates the module ncio and not fv3gfs_ncio. add cmake build capability for workflow utilities Update Fit2Obs tag to newm.1.3 for bugfix Update Fit2Obs tag to newm.1.3 for bugfix Update EMC_verif-global tag for Hera bug Pull in nwpara/gfsv16.0.6 updates for parse-storm-type.pl HOTFIX: Update EMC_verif-global tag for Hera bug Issue #1 and issue #238 - update Externals.cfg to match checkout.sh updates for v16.0.6 move errchk definition from script to job for wave prdgen and gempak adding definition of errchk which was undefined in these scripts Issue #179 and issue #243 - update Fit2Obs to newm.1.2 tag and correct COMROOT path for Hera HOTFIX: Issue #241 - update EMC_verif-global tag to remove use of /tmp space Issue #1 and issue #233 - update GLDAS tag to gldas_gfsv16_release.v1.13.0 Issue #1 and issue #241 - update EMC_verif-global tag Issue #1 and issue #238 - remove ak_10m grid from config.wave and update checkout.sh tags for ufs-weather-model and EMC_gfs_wafs Issue #179 - update to config.vrfy for Fit2Obs tag which supports Orion Issue #1 and issue #226 - update UPP tag to upp_gfsv16_release.v1.1.3 in Externals.cfg Issue #1 and issue #226 - update UPP tag to upp_gfsv16_release.v1.1.3 Issue #233 - remove unnecessary extra space in tag line for gldas Issue #233 - update GLDAS tag to gldas_gfsv16_release.v1.13.0 Issue #1 and issue #226 - update exgfs_atmos_grib2_special_npoess.sh for dbn_alert modified: exglobal_forecast.sh The breakpoint restart only works for the first restart from a breakpoint. Restart files written in RERUN_RESTRAT after the first restart has a 3-hour time shift for DO_IAU=YES cases. Forecasts starting from the 2nd breakpoint and beyond will fail becasue of incorrect initial conditins. This commit fixes this bug. issue #227 reducing output bufr files to 64 levels per NCO request issue #227 reducing output bufr files to 64 levels per NCO request Issue #1: update ecflow to be consistent with NCO's gfs.v16.0.4 and update checkout to bring in new UPP tag (see issue #226) Upaded ush script scale_dec.sh Updated scripts gfs_v16.0 Issue #1 and issue #220 - set C192/C96/C48 npe_eobs back to dev values for develop Issue #1 - add grib_util module load to several analysis ecflow scripts Issue #189 - update ufs-weather-model hash Issue #201 - workaround for failing post000 job before hpc-stack solution Issue #1 - update WAFS tag to gfs_wafs.v6.0.17 for dbn_alert change Issue #1 - correct gridded wave parm files for v16.0.3 Issue #1 - changes from NCO for GFSv16.0.3 Issue #1 - update Externals.cfg with final tags for GFSv16.0.2 Fixes for issue #202 (FINDDATE) and issue #208 (postsnd.sh permissions) Issue #1 - correct permissions on jobs/rocoto/postsnd.sh Issue #1 - update gempak version to 7.3.3 in the ecflow gfs.ver file Issue #1 - update gempak and dumpjb versions to 7.3.3 and 5.1.0 respectively Script alert updates from NCO for wave downstream Add override for COMIN_WAV_RTOFS in emc mode for waveprep job Issue #197: place CDATE specific sections of config.anal and config.prep inside RUN_ENVIR=emc blocks. These sections are use for retrospective parallels and therefore do not need to be executed in operations (NCO). modified: JGLOBAL_FORECAST modified: JGLOBAL_FORECAST to make it work for both emc and nco running environments. modified: JGLOBAL_FORECAST A test showed that jobid is not defined in JGLOBAL_FORECAST running in the Rocoto environment. jobid is defined in ./env files. Defining DATA without sourcing ./env/$nachine.env caused the script to fail. Move the definitin of DATA after sourcing env parameters modified: checkout.sh to use WAFS tag gfs_wafs.v6.0.16 modified: checkout.sh to update UPP to upp_gfsv16_release.v1.1.1, a minor syntax bug fix modified: link_fv3gfs.sh to 1) use hard copies of external fix fields and executable for NCO installation 2) use soft links for all other files and directories for both NCO and EMC installations Compared local files in NCO implementation directory with release/gfs.v16.0.0 branch, changes made by NCO(Jen Yang) in the following files are either accepted or rejected. create a new branch release/gfsv16.0.0.nco to merge changes made by NCO in /gpfs/dell1/nco/ops/nwpara/gfs-v16/gfs.v16.0.1 back to EMC's repository update for the wave parm so that the wave model will look for the correct restart for when gfs is not run every cycle updates for checking if RTOFS files exist and only processing RTOFS files for needed fhr commit b644f792bbb939d6ab25957b93f812aa02b497a9 Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon Mar 8 15:07:34 2021 +0000 Bufr sounding job update - set DO_BUFRSND to NO by default - in config.postsnd, if FHMAX_GFS is less than 180 then set DO_BUFRSND to FHMAX_GFS Refs: #238 commit 86b0345a550a7128fd6420befcb793a94411e4db Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon Mar 8 14:09:40 2021 +0000 Add pull of IAU increment files off HPSS for free-forecast Refs: #178 commit efdf917a843cc301a2fe7d5386aea1e29dd02c46 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Fri Mar 5 21:29:22 2021 +0000 Update in wave prep script and add ability to pull warm starts - Update getic job to detect warm start config info and pull warm start RESTART files off HPSS and place in ROTDIR; just for retro ICs, will add ops after implementation - Add check to JGLOBAL_WAVE_PREP for prior cycle rtofs ROTDIR symlink; normally cycled mode would have already created this during prior cycle so added check for use in free-forecast mode Refs: #178 commit 65fce4ce9b2d7e63a0bd038fff1a206f8b4a5815 Merge: 084cb6aa 9027452b Author: kate.friedman <kate.friedman@noaa.gov> Date: Fri Mar 5 17:13:37 2021 +0000 Merge remote-tracking branch 'origin/release/gfsv16.0.0' into feature/issue238 * origin/release/gfsv16.0.0: Add config.resources.nco.static ecflow forecast job resource updates from NCO v16.0.7 install Refs: #238 commit be0ed38a53d2422923ccd5380d610785e61deafa Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Mar 4 18:06:24 2021 +0000 Consolidate/cleanup init config and script Refs: #178 commit d32199cd58329b4b2c9c5c3e84e7d8d0801305e0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Mar 4 17:43:58 2021 +0000 Move getic/init settings from scripts to configs - consolidate RETRO variable in config.getic - move configuration settings from getic/init scripts to configs - add dependency to setup_workflow_fcstonly.py - add getic and init to task list at top of config.resources Refs: #178 commit 084cb6aacc0c65440c5fecd3010a1b691ee98d87 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Mar 4 15:22:42 2021 +0000 Update EMC_verif-global tag to verif_global_v1.13.5 Refs: #238,#279 co…

Squashed commit of the following: commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d11 e08f55583 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb39 e08f55583 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f1 b2879fe9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature branch for testing Refs: #178 commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:41:32 2021 +0000 Correct if-statement syntax in config.init Refs: #178 commit 005d33d7b100b279e0db5290824c3e7acabfa4ba Merge: 5ec376bab e09a398f1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 15:23:05 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit b2879fe9f90def631047f533db2144858d827023 Merge: 68b9157bd a8ed770d9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 10:07:05 2021 -0400 Merge pull request #326 from NOAA-EMC/release/gfsv16.1.1 GFSv16.1.1 commit e09a398f1cedc7252219e75bf0b319d2601bc8df Merge: e3fcfebc1 6bad810bc Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri May 21 09:58:49 2021 -0400 Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade EMC_verif-global v2.0.0 major release updates commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a Author: Mallory Row <mallory.row@noaa.gov> Date: Fri May 21 13:55:13 2021 +0000 Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit 9cf615d11b096ea4843f4e5938a6a65f3500df49 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 20 20:10:18 2021 +0000 Modulefile updates for testing with waves on - updated ww3 and base modulefiles to add modules and update some - added new: pio/2.5.2i, fms/2020.04.03 - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6 Refs: #164 commit b155ff37040658703168268d4e58fe4e6b45a50d Author: Mallory Row <mallory.row@noaa.gov> Date: Thu May 20 15:00:04 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit cae62e3f47e245e70fcf3721fb4c022ea11c059f Merge: 8def77afd e3fcfebc1 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 19 19:45:05 2021 +0000 Sync merge with develop and WW3 build updates - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack - WW3 build updates: revert back to separate module files for build; address modulefile reorganization in separate issue - remove CCPP option with system build, doing CCPP by default now Refs: #164 commit 5ec376bababd935e4f3b15c4754105f5bd750657 Merge: 6b6b9ed39 e3fcfebc1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed May 19 18:24:31 2021 +0000 Merge remote-tracking branch 'origin/develop' into issue178 * origin/develop: change fv3gfs checkout head fixed a compilation error, NEMs/exe existing, in hera build_fv3.sh with ATM fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 bugfix for not removing last point from list in wave post pnt jobs changes added in link_fv3gfs for fix_aer changed fix dir for link_fv3gfs changes on build_fv3.sh and symlinks to optical data files instead of cp Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination updated config.fcst testing merra2 workflow in hera update merra2 before a new pull request Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions udate config.base.emc.dyn high resolution MERRA2 data used fixed a bug related to orion added merra2 input and update diag_table merra2 workflow for orion Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) commit 4641c5d206a95e0e66276fa86d46ecd580213fd5 Merge: eff8a1258 e3fcfebc1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 19 14:51:19 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit e3fcfebc1ff9c9f9ceda7b775de0c34117de6459 Merge: 95e0dffea fa5d1e2ba Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 19 10:02:19 2021 -0400 Merge pull request #254 from AnningCheng-NOAA/merra2 Addition of support for MERRA2 commit fa5d1e2ba242a08e26cb7bac8c68b700a83d1d60 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue May 18 10:41:16 2021 -0400 change fv3gfs checkout head commit 283c4a044847bbadd0cef46e14dde4de97abe986 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 17 15:56:56 2021 -0400 fixed a compilation error, NEMs/exe existing, in hera commit 6b574160f94329754677e7f4541ab07c44185bb0 Author: anning.cheng <anning.cheng@noaa.gov> Date: Fri May 14 13:44:18 2021 +0000 build_fv3.sh with ATM commit dfc8aa9a2cf5370fff38520d2a28f3960be3b583 Merge: bf5d11063 95e0dffea Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed May 12 20:11:44 2021 +0000 Merge remote-tracking branch 'upstream/develop' into merra2 commit eff8a1258aa70c061fe69697388f8914935726ee Merge: b1ad0b963 95e0dffea Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 12 19:15:17 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit 95e0dffea435af17be9150fcd0c842763768b45f Merge: fc727f405 dd4d18790 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 12 14:51:10 2021 -0400 Merge pull request #323 from NOAA-EMC/sync/operations_v16.0.9 Bring operations branch v16.0.9 changes into develop commit dd4d1879093516a7950c9e0e59f6e44e462199f6 Merge: fc727f405 68b9157bd Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 10 16:40:13 2021 +0000 Merge remote-tracking branch 'origin/operations' into sync/operations_v16.0.9 * origin/operations: bugfix for not removing last point from list in wave post pnt jobs Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) Refs: #309 commit 8def77afd4a9f1cd6cdca42c956bc7ebf675a58d Merge: c6e2a96e8 d46e8cf49 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 10 11:45:02 2021 -0400 Merge pull request #322 from JessicaMeixner-NOAA/hpcstackww3 Updates for ww3 pre and post exec builds for hpc-stack commit d46e8cf49aff0dbf72e457f1177e10e6f50252a6 Author: Jessica Meixner <Jessica.Meixner@noaa.gov> Date: Mon May 10 15:31:56 2021 +0000 update for ww3_pre/post build: -- remove ww3 specific module files -- updated module base files to be in sync with ufs-weather-model except that jasper is a more recent version which is needed for ww3_grib -- added extra ww3 execs needed for this branch -- added ww3prepost build to build_all and partial build commit c6e2a96e86611cce00455609d9be803d580e7bc0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:30:13 2021 +0000 Change fix file linking to scan for possible subfolders in set - instead of providing subfolder names, scan for subfolders in FIX_DIR path and then create symlinks based on existing subfolders in set - will not have to keep updating list of subfolders now Refs: #164 commit aa1d1e9ca1d8521ef22e1bdb654d4a70e7b1e29e Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:27:13 2021 +0000 Change CCPP_SUITE from FV3_GFS_v16beta to FV3_GFS_v16 - newer ufs-weather-model hash supports FV3_GFS_v16 suite Refs: #164 commit a8ed770d9c1e8614c5477d0129d6eaf5fe4e2085 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:32:36 2021 +0000 Companion update to Externals.cfg for WAFS tag update to gfs_wafs.v6.0.22 Refs: #1,#321 commit 68d9b5b5ff072b1f62131a9f7495c33c14c4a850 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:28:17 2021 +0000 WAFS tag update to gfs_wafs.v6.0.22 for bug fix Refs: #1,#321 commit 68b9157bd59278dc07369d316999d3c8485ebf7c Merge: 1f5af6283 97fe99096 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 5 10:50:42 2021 -0400 Merge pull request #306 from NOAA-EMC/release/gfsv16.0.0_to_ops GFSv16.0.9 commit 1aea3ee393c99d4f76556fbbdbebc43f629558c2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:30:06 2021 +0000 Add build script and modulefiles for WW3 build - WW3 execs no longer built by FV3 build, need separate build now - add new build_ww3prepost.sh script for building WW3 execs in ufs-weather-model checkout - add modulefiles for WCOSS-Dell, Hera, and Orion Refs: #164 commit 214431a2c04f6e685e966810621fc2fae771d2f5 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:26:00 2021 +0000 Update WAFS execs to include .x - update WAFS exec names in link_fv3gfs.sh to include ".x" extension that was added with new version Refs: #164 commit eb1613764794a35d165e55423682ed592b2aaacb Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:22:06 2021 +0000 ufs-weather-model hash update for WW3 support with hpc-stack - update ufs-weather-model hash to 554aedcd63e4a7c5012570406132eaf76e249ca9 - update build_fv3.sh for new compile arguments for CCPP/WW3 build Refs: #164 commit b1ad0b96328a54112ecc13ff4b71dcc08556a8c1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 5 14:13:58 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.1 Refs: #315 commit c206e8d2606f14ee6188740f881673ff512b866b Author: Mallory Row <mallory.row@noaa.gov> Date: Mon May 3 19:16:42 2021 +0000 Fix typo in config.metp There was a typo in the grid-to-obs METviewer related config variables. The variables started with "g2g1" instead of "g2o1". Refs: #315 commit f9013decd5af75f66eda619175bacc7549f4746a Author: Brian Curtis <Brian.Curtis@noaa.gov> Date: Mon May 3 14:37:13 2021 -0400 Files to test for python3 compatibility commit 0b9607711900e0da0de3d3dc1af91cc4dc9dd04d Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 12:31:01 2021 -0400 Update v16.1 release notes with wave script fix Refs: #301 commit fda26e9010ef59f69cd378c3092bdc82e57e4ec2 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon May 3 12:08:12 2021 -0400 Update config.base.nco.static Change HOMEobsproc_prep and HOMEobsproc_network to point at NCO installation of these packages. commit f9a6dd71ef7d580d6b83f50eb53814a06a944577 Merge: 173bb4814 97fe99096 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 11:55:09 2021 -0400 Merge branch 'release/gfsv16.0.0_to_ops' into release/gfsv16.1 Include wave fixes in v16.1 Refs: #301 commit 173bb4814ed2d2bc6e3436263f55c199f8dc8721 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 11:52:42 2021 -0400 Update v16.1 release notes for wave fixes Refs: #301 commit 858f216330d7ab71137afe6331f6576fec413aee Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:19:56 2021 +0000 Update EMC_post, UFS_UTILS, EMC_gfs_wafs versions in Externals.cfg Refs: #164 commit 6ce83363726ece6dbd34719430dd44f5e63bbc3c Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:14:54 2021 +0000 Component updates for UPP, WAFS, UFS_UTILS - new tag in checkout for UFS_UTILS to use hpc/1.1.0 - new hash in checkout for UPP/EMC_post to support GTG and GTG code copy fix - new hash in checkout for WAFS/EMC_gfs_wafs to support hpc-stack - build script update for WAFS (cmake/stack) - WAFS GCIP config update to fix runtime error Refs: #164 commit 709095709ca60498d05ea0f519b494501e1ecdf2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:11:51 2021 +0000 Update util_shared to 1.3.0 on WCOSS-Dell - version changed in production for v16.0.9 footer fix Refs: #164 commit bf5d110632fc67653441e6830bfdcdddda906706 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 3 10:53:37 2021 -0400 fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 commit 97fe990968955486fe2b7f3035c9d9423cef5e3e Merge: c582db288 f0fd3d410 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 3 09:15:15 2021 -0400 Merge pull request #318 from JessicaMeixner-NOAA/v16/bugforpnt Bug fix for missing buoy in wave post point commit f0fd3d4108debaa61f000ac700fd90904f1b600b Author: jessica.meixner <Jessica.Meixner@noaa.gov> Date: Fri Apr 30 17:56:34 2021 +0000 bugfix for not removing last point from list in wave post pnt jobs commit fb47a5a0f7391f670461b00eaf324c3b0102ef1f Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Apr 28 17:50:15 2021 +0000 Update TC_tracker version in config.vrfy - new TC_tracker.v1.1.15.4 was made available by Jiayi Peng - new version supports hpc-stack on supported platforms - installed locally on WCOSS-Dells, Hera, and Orion Refs: #164 commit 587ac0c914430d5b887327d7c566c452d2eace62 Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed Apr 28 10:36:49 2021 -0400 changes added in link_fv3gfs for fix_aer commit 48690cd07ceeb90c6808346a04a31a6166505c86 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed Apr 28 14:00:46 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.0 commit 1d0e0c29979101b451f1fda265af3f9a716bb9de Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Apr 27 19:33:09 2021 +0000 Reverting resource related changes - will commit resource adjustments separately Refs: #164 commit 101905ce4d92a544d353700b0acdc137aa61b088 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue Apr 27 14:15:59 2021 -0400 changed fix dir for link_fv3gfs commit 3271bac5b2072bfa2c0c0d229f050b647cd28925 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Tue Apr 27 10:08:54 2021 -0400 Update Externals.cfg and release notes for v16.1 Updated Externals.cfg GSI tag to gfsda.v16.1.0. Added sections in the release notes to explicitly say no changes to parm/config and scripts. Refs: #301 commit 31389bc23b89b1713712da17c8f226b649286b40 Merge: b1e924cd4 c582db288 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Tue Apr 27 08:31:41 2021 -0400 Merge branch 'release/gfsv16.0.0_to_ops' into release/gfsv16.1 This update brings in the wave foot fix for GFSv16.0.9. Refs: #301 commit b1e924cd44eba056443cb2a6789b1dc8040a02e1 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Tue Apr 27 07:31:44 2021 -0400 Change GSI tag to gfsda.v16.1.0 The GSI tag has been updated for the v16.1 implementation. This implementation turns on commercial RO data from GeoOptics. See release notes docs/Release_Notes.gfs.v16.1.0.txt in the global-workflow and release notes doc/Release_Notes.gfsda.v16.1.0.txt in the GSI for details. Refs: #301 commit 3142a8219c74b7b33a2bee1aed4ed7acd34ed0dc Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon Apr 26 16:59:43 2021 -0400 Add Release Notes for GFSv16.1 Added the file docs/Release_Notes.gfs.v16.1.0.txt to release branch release/gfsv16.1. Refs: #301 commit 7cd6e0e3000a47b39fa0c7e75ad66150e96385d8 Author: Mallory Row <mallory.row@noaa.gov> Date: Fri Apr 23 14:44:03 2021 +0000 Fix setting of 'SDATE_GFS' for free forecast XML In the workflow XML for free forecasts there is no SDATE_GFS variable. The 'SDATE_GFS' variable was changed to be set to the value of 'SDATE'. Refs: #315 commit d34b99d4e3d369b784fd9d2c639a0bddd1bbfc0c Author: Mallory Row <mallory.row@noaa.gov> Date: Fri Apr 23 12:59:51 2021 +0000 Clean up and add new settings in metp.sh SDATE_GFS was added into the script preamble following the addition of the variable being added as a rocoto exported environment variable for metp tasks. Config.vrfy was removed from the list of relevant configs to source. Variables CDATEm1 and PDYm1 were removed and replaced with VDATE. VDATE is the verification date to be done by the metp tasks based on VRFYBACK_HRS set in config.metp. Lines were added to catch the exit status of VERIFGLOBAL_SH and to exit if not succesfully run so it can be caught by rocoto. Refs: #315 commit 998f1a454427dedd46bb20b36e381bedbdf3e349 Author: Mallory Row <mallory.row@noaa.gov> Date: Fri Apr 23 12:49:38 2021 +0000 Revamp of config.metp Following the EMC_verif-global configuration remake, config.metp has been revamped to support the new configuration settings. Refs: #315 commit 6a01ae405202b8984fe8efa73573d7fdba2b74d2 Author: Mallory Row <mallory.row@noaa.gov> Date: Thu Apr 22 17:17:14 2021 +0000 Add 'SDATE_GFS' rocoto env var for metp tasks The connector script between EMC_verif-global and global-workflow run_verif_global_in_global_workflow.sh (housed in EMC_verif-global) contains a new feature that checks the maximum forecast hour for verification is the hour's initialization date is equal to or after the first GFS cycle initialization. If the date is before, the maximum forecast hour is adjusted to the maximum hour relative to the forecast verification date and the first GFS cycle initialization. This feature was added to cut down on METplus calls being done on data that don't exist. Refs: #315 commit dfec5816add3c56721360a418ec9f3459cfd4d8c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 15:27:56 2021 +0000 Update UFS_UTILS hash to 9d9dd23e37a51fcc5ff6b7499b834c85ab32e5f3 Refs: #164 commit be564bb85eeefbb1699992e0ed4f0705e4e2ee24 Author: anning.cheng <anning.cheng@noaa.gov> Date: Thu Apr 22 11:22:02 2021 -0400 changes on build_fv3.sh and symlinks to optical data files instead of cp commit 15c6619c6e211eb67ca6aa5c995e4a3bf4cf586f Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 14:03:46 2021 +0000 Adjust C768 fcst thread value for reduced node usage - change C768 nth_fv3_gfs value from 7 to 2 Refs: #164 commit ece41632a76e697184a46bb2a428c35ccdf08305 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Apr 22 13:58:22 2021 +0000 Add separate gfs resource variables to fcst in config.resources Refs: #164 commit 00c18b5e341d601fd83da2f9df2ac928e8dcf7c8 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 13:44:13 2021 +0000 Update FIX_DIR paths in link_fv3gfs.sh - change p…

…2 branch + 18Mar22 updates) ** 01Mar22 NOAA-EMC/develop branch + GSL updates ** default suite is FV3_RAP_noah_sfcdiff_unified_ugwp ** v5 namelist ** UFS version: tag global-24Feb2022 from NOAA-GSL:gsl/develop branch Squashed commit of the following: commit 463658317bd968fe43e25b8deea5d6bea3433bc6 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 18 00:25:34 2022 +0000 Updates for GSL - restored config.base.emc.dyn to original settings -- added STEP_GFS -- set DO_VRFY back to "YES" - added instantaneous flux variables to grib2 files -- added files to gfs_post.fd_gsl -- different configuration file used if running with inline POST - deleted obsolete files - deleted older experiment directories commit dbaadf28f9f41659bdba00f170b8db630a601de7 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Mar 16 21:14:00 2022 +0000 Merge 07Mar2022 gslv16_dev branch into gslv16_dev_cyc Squashed commit of the following: commit 25bb23710433d0a3d21659b4e8f599ac0b372d84 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 18:07:51 2022 +0000 Additional updates for GSL - added FV3_RAP_noah_sfcdiff_ugwpv1 to if CCPP_SUITE statements - corrected path for init dependencies in GSL setup workflow forecast-only script commit c7f02007d2d1a1817aa8d12cf7341b60778419b6 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 16:46:56 2022 +0000 Updated GSL archive script commit fad24c0b7c507f4f8fa8da30157935cc0869e0bb Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:50:09 2022 +0000 Add link for config.base.emc.dyn under parm/config so link_workflow.sh runs successfully commit 6fd8fa391ddf055a160e50dddc5badddc2b089c7 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:39:53 2022 +0000 Add experiment directory FV3GFSwfm/gsl_v5 to be used as reference commit 84941c8f059a30523e0e9c97240137c6f07cf3e1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:38:22 2022 +0000 Add dt_inner namelist parameter for GSL suites commit e8ec42ec61d00523caf7fba0ca70f8408f9f529d Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 18:54:55 2022 +0000 Correct syntax error in parsing_namelist_FV3.sh Correct suite name in build_ufs.sh Set default CCPP suite to FV3_RAP_noah_sfcdiff_unified_ugwp in config.base.emc.dyn* files Set DO_VRFY to NO in config.base.emc.dyn* files Rename GSL archive script to jobs/rocoto/arch_gsl.sh Changes for running without GF shallow - comment out consistency check in cu_gf_driver.F90 - set imfshalcnv to -1 in config.fcst Updates to experiment setup scripts - created GSL specific files workflow_utils.py_gsl setup_workflow_fcstonly_gsl_ics.py setup_workflow_fcstonly_gsl.py - pointed workflow_utils.py to GSL version - added example setup scripts, ffl127.sh and testics.sh commit 3f736afabc7956d1cf3c3941519116742ac97608 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:20:44 2022 +0000 Added GSL specific getic scripts commit e8cb894178ac7978fbe4fd5a9851db77ed0032bd Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:16:20 2022 +0000 Add GSL suite definition files to build_ufs.sh commit 38c354b976be0e445922a18816f59939d31e8c40 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:12:27 2022 +0000 Updates for GSL - cleaned up checkout.sh - renamed fv3gfs.fd_gsl to ufs_model.fd_gsl - renamed suite definition files from FV3_GSD to FV3_RAP commit 8ea7fd81c914725d453c2c770d3881f04f237215 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 00:40:23 2022 +0000 Updates for GSL - updated INFO file - updated GSL Suite Definition Files renamed FV3_GSD_v0 FV3_RAP_cires_ugwp renamed FV3_GSD_noah FV3_RAP_sfcdiff_unified_ugwp added FV3_RAP_sfcdiff_ugwpv1 - renamed GSL diag tables diag_table_da_gsd => diag_table_da_gsl diag_table_gsd => diag_table_gsl diag_table_gsd_ruc => diag_table_gsl_ruc - renamed GSL field table field_table_gsd => field_table_thompson_aero_tke - change cdmbgwd values for SDF FV3_RAP_noah_sfcdiff_ugwpv1 commit b0ea869ef9d11662b0710e4763f9f36064efab55 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 3 20:50:41 2022 +0000 Merge 01Mar2022 NOAA-EMC/develop branch into gslv16_dev Squashed commit of the following: commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d11 e08f55583 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb39 e08f55583 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f1 b2879fe9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature branch for testing Refs: #178 commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:41:32 2021 +0000 Correct if-statement syntax in config.init Refs: #178 commit 005d33d7b100b279e0db5290824c3e7acabfa4ba Merge: 5ec376bab e09a398f1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 15:23:05 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit b2879fe9f90def631047f533db2144858d827023 Merge: 68b9157bd a8ed770d9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 10:07:05 2021 -0400 Merge pull request #326 from NOAA-EMC/release/gfsv16.1.1 GFSv16.1.1 commit e09a398f1cedc7252219e75bf0b319d2601bc8df Merge: e3fcfebc1 6bad810bc Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri May 21 09:58:49 2021 -0400 Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade EMC_verif-global v2.0.0 major release updates commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a Author: Mallory Row <mallory.row@noaa.gov> Date: Fri May 21 13:55:13 2021 +0000 Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit 9cf615d11b096ea4843f4e5938a6a65f3500df49 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 20 20:10:18 2021 +0000 Modulefile updates for testing with waves on - updated ww3 and base modulefiles to add modules and update some - added new: pio/2.5.2i, fms/2020.04.03 - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6 Refs: #164 commit b155ff37040658703168268d4e58fe4e6b45a50d Author: Mallory Row <mallory.row@noaa.gov> Date: Thu May 20 15:00:04 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit cae62e3f47e245e70fcf3721fb4c022ea11c059f Merge: 8def77afd e3fcfebc1 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 19 19:45:05 2021 +0000 Sync merge with develop and WW3 build updates - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack - WW3 build updates: revert back to separate module files for build; address modulefile reorganization in separate issue - remove CCPP option with system build, doing CCPP by default now Refs: #164 commit 5ec376bababd935e4f3b15c4754105f5bd750657 Merge: 6b6b9ed39 e3fcfebc1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed May 19 18:24:31 2021 +0000 Merge remote-tracking branch 'origin/develop' into issue178 * origin/develop: change fv3gfs checkout head fixed a compilation error, NEMs/exe existing, in hera build_fv3.sh with ATM fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 bugfix for not removing last point from list in wave post pnt jobs changes added in link_fv3gfs for fix_aer changed fix dir for link_fv3gfs changes on build_fv3.sh and symlinks to optical data files instead of cp Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination updated config.fcst testing merra2 workflow in hera update merra2 before a new pull request Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions udate config.base.emc.dyn high resolution MERRA2 data used fixed a bug related to orion added merra2 input and update diag_table merra2 workflow for orion Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) commit 4641c5d206a95e0e66276fa86d46ecd580213fd5 Merge: eff8a1258 e3fcfebc1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 19 14:51:19 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit e3fcfebc1ff9c9f9ceda7b775de0c34117de6459 Merge: 95e0dffea fa5d1e2ba Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 19 10:02:19 2021 -0400 Merge pull request #254 from AnningCheng-NOAA/merra2 Addition of support for MERRA2 commit fa5d1e2ba242a08e26cb7bac8c68b700a83d1d60 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue May 18 10:41:16 2021 -0400 change fv3gfs checkout head commit 283c4a044847bbadd0cef46e14dde4de97abe986 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 17 15:56:56 2021 -0400 fixed a compilation error, NEMs/exe existing, in hera commit 6b574160f94329754677e7f4541ab07c44185bb0 Author: anning.cheng <anning.cheng@noaa.gov> Date: Fri May 14 13:44:18 2021 +0000 build_fv3.sh with ATM commit dfc8aa9a2cf5370fff38520d2a28f3960be3b583 Merge: bf5d11063 95e0dffea Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed May 12 20:11:44 2021 +0000 Merge remote-tracking branch 'upstream/develop' into merra2 commit eff8a1258aa70c061fe69697388f8914935726ee Merge: b1ad0b963 95e0dffea Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 12 19:15:17 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit 95e0dffea435af17be9150fcd0c842763768b45f Merge: fc727f405 dd4d18790 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 12 14:51:10 2021 -0400 Merge pull request #323 from NOAA-EMC/sync/operations_v16.0.9 Bring operations branch v16.0.9 changes into develop commit dd4d1879093516a7950c9e0e59f6e44e462199f6 Merge: fc727f405 68b9157bd Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 10 16:40:13 2021 +0000 Merge remote-tracking branch 'origin/operations' into sync/operations_v16.0.9 * origin/operations: bugfix for not removing last point from list in wave post pnt jobs Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) Refs: #309 commit 8def77afd4a9f1cd6cdca42c956bc7ebf675a58d Merge: c6e2a96e8 d46e8cf49 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 10 11:45:02 2021 -0400 Merge pull request #322 from JessicaMeixner-NOAA/hpcstackww3 Updates for ww3 pre and post exec builds for hpc-stack commit d46e8cf49aff0dbf72e457f1177e10e6f50252a6 Author: Jessica Meixner <Jessica.Meixner@noaa.gov> Date: Mon May 10 15:31:56 2021 +0000 update for ww3_pre/post build: -- remove ww3 specific module files -- updated module base files to be in sync with ufs-weather-model except that jasper is a more recent version which is needed for ww3_grib -- added extra ww3 execs needed for this branch -- added ww3prepost build to build_all and partial build commit c6e2a96e86611cce00455609d9be803d580e7bc0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:30:13 2021 +0000 Change fix file linking to scan for possible subfolders in set - instead of providing subfolder names, scan for subfolders in FIX_DIR path and then create symlinks based on existing subfolders in set - will not have to keep updating list of subfolders now Refs: #164 commit aa1d1e9ca1d8521ef22e1bdb654d4a70e7b1e29e Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:27:13 2021 +0000 Change CCPP_SUITE from FV3_GFS_v16beta to FV3_GFS_v16 - newer ufs-weather-model hash supports FV3_GFS_v16 suite Refs: #164 commit a8ed770d9c1e8614c5477d0129d6eaf5fe4e2085 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:32:36 2021 +0000 Companion update to Externals.cfg for WAFS tag update to gfs_wafs.v6.0.22 Refs: #1,#321 …

-- bring workflow up to 01Mar2022 NOAA-EMC/develop branch Squashed commit of the following: commit b90c2ce84374a7207044d8172a611d38c1000c4c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Mar 23 21:26:57 2022 +0000 Updates for GSL - added STEP_GFS back to config.base.emc.dyn_jet - modified link_workflow.sh to copy machine-specific config.base.emc.dyn in parm/config - removed linking of config.base.emc.dyn in experiment setup script, ffl127.sh commit 9513a6d569a548e93c4f678741f80c6891ed7725 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 22 00:11:00 2022 +0000 Turn off DO_VRFY in config.base.emc.dyn so correct XML file gets created commit 776651b573d3b6dc07729fda58d029103dc3a9c9 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 22 00:00:04 2022 +0000 Update experiment setup script and example directory - corrected syntax error in setup_workflow_fcstonly_gsl.py - updated files in FV3GFSwfm/gsl_v5 experiment directory to be used as reference commit ae66f75d310e4163853614738883278cd7d167c1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 18 00:37:07 2022 +0000 Updates for GSL - restored config.base.emc.dyn to original settings -- added STEP_GFS -- set DO_VRFY back to "YES" - updated jobs/JGLOBAL_WAVE_PREP to correct version - added GSL-specific vrfy shell script, vrfy_gsl.sh - deleted obsolete files - added instantaneous flux variables to grib2 files -- added files to gfs_post.fd_gsl (different configuration file used if running with inline POST) commit 25bb23710433d0a3d21659b4e8f599ac0b372d84 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 18:07:51 2022 +0000 Additional updates for GSL - added FV3_RAP_noah_sfcdiff_ugwpv1 to if CCPP_SUITE statements - corrected path for init dependencies in GSL setup workflow forecast-only script commit c7f02007d2d1a1817aa8d12cf7341b60778419b6 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 16:46:56 2022 +0000 Updated GSL archive script commit fad24c0b7c507f4f8fa8da30157935cc0869e0bb Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:50:09 2022 +0000 Add link for config.base.emc.dyn under parm/config so link_workflow.sh runs successfully commit 6fd8fa391ddf055a160e50dddc5badddc2b089c7 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:39:53 2022 +0000 Add experiment directory FV3GFSwfm/gsl_v5 to be used as reference commit 84941c8f059a30523e0e9c97240137c6f07cf3e1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:38:22 2022 +0000 Add dt_inner namelist parameter for GSL suites commit e8ec42ec61d00523caf7fba0ca70f8408f9f529d Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 18:54:55 2022 +0000 Correct syntax error in parsing_namelist_FV3.sh Correct suite name in build_ufs.sh Set default CCPP suite to FV3_RAP_noah_sfcdiff_unified_ugwp in config.base.emc.dyn* files Set DO_VRFY to NO in config.base.emc.dyn* files Rename GSL archive script to jobs/rocoto/arch_gsl.sh Changes for running without GF shallow - comment out consistency check in cu_gf_driver.F90 - set imfshalcnv to -1 in config.fcst Updates to experiment setup scripts - created GSL specific files workflow_utils.py_gsl setup_workflow_fcstonly_gsl_ics.py setup_workflow_fcstonly_gsl.py - pointed workflow_utils.py to GSL version - added example setup scripts, ffl127.sh and testics.sh commit 3f736afabc7956d1cf3c3941519116742ac97608 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:20:44 2022 +0000 Added GSL specific getic scripts commit e8cb894178ac7978fbe4fd5a9851db77ed0032bd Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:16:20 2022 +0000 Add GSL suite definition files to build_ufs.sh commit 38c354b976be0e445922a18816f59939d31e8c40 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:12:27 2022 +0000 Updates for GSL - cleaned up checkout.sh - renamed fv3gfs.fd_gsl to ufs_model.fd_gsl - renamed suite definition files from FV3_GSD to FV3_RAP commit 8ea7fd81c914725d453c2c770d3881f04f237215 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 00:40:23 2022 +0000 Updates for GSL - updated INFO file - updated GSL Suite Definition Files renamed FV3_GSD_v0 FV3_RAP_cires_ugwp renamed FV3_GSD_noah FV3_RAP_sfcdiff_unified_ugwp added FV3_RAP_sfcdiff_ugwpv1 - renamed GSL diag tables diag_table_da_gsd => diag_table_da_gsl diag_table_gsd => diag_table_gsl diag_table_gsd_ruc => diag_table_gsl_ruc - renamed GSL field table field_table_gsd => field_table_thompson_aero_tke - change cdmbgwd values for SDF FV3_RAP_noah_sfcdiff_ugwpv1 commit b0ea869ef9d11662b0710e4763f9f36064efab55 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 3 20:50:41 2022 +0000 Merge 01Mar2022 NOAA-EMC/develop branch into gslv16_dev Squashed commit of the following: commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d11 e08f55583 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb39 e08f55583 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f1 b2879fe9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature branch for testing Refs: #178 commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:41:32 2021 +0000 Correct if-statement syntax in config.init Refs: #178 commit 005d33d7b100b279e0db5290824c3e7acabfa4ba Merge: 5ec376bab e09a398f1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 15:23:05 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit b2879fe9f90def631047f533db2144858d827023 Merge: 68b9157bd a8ed770d9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 10:07:05 2021 -0400 Merge pull request #326 from NOAA-EMC/release/gfsv16.1.1 GFSv16.1.1 commit e09a398f1cedc7252219e75bf0b319d2601bc8df Merge: e3fcfebc1 6bad810bc Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri May 21 09:58:49 2021 -0400 Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade EMC_verif-global v2.0.0 major release updates commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a Author: Mallory Row <mallory.row@noaa.gov> Date: Fri May 21 13:55:13 2021 +0000 Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit 9cf615d11b096ea4843f4e5938a6a65f3500df49 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 20 20:10:18 2021 +0000 Modulefile updates for testing with waves on - updated ww3 and base modulefiles to add modules and update some - added new: pio/2.5.2i, fms/2020.04.03 - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6 Refs: #164 commit b155ff37040658703168268d4e58fe4e6b45a50d Author: Mallory Row <mallory.row@noaa.gov> Date: Thu May 20 15:00:04 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit cae62e3f47e245e70fcf3721fb4c022ea11c059f Merge: 8def77afd e3fcfebc1 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 19 19:45:05 2021 +0000 Sync merge with develop and WW3 build updates - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack - WW3 build updates: revert back to separate module files for build; address modulefile reorganization in separate issue - remove CCPP option with system build, doing CCPP by default now Refs: #164 commit 5ec376bababd935e4f3b15c4754105f5bd750657 Merge: 6b6b9ed39 e3fcfebc1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed May 19 18:24:31 2021 +0000 Merge remote-tracking branch 'origin/develop' into issue178 * origin/develop: change fv3gfs checkout head fixed a compilation error, NEMs/exe existing, in hera build_fv3.sh with ATM fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 bugfix for not removing last point from list in wave post pnt jobs changes added in link_fv3gfs for fix_aer changed fix dir for link_fv3gfs changes on build_fv3.sh and symlinks to optical data files instead of cp Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination updated config.fcst testing merra2 workflow in hera update merra2 before a new pull request Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions udate config.base.emc.dyn high resolution MERRA2 data used fixed a bug related to orion added merra2 input and update diag_table merra2 workflow for orion Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) commit 4641c5d206a95e0e66276fa86d46ecd580213fd5 Merge: eff8a1258 e3fcfebc1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 19 14:51:19 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit e3fcfebc1ff9c9f9ceda7b775de0c34117de6459 Merge: 95e0dffea fa5d1e2ba Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 19 10:02:19 2021 -0400 Merge pull request #254 from AnningCheng-NOAA/merra2 Addition of support for MERRA2 commit fa5d1e2ba242a08e26cb7bac8c68b700a83d1d60 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue May 18 10:41:16 2021 -0400 change fv3gfs checkout head commit 283c4a044847bbadd0cef46e14dde4de97abe986 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 17 15:56:56 2021 -0400 fixed a compilation error, NEMs/exe existing, in hera commit 6b574160f94329754677e7f4541ab07c44185bb0 Author: anning.cheng <anning.cheng@noaa.gov> Date: Fri May 14 13:44:18 2021 +0000 build_fv3.sh with ATM commit dfc8aa9a2cf5370fff38520d2a28f3960be3b583 Merge: bf5d11063 95e0dffea Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed May 12 20:11:44 2021 +0000 Merge remote-tracking branch 'upstream/develop' into merra2 commit eff8a1258aa70c061fe69697388f8914935726ee Merge: b1ad0b963 95e0dffea Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 12 19:15:17 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit 95e0dffea435af17be9150fcd0c842763768b45f Merge: fc727f405 dd4d18790 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 12 14:51:10 2021 -0400 Merge pull request #323 from NOAA-EMC/sync/operations_v16.0.9 Bring operations branch v16.0.9 changes into develop commit dd4d1879093516a7950c9e0e59f6e44e462199f6 Merge: fc727f405 68b9157bd Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 10 16:40:13 2021 +0000 Merge remote-tracking branch 'origin/operations' into sync/operations_v16.0.9 * origin/operations: bugfix for not removing last point from list in wave post pnt jobs Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) Refs: #309 commit 8def77afd4a9f1cd6cdca42c956bc7ebf675a58d Merge: c6e2a96e8 d46e8cf49 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 10 11:45:02 2021 -0400 Merge pull request #322 from JessicaMeixner-NOAA/hpcstackww3 Updates for ww3 pre and post exec builds for hpc-stack commit d46e8cf49aff0dbf72e457f1177e10e6f50252a6 Author: Jessica Meixner <Jessica.Meixner@noaa.gov> Date: Mon May 10 15:31:56 2021 +0000 update for ww3_pre/post build: -- remove ww3 specific module files -- updated module base files to be in sync with ufs-weather-model except that jasper is a more recent version which is needed for ww3_grib -- added extra ww3 execs needed for this branch -- added ww3prepost build to build_all and partial build commit c6e2a96e86611cce00455609d9be803d580e7bc0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:30:13 2021 +0000 Change fix file linking to scan for possible subfolders in set - instead of providing subfolder names, scan for subfolders in FIX_DIR path and then create symlinks based on existing subfolders in set - will not have to keep updating list of subfolders now Refs: #164 commit aa1d1e9ca1d8521ef22e1bdb654d4a70e7b1e29e Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:27:13 2021 +0000 Change CCPP_SUITE from FV3_GFS_v16beta to FV3_GFS_v16 - newer ufs-weather-model hash supports FV3_GFS_v16 suite Refs: #164 commit a8ed770d9c1e8614c5477d0129d6eaf5fe4e2085 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:32:36 2021 +0000 Companion update to Externals.cfg for WAFS tag update to gfs_wafs.v6.0.22 Refs: #1,#321 commit 68d9b5b5ff072b1f62131a9f7495c33c14c4a850 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:28:17 2021 +0000 WAFS tag update to gfs_wafs.v6.0.22 for bug fix Refs: #1,#321 commit 68b9157bd59278dc07369d316999d3c8485ebf7c Merge: 1f5af6283 97fe99096 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 5 10:50:42 2021 -0400 Merge pull request #306 from NOAA-EMC/release/gfsv16.0.0_to_ops GFSv16.0.9 commit 1aea3ee393c99d4f76556fbbdbebc43f629558c2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:30:06 2021 +0000 Add build script and modulefiles for WW3 build - WW3 execs no longer built by FV3 build, need separate build now - add new build_ww3prepost.sh script for building WW3 execs in ufs-weather-model checkout - add modulefiles for WCOSS-Dell, Hera, and Orion Refs: #164 commit 214431a2c04f6e685e966810621fc2fae771d2f5 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:26:00 2021 +0000 Update WAFS execs to include .x - update WAFS exec names in link_fv3gfs.sh to include ".x" extension that was added with new version Refs: #164 commit eb1613764794a35d165e55423682ed592b2aaacb Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:22:06 2021 +0000 ufs-weather-model hash update for WW3 support with hpc-stack - update ufs-weather-model hash to 554aedcd63e4a7c5012570406132eaf76e249ca9 - update build_fv3.sh for new compile arguments for CCPP/WW3 build Refs: #164 commit b1ad0b96328a54112ecc13ff4b71dcc08556a8c1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 5 14:13:58 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.1 Refs: #315 commit c206e8d2606f14ee6188740f881673ff512b866b Author: Mallory Row <mallory.row@noaa.gov> Date: Mon May 3 19:16:42 2021 +0000 Fix typo in config.metp There was a typo in the grid-to-obs METviewer related config variables. The variables started with "g2g1" instead of "g2o1". Refs: #315 commit f9013decd5af75f66eda619175bacc7549f4746a Author: Brian Curtis <Brian.Curtis@noaa.gov> Date: Mon May 3 14:37:13 2021 -0400 Files to test for python3 compatibility commit 0b9607711900e0da0de3d3dc1af91cc4dc9dd04d Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 12:31:01 2021 -0400 Update v16.1 release notes with wave script fix Refs: #301 commit fda26e9010ef59f69cd378c3092bdc82e57e4ec2 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon May 3 12:08:12 2021 -0400 Update config.base.nco.static Change HOME…

-- 01Mar22 NOAA-EMC/global-workflow develop branch, a0e23e2 post: c939eae (10Nov21) ufs_utils: 26cd024 (31Jan22) -- 24Feb22 gsl/develop branch, a2a6a22, tag global-24Feb2022 v5 namelist unified UGWP ( FV3_RAP_noah_sfcdiff_unified_ugwp SDF ) no GF shallow convection Squashed commit of the following: commit 34fd1fc2b2d33c3799357dc4f031870e0247b337 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 29 00:48:48 2022 +0000 Modified realtime experiment setup scripts commit 3fb2b1cb4189cd2f066e0f4a5925e3854283189c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 29 00:37:36 2022 +0000 Updates for GSL - added experiment setup scripts for jet - changed default STMP and PTMP paths - change resources for gfsgetic task commit 1134dd4b98142b2e0fafa0043f4fc0c28a2004d7 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 19:06:44 2022 +0000 Correct paths for logfiles in checkout scripts commit b7df605d3ea1912d36f7521fca3869edc585048f Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 18:41:11 2022 +0000 Updated INFO file and checkout_jet.sh commit e56dd9a6d4e7d47efbd2d54ec9c3420b66bfc7c0 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 18:40:17 2022 +0000 Remove obsolete lines from experiment setup scripts commit f3ca5e5d3a17181da1c2e84d6b5b2c5edba0524e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 18:33:44 2022 +0000 Update realtime experiment setup scripts commit 564c721e3f4a40f5cfd05900c8f08d386d2e1523 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 02:46:14 2022 +0000 Merge gslv16_dev into gslv16_rt -- bring workflow up to 01Mar2022 NOAA-EMC/develop branch Squashed commit of the following: commit b90c2ce84374a7207044d8172a611d38c1000c4c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Mar 23 21:26:57 2022 +0000 Updates for GSL - added STEP_GFS back to config.base.emc.dyn_jet - modified link_workflow.sh to copy machine-specific config.base.emc.dyn in parm/config - removed linking of config.base.emc.dyn in experiment setup script, ffl127.sh commit 9513a6d569a548e93c4f678741f80c6891ed7725 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 22 00:11:00 2022 +0000 Turn off DO_VRFY in config.base.emc.dyn so correct XML file gets created commit 776651b573d3b6dc07729fda58d029103dc3a9c9 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 22 00:00:04 2022 +0000 Update experiment setup script and example directory - corrected syntax error in setup_workflow_fcstonly_gsl.py - updated files in FV3GFSwfm/gsl_v5 experiment directory to be used as reference commit ae66f75d310e4163853614738883278cd7d167c1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 18 00:37:07 2022 +0000 Updates for GSL - restored config.base.emc.dyn to original settings -- added STEP_GFS -- set DO_VRFY back to "YES" - updated jobs/JGLOBAL_WAVE_PREP to correct version - added GSL-specific vrfy shell script, vrfy_gsl.sh - deleted obsolete files - added instantaneous flux variables to grib2 files -- added files to gfs_post.fd_gsl (different configuration file used if running with inline POST) commit 25bb23710433d0a3d21659b4e8f599ac0b372d84 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 18:07:51 2022 +0000 Additional updates for GSL - added FV3_RAP_noah_sfcdiff_ugwpv1 to if CCPP_SUITE statements - corrected path for init dependencies in GSL setup workflow forecast-only script commit c7f02007d2d1a1817aa8d12cf7341b60778419b6 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 16:46:56 2022 +0000 Updated GSL archive script commit fad24c0b7c507f4f8fa8da30157935cc0869e0bb Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:50:09 2022 +0000 Add link for config.base.emc.dyn under parm/config so link_workflow.sh runs successfully commit 6fd8fa391ddf055a160e50dddc5badddc2b089c7 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:39:53 2022 +0000 Add experiment directory FV3GFSwfm/gsl_v5 to be used as reference commit 84941c8f059a30523e0e9c97240137c6f07cf3e1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:38:22 2022 +0000 Add dt_inner namelist parameter for GSL suites commit e8ec42ec61d00523caf7fba0ca70f8408f9f529d Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 18:54:55 2022 +0000 Correct syntax error in parsing_namelist_FV3.sh Correct suite name in build_ufs.sh Set default CCPP suite to FV3_RAP_noah_sfcdiff_unified_ugwp in config.base.emc.dyn* files Set DO_VRFY to NO in config.base.emc.dyn* files Rename GSL archive script to jobs/rocoto/arch_gsl.sh Changes for running without GF shallow - comment out consistency check in cu_gf_driver.F90 - set imfshalcnv to -1 in config.fcst Updates to experiment setup scripts - created GSL specific files workflow_utils.py_gsl setup_workflow_fcstonly_gsl_ics.py setup_workflow_fcstonly_gsl.py - pointed workflow_utils.py to GSL version - added example setup scripts, ffl127.sh and testics.sh commit 3f736afabc7956d1cf3c3941519116742ac97608 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:20:44 2022 +0000 Added GSL specific getic scripts commit e8cb894178ac7978fbe4fd5a9851db77ed0032bd Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:16:20 2022 +0000 Add GSL suite definition files to build_ufs.sh commit 38c354b976be0e445922a18816f59939d31e8c40 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:12:27 2022 +0000 Updates for GSL - cleaned up checkout.sh - renamed fv3gfs.fd_gsl to ufs_model.fd_gsl - renamed suite definition files from FV3_GSD to FV3_RAP commit 8ea7fd81c914725d453c2c770d3881f04f237215 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 00:40:23 2022 +0000 Updates for GSL - updated INFO file - updated GSL Suite Definition Files renamed FV3_GSD_v0 FV3_RAP_cires_ugwp renamed FV3_GSD_noah FV3_RAP_sfcdiff_unified_ugwp added FV3_RAP_sfcdiff_ugwpv1 - renamed GSL diag tables diag_table_da_gsd => diag_table_da_gsl diag_table_gsd => diag_table_gsl diag_table_gsd_ruc => diag_table_gsl_ruc - renamed GSL field table field_table_gsd => field_table_thompson_aero_tke - change cdmbgwd values for SDF FV3_RAP_noah_sfcdiff_ugwpv1 commit b0ea869ef9d11662b0710e4763f9f36064efab55 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 3 20:50:41 2022 +0000 Merge 01Mar2022 NOAA-EMC/develop branch into gslv16_dev Squashed commit of the following: commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d11 e08f55583 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb39 e08f55583 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f1 b2879fe9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature branch for testing Refs: #178 commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:41:32 2021 +0000 Correct if-statement syntax in config.init Refs: #178 commit 005d33d7b100b279e0db5290824c3e7acabfa4ba Merge: 5ec376bab e09a398f1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 15:23:05 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit b2879fe9f90def631047f533db2144858d827023 Merge: 68b9157bd a8ed770d9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 10:07:05 2021 -0400 Merge pull request #326 from NOAA-EMC/release/gfsv16.1.1 GFSv16.1.1 commit e09a398f1cedc7252219e75bf0b319d2601bc8df Merge: e3fcfebc1 6bad810bc Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri May 21 09:58:49 2021 -0400 Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade EMC_verif-global v2.0.0 major release updates commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a Author: Mallory Row <mallory.row@noaa.gov> Date: Fri May 21 13:55:13 2021 +0000 Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit 9cf615d11b096ea4843f4e5938a6a65f3500df49 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 20 20:10:18 2021 +0000 Modulefile updates for testing with waves on - updated ww3 and base modulefiles to add modules and update some - added new: pio/2.5.2i, fms/2020.04.03 - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6 Refs: #164 commit b155ff37040658703168268d4e58fe4e6b45a50d Author: Mallory Row <mallory.row@noaa.gov> Date: Thu May 20 15:00:04 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit cae62e3f47e245e70fcf3721fb4c022ea11c059f Merge: 8def77afd e3fcfebc1 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 19 19:45:05 2021 +0000 Sync merge with develop and WW3 build updates - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack - WW3 build updates: revert back to separate module files for build; address modulefile reorganization in separate issue - remove CCPP option with system build, doing CCPP by default now Refs: #164 commit 5ec376bababd935e4f3b15c4754105f5bd750657 Merge: 6b6b9ed39 e3fcfebc1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed May 19 18:24:31 2021 +0000 Merge remote-tracking branch 'origin/develop' into issue178 * origin/develop: change fv3gfs checkout head fixed a compilation error, NEMs/exe existing, in hera build_fv3.sh with ATM fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 bugfix for not removing last point from list in wave post pnt jobs changes added in link_fv3gfs for fix_aer changed fix dir for link_fv3gfs changes on build_fv3.sh and symlinks to optical data files instead of cp Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination updated config.fcst testing merra2 workflow in hera update merra2 before a new pull request Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions udate config.base.emc.dyn high resolution MERRA2 data used fixed a bug related to orion added merra2 input and update diag_table merra2 workflow for orion Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) commit 4641c5d206a95e0e66276fa86d46ecd580213fd5 Merge: eff8a1258 e3fcfebc1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 19 14:51:19 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit e3fcfebc1ff9c9f9ceda7b775de0c34117de6459 Merge: 95e0dffea fa5d1e2ba Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 19 10:02:19 2021 -0400 Merge pull request #254 from AnningCheng-NOAA/merra2 Addition of support for MERRA2 commit fa5d1e2ba242a08e26cb7bac8c68b700a83d1d60 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue May 18 10:41:16 2021 -0400 change fv3gfs checkout head commit 283c4a044847bbadd0cef46e14dde4de97abe986 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 17 15:56:56 2021 -0400 fixed a compilation error, NEMs/exe existing, in hera commit 6b574160f94329754677e7f4541ab07c44185bb0 Author: anning.cheng <anning.cheng@noaa.gov> Date: Fri May 14 13:44:18 2021 +0000 build_fv3.sh with ATM commit dfc8aa9a2cf5370fff38520d2a28f3960be3b583 Merge: bf5d11063 95e0dffea Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed May 12 20:11:44 2021 +0000 Merge remote-tracking branch 'upstream/develop' into merra2 commit eff8a1258aa70c061fe69697388f8914935726ee Merge: b1ad0b963 95e0dffea Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 12 19:15:17 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit 95e0dffea435af17be9150fcd0c842763768b45f Merge: fc727f405 dd4d18790 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 12 14:51:10 2021 -0400 Merge pull request #323 from NOAA-EMC/sync/operations_v16.0.9 Bring operations branch v16.0.9 changes into develop commit dd4d1879093516a7950c9e0e59f6e44e462199f6 Merge: fc727f405 68b9157bd Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 10 16:40:13 2021 +0000 Merge remote-tracking branch 'origin/operations' into sync/operations_v16.0.9 * origin/operations: bugfix for not removing last point from list in wave post pnt jobs Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file change…

Squashed commit of the following: commit 9c46b419f6bdabc96a5da008920046a6f1f27912 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 29 01:00:19 2022 +0000 Merge gw_merge_mar01 into gslv16_rt branch -- 01Mar22 NOAA-EMC/global-workflow develop branch, a0e23e2 post: c939eae (10Nov21) ufs_utils: 26cd024 (31Jan22) -- 24Feb22 gsl/develop branch, a2a6a22, tag global-24Feb2022 v5 namelist unified UGWP ( FV3_RAP_noah_sfcdiff_unified_ugwp SDF ) no GF shallow convection Squashed commit of the following: commit 34fd1fc2b2d33c3799357dc4f031870e0247b337 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 29 00:48:48 2022 +0000 Modified realtime experiment setup scripts commit 3fb2b1cb4189cd2f066e0f4a5925e3854283189c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 29 00:37:36 2022 +0000 Updates for GSL - added experiment setup scripts for jet - changed default STMP and PTMP paths - change resources for gfsgetic task commit 1134dd4b98142b2e0fafa0043f4fc0c28a2004d7 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 19:06:44 2022 +0000 Correct paths for logfiles in checkout scripts commit b7df605d3ea1912d36f7521fca3869edc585048f Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 18:41:11 2022 +0000 Updated INFO file and checkout_jet.sh commit e56dd9a6d4e7d47efbd2d54ec9c3420b66bfc7c0 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 18:40:17 2022 +0000 Remove obsolete lines from experiment setup scripts commit f3ca5e5d3a17181da1c2e84d6b5b2c5edba0524e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 18:33:44 2022 +0000 Update realtime experiment setup scripts commit 564c721e3f4a40f5cfd05900c8f08d386d2e1523 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 02:46:14 2022 +0000 Merge gslv16_dev into gslv16_rt -- bring workflow up to 01Mar2022 NOAA-EMC/develop branch Squashed commit of the following: commit b90c2ce84374a7207044d8172a611d38c1000c4c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Mar 23 21:26:57 2022 +0000 Updates for GSL - added STEP_GFS back to config.base.emc.dyn_jet - modified link_workflow.sh to copy machine-specific config.base.emc.dyn in parm/config - removed linking of config.base.emc.dyn in experiment setup script, ffl127.sh commit 9513a6d569a548e93c4f678741f80c6891ed7725 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 22 00:11:00 2022 +0000 Turn off DO_VRFY in config.base.emc.dyn so correct XML file gets created commit 776651b573d3b6dc07729fda58d029103dc3a9c9 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 22 00:00:04 2022 +0000 Update experiment setup script and example directory - corrected syntax error in setup_workflow_fcstonly_gsl.py - updated files in FV3GFSwfm/gsl_v5 experiment directory to be used as reference commit ae66f75d310e4163853614738883278cd7d167c1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 18 00:37:07 2022 +0000 Updates for GSL - restored config.base.emc.dyn to original settings -- added STEP_GFS -- set DO_VRFY back to "YES" - updated jobs/JGLOBAL_WAVE_PREP to correct version - added GSL-specific vrfy shell script, vrfy_gsl.sh - deleted obsolete files - added instantaneous flux variables to grib2 files -- added files to gfs_post.fd_gsl (different configuration file used if running with inline POST) commit 25bb23710433d0a3d21659b4e8f599ac0b372d84 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 18:07:51 2022 +0000 Additional updates for GSL - added FV3_RAP_noah_sfcdiff_ugwpv1 to if CCPP_SUITE statements - corrected path for init dependencies in GSL setup workflow forecast-only script commit c7f02007d2d1a1817aa8d12cf7341b60778419b6 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 16:46:56 2022 +0000 Updated GSL archive script commit fad24c0b7c507f4f8fa8da30157935cc0869e0bb Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:50:09 2022 +0000 Add link for config.base.emc.dyn under parm/config so link_workflow.sh runs successfully commit 6fd8fa391ddf055a160e50dddc5badddc2b089c7 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:39:53 2022 +0000 Add experiment directory FV3GFSwfm/gsl_v5 to be used as reference commit 84941c8f059a30523e0e9c97240137c6f07cf3e1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:38:22 2022 +0000 Add dt_inner namelist parameter for GSL suites commit e8ec42ec61d00523caf7fba0ca70f8408f9f529d Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 18:54:55 2022 +0000 Correct syntax error in parsing_namelist_FV3.sh Correct suite name in build_ufs.sh Set default CCPP suite to FV3_RAP_noah_sfcdiff_unified_ugwp in config.base.emc.dyn* files Set DO_VRFY to NO in config.base.emc.dyn* files Rename GSL archive script to jobs/rocoto/arch_gsl.sh Changes for running without GF shallow - comment out consistency check in cu_gf_driver.F90 - set imfshalcnv to -1 in config.fcst Updates to experiment setup scripts - created GSL specific files workflow_utils.py_gsl setup_workflow_fcstonly_gsl_ics.py setup_workflow_fcstonly_gsl.py - pointed workflow_utils.py to GSL version - added example setup scripts, ffl127.sh and testics.sh commit 3f736afabc7956d1cf3c3941519116742ac97608 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:20:44 2022 +0000 Added GSL specific getic scripts commit e8cb894178ac7978fbe4fd5a9851db77ed0032bd Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:16:20 2022 +0000 Add GSL suite definition files to build_ufs.sh commit 38c354b976be0e445922a18816f59939d31e8c40 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:12:27 2022 +0000 Updates for GSL - cleaned up checkout.sh - renamed fv3gfs.fd_gsl to ufs_model.fd_gsl - renamed suite definition files from FV3_GSD to FV3_RAP commit 8ea7fd81c914725d453c2c770d3881f04f237215 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 00:40:23 2022 +0000 Updates for GSL - updated INFO file - updated GSL Suite Definition Files renamed FV3_GSD_v0 FV3_RAP_cires_ugwp renamed FV3_GSD_noah FV3_RAP_sfcdiff_unified_ugwp added FV3_RAP_sfcdiff_ugwpv1 - renamed GSL diag tables diag_table_da_gsd => diag_table_da_gsl diag_table_gsd => diag_table_gsl diag_table_gsd_ruc => diag_table_gsl_ruc - renamed GSL field table field_table_gsd => field_table_thompson_aero_tke - change cdmbgwd values for SDF FV3_RAP_noah_sfcdiff_ugwpv1 commit b0ea869ef9d11662b0710e4763f9f36064efab55 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 3 20:50:41 2022 +0000 Merge 01Mar2022 NOAA-EMC/develop branch into gslv16_dev Squashed commit of the following: commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d11 e08f55583 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb39 e08f55583 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f1 b2879fe9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature branch for testing Refs: #178 commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:41:32 2021 +0000 Correct if-statement syntax in config.init Refs: #178 commit 005d33d7b100b279e0db5290824c3e7acabfa4ba Merge: 5ec376bab e09a398f1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 15:23:05 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit b2879fe9f90def631047f533db2144858d827023 Merge: 68b9157bd a8ed770d9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 10:07:05 2021 -0400 Merge pull request #326 from NOAA-EMC/release/gfsv16.1.1 GFSv16.1.1 commit e09a398f1cedc7252219e75bf0b319d2601bc8df Merge: e3fcfebc1 6bad810bc Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri May 21 09:58:49 2021 -0400 Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade EMC_verif-global v2.0.0 major release updates commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a Author: Mallory Row <mallory.row@noaa.gov> Date: Fri May 21 13:55:13 2021 +0000 Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit 9cf615d11b096ea4843f4e5938a6a65f3500df49 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 20 20:10:18 2021 +0000 Modulefile updates for testing with waves on - updated ww3 and base modulefiles to add modules and update some - added new: pio/2.5.2i, fms/2020.04.03 - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6 Refs: #164 commit b155ff37040658703168268d4e58fe4e6b45a50d Author: Mallory Row <mallory.row@noaa.gov> Date: Thu May 20 15:00:04 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit cae62e3f47e245e70fcf3721fb4c022ea11c059f Merge: 8def77afd e3fcfebc1 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 19 19:45:05 2021 +0000 Sync merge with develop and WW3 build updates - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack - WW3 build updates: revert back to separate module files for build; address modulefile reorganization in separate issue - remove CCPP option with system build, doing CCPP by default now Refs: #164 commit 5ec376bababd935e4f3b15c4754105f5bd750657 Merge: 6b6b9ed39 e3fcfebc1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed May 19 18:24:31 2021 +0000 Merge remote-tracking branch 'origin/develop' into issue178 * origin/develop: change fv3gfs checkout head fixed a compilation error, NEMs/exe existing, in hera build_fv3.sh with ATM fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 bugfix for not removing last point from list in wave post pnt jobs changes added in link_fv3gfs for fix_aer changed fix dir for link_fv3gfs changes on build_fv3.sh and symlinks to optical data files instead of cp Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination updated config.fcst testing merra2 workflow in hera update merra2 before a new pull request Issue #215 - GFSv15.3.5 ops update…

-- 01Mar22 NOAA-EMC/global-workflow develop branch, a0e23e2 post: c939eae (10Nov21) ufs_utils: 26cd024 (31Jan22) -- 29Mar22 gsl/develop branch, c31f633, tag global-29Mar2022 v5 namelist unified UGWP ( FV3_RAP_noah_sfcdiff_unified_ugwp SDF ) no GF shallow convection Squashed commit of the following: commit b1d1dc49e4ae8914f181186fbff1fd1b6c542cbb Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Apr 6 20:19:47 2022 +0000 Updates for GSL - removed EMCDIR and added SCR_DIR entities in setup_workflow_fcstonly_gsl_ics_jet.py - call setup_workflow_fcstonly_gsl_ics_jet.py in jet experiment setup script (handle path differences) - set Build_gsi to false for jet in build_all.sh - change FHMAX to 120 in config.base.emc.dyn_jet commit deace8e07d6621fb7168b2524b9db96da43d6e2a Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Apr 6 17:43:15 2022 +0000 Updates for GSL - changed default stmp/ptmp directories for jet in workflow_utils.py_gsl commit 17edcddd31579b8d214cce1ec48a518d3a327e67 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Apr 6 07:16:20 2022 +0000 Updates for GSL - changed default stmp/ptmp directories in workflow_utils.py_gsl - updated UFS hash to 29Mar22 gsl/develop branch, c31f633, in checkout_jet.sh - updated sample experiment setup script, ffl127.sh commit 59047458a7504f2bca7f6daf32ecada2abbee928 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Apr 6 01:18:04 2022 +0000 Updates for new GSL dev1 experiment - updated INFO file - updated UFS to 29Mar22 gsl/develop branch, c31f633 - modified experiment setup scripts for PSLOT=rt_ufscam_l127_dev1 commit ef63ce8cfb71236a182c0d735df8abb944b99081 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Apr 6 01:02:58 2022 +0000 Merge 29Mar2022 gslv16_rt branch into gw_mar01_rtdev1 branch Squashed commit of the following: commit 9c46b419f6bdabc96a5da008920046a6f1f27912 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 29 01:00:19 2022 +0000 Merge gw_merge_mar01 into gslv16_rt branch -- 01Mar22 NOAA-EMC/global-workflow develop branch, a0e23e2 post: c939eae (10Nov21) ufs_utils: 26cd024 (31Jan22) -- 24Feb22 gsl/develop branch, a2a6a22, tag global-24Feb2022 v5 namelist unified UGWP ( FV3_RAP_noah_sfcdiff_unified_ugwp SDF ) no GF shallow convection Squashed commit of the following: commit 34fd1fc2b2d33c3799357dc4f031870e0247b337 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 29 00:48:48 2022 +0000 Modified realtime experiment setup scripts commit 3fb2b1cb4189cd2f066e0f4a5925e3854283189c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 29 00:37:36 2022 +0000 Updates for GSL - added experiment setup scripts for jet - changed default STMP and PTMP paths - change resources for gfsgetic task commit 1134dd4b98142b2e0fafa0043f4fc0c28a2004d7 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 19:06:44 2022 +0000 Correct paths for logfiles in checkout scripts commit b7df605d3ea1912d36f7521fca3869edc585048f Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 18:41:11 2022 +0000 Updated INFO file and checkout_jet.sh commit e56dd9a6d4e7d47efbd2d54ec9c3420b66bfc7c0 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 18:40:17 2022 +0000 Remove obsolete lines from experiment setup scripts commit f3ca5e5d3a17181da1c2e84d6b5b2c5edba0524e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 18:33:44 2022 +0000 Update realtime experiment setup scripts commit 564c721e3f4a40f5cfd05900c8f08d386d2e1523 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 24 02:46:14 2022 +0000 Merge gslv16_dev into gslv16_rt -- bring workflow up to 01Mar2022 NOAA-EMC/develop branch Squashed commit of the following: commit b90c2ce84374a7207044d8172a611d38c1000c4c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Mar 23 21:26:57 2022 +0000 Updates for GSL - added STEP_GFS back to config.base.emc.dyn_jet - modified link_workflow.sh to copy machine-specific config.base.emc.dyn in parm/config - removed linking of config.base.emc.dyn in experiment setup script, ffl127.sh commit 9513a6d569a548e93c4f678741f80c6891ed7725 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 22 00:11:00 2022 +0000 Turn off DO_VRFY in config.base.emc.dyn so correct XML file gets created commit 776651b573d3b6dc07729fda58d029103dc3a9c9 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Mar 22 00:00:04 2022 +0000 Update experiment setup script and example directory - corrected syntax error in setup_workflow_fcstonly_gsl.py - updated files in FV3GFSwfm/gsl_v5 experiment directory to be used as reference commit ae66f75d310e4163853614738883278cd7d167c1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 18 00:37:07 2022 +0000 Updates for GSL - restored config.base.emc.dyn to original settings -- added STEP_GFS -- set DO_VRFY back to "YES" - updated jobs/JGLOBAL_WAVE_PREP to correct version - added GSL-specific vrfy shell script, vrfy_gsl.sh - deleted obsolete files - added instantaneous flux variables to grib2 files -- added files to gfs_post.fd_gsl (different configuration file used if running with inline POST) commit 25bb23710433d0a3d21659b4e8f599ac0b372d84 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 18:07:51 2022 +0000 Additional updates for GSL - added FV3_RAP_noah_sfcdiff_ugwpv1 to if CCPP_SUITE statements - corrected path for init dependencies in GSL setup workflow forecast-only script commit c7f02007d2d1a1817aa8d12cf7341b60778419b6 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Mar 7 16:46:56 2022 +0000 Updated GSL archive script commit fad24c0b7c507f4f8fa8da30157935cc0869e0bb Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:50:09 2022 +0000 Add link for config.base.emc.dyn under parm/config so link_workflow.sh runs successfully commit 6fd8fa391ddf055a160e50dddc5badddc2b089c7 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:39:53 2022 +0000 Add experiment directory FV3GFSwfm/gsl_v5 to be used as reference commit 84941c8f059a30523e0e9c97240137c6f07cf3e1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 22:38:22 2022 +0000 Add dt_inner namelist parameter for GSL suites commit e8ec42ec61d00523caf7fba0ca70f8408f9f529d Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 18:54:55 2022 +0000 Correct syntax error in parsing_namelist_FV3.sh Correct suite name in build_ufs.sh Set default CCPP suite to FV3_RAP_noah_sfcdiff_unified_ugwp in config.base.emc.dyn* files Set DO_VRFY to NO in config.base.emc.dyn* files Rename GSL archive script to jobs/rocoto/arch_gsl.sh Changes for running without GF shallow - comment out consistency check in cu_gf_driver.F90 - set imfshalcnv to -1 in config.fcst Updates to experiment setup scripts - created GSL specific files workflow_utils.py_gsl setup_workflow_fcstonly_gsl_ics.py setup_workflow_fcstonly_gsl.py - pointed workflow_utils.py to GSL version - added example setup scripts, ffl127.sh and testics.sh commit 3f736afabc7956d1cf3c3941519116742ac97608 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:20:44 2022 +0000 Added GSL specific getic scripts commit e8cb894178ac7978fbe4fd5a9851db77ed0032bd Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:16:20 2022 +0000 Add GSL suite definition files to build_ufs.sh commit 38c354b976be0e445922a18816f59939d31e8c40 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 01:12:27 2022 +0000 Updates for GSL - cleaned up checkout.sh - renamed fv3gfs.fd_gsl to ufs_model.fd_gsl - renamed suite definition files from FV3_GSD to FV3_RAP commit 8ea7fd81c914725d453c2c770d3881f04f237215 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Mar 4 00:40:23 2022 +0000 Updates for GSL - updated INFO file - updated GSL Suite Definition Files renamed FV3_GSD_v0 FV3_RAP_cires_ugwp renamed FV3_GSD_noah FV3_RAP_sfcdiff_unified_ugwp added FV3_RAP_sfcdiff_ugwpv1 - renamed GSL diag tables diag_table_da_gsd => diag_table_da_gsl diag_table_gsd => diag_table_gsl diag_table_gsd_ruc => diag_table_gsl_ruc - renamed GSL field table field_table_gsd => field_table_thompson_aero_tke - change cdmbgwd values for SDF FV3_RAP_noah_sfcdiff_ugwpv1 commit b0ea869ef9d11662b0710e4763f9f36064efab55 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Mar 3 20:50:41 2022 +0000 Merge 01Mar2022 NOAA-EMC/develop branch into gslv16_dev Squashed commit of the following: commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d11 e08f55583 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb39 e08f55583 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f1 b2879fe9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature b…

Squashed commit of the following: commit cabf437044cb937caf7a7830068fd9e413c5921f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Mar 30 21:28:50 2022 -0400 Update model and settings for Prototype P8b (#681) Updates model and setting defaults for prototype 8b. The UFS version is updated to a recent version of UFS (tag Prototype-P8b). As part of this, the print_esmf option is removed from the model configure file and replaced with a new setting in nems.configure. We have not made this option user-configurable at this point, but that may come in the future. The default CCPP suites have been updated for all modes to either FV3_GFS_v17_p8 or FV3_GFS_v17_coupled_p8. This involves changing the microphysics to Thompson and changes the gravity wave drag version (knob_ugwp_version) to 0. This change breaks cycled mode for the time being. A future PR will revert the defaults to ones that allow cycled to run along with a more robust system for changing settings. Tiled fix files are now used for all modes instead of just coupled. Cellular automata now defaults on ON. There are also other miscellaneous settings that have had their defaults changed. Fixes #641, #687 commit e3f707cb9c05b45e9d4019679e406f54008279a5 Author: XuLi-NOAA <55100838+XuLi-NOAA@users.noreply.github.com> Date: Thu Mar 24 05:43:31 2022 -0400 Modify eobs for EnKF thinning In the Hybrid EnKF GSI, the thinning box size, dmesh, is different for the full resolution analysis and EnKF respectively. There are set in GSI scripts for the full resolution analysis, and reset in global workflow in config.eobs. Only two thinning box sizes, dmesh(1) & dmesh(2), are defined in GSI scripts before, recently, two more, dmesh(3) & dmesh(4) are added. Accordingly, these two need to be added in config.eobs as well. Specifically, add dmesh(3)=225.0,demsh(4)=100.0 to config.eobs. Fixes #595 commit c32eea459af3177cee28e151b43fe5e12bdfc412 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 22 11:18:10 2022 -0400 Update ocean resolution for C48 (#651) The ocean resolution for C48 was set as 1-deg, but the fractional grid fix files available at C48 are for a 4-deg ocean grid. The ocean resolution is now set to this value when FV3 is C48. Also commented out a currently redundant block setting OCNRES in config.ocn. The one in ecfs has to stay as it recalculates the ocean resolution based on the EnKF resolution. Fixes #650 commit d758e8b227fca7b5a3320adc43c29ba492c3bfe9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Mar 10 05:54:49 2022 -0500 Add single forecast GOCART support (#659) Adds support for running single coupled free forecasts with GOCART aerosols. Support for continuous aerosol fields from cycle to cycle will be added in a future PR. To turn on aerosols, there is a new --aerosols option for setup_expt.py. The option takes no arguments. When it is used, aerosols will be turned on by setting DO_AERO="YES" in config.base. GOCART output files are placed in the chem directory in COM. There is a new tarball archived, chem.tar, that contains the GOCART output. Partially addresses #516 Fixes #403 commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d11 e08f55583 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb39 e08f55583 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f1 b2879fe9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature branch for testing Refs: #178 commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:41:32 2021 +0000 Correct if-statement syntax in config.init Refs: #178 commit 005d33d7b100b279e0db5290824c3e7acabfa4ba Merge: 5ec376bab e09a398f1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 15:23:05 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit b2879fe9f90def631047f533db2144858d827023 Merge: 68b9157bd a8ed770d9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 10:07:05 2021 -0400 Merge pull request #326 from NOAA-EMC/release/gfsv16.1.1 GFSv16.1.1 commit e09a398f1cedc7252219e75bf0b319d2601bc8df Merge: e3fcfebc1 6bad810bc Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri May 21 09:58:49 2021 -0400 Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade EMC_verif-global v2.0.0 major release updates commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a Author: Mallory Row <mallory.row@noaa.gov> Date: Fri May 21 13:55:13 2021 +0000 Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit 9cf615d11b096ea4843f4e5938a6a65f3500df49 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 20 20:10:18 2021 +0000 Modulefile updates for testing with waves on - updated ww3 and base modulefiles to add modules and update some - added new: pio/2.5.2i, fms/2020.04.03 - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6 Refs: #164 commit b155ff37040658703168268d4e58fe4e6b45a50d Author: Mallory Row <mallory.row@noaa.gov> Date: Thu May 20 15:00:04 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit cae62e3f47e245e70fcf3721fb4c022ea11c059f Merge: 8def77afd e3fcfebc1 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 19 19:45:05 2021 +0000 Sync merge with develop and WW3 build updates - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack - WW3 build updates: revert back to separate module files for build; address modulefile reorganization in separate issue - remove CCPP option with system build, doing CCPP by default now Refs: #164 commit 5ec376bababd935e4f3b15c4754105f5bd750657 Merge: 6b6b9ed39 e3fcfebc1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed May 19 18:24:31 2021 +0000 Merge remote-tracking branch 'origin/develop' into issue178 * origin/develop: change fv3gfs checkout head fixed a compilation error, NEMs/exe existing, in hera build_fv3.sh with ATM fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 bugfix for not removing last point from list in wave post pnt jobs changes added in link_fv3gfs for fix_aer changed fix dir for link_fv3gfs changes on build_fv3.sh and symlinks to optical data files instead of cp Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination updated config.fcst testing merra2 workflow in hera update merra2 before a new pull request Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions udate config.base.emc.dyn high resolution MERRA2 data used fixed a bug related to orion added merra2 input and update diag_table merra2 workflow for orion Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) commit 4641c5d206a95e0e66276fa86d46ecd580213fd5 Merge: eff8a1258 e3fcfebc1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 19 14:51:19 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit e3fcfebc1ff9c9f9ceda7b775de0c34117de6459 Merge: 95e0dffea fa5d1e2ba Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 19 10:02:19 2021 -0400 Merge pull request #254 from AnningCheng-NOAA/merra2 Addition of support for MERRA2 commit fa5d1e2ba242a08e26cb7bac8c68b700a83d1d60 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue May 18 10:41:16 2021 -0400 change fv3gfs checkout head commit 283c4a044847bbadd0cef46e14dde4de97abe986 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 17 15:56:56 2021 -0400 fixed a compilation error, NEMs/exe existing, in hera commit 6b574160f94329754677e7f4541ab07c44185bb0 Author: anning.cheng <anning.cheng@noaa.gov> Date: Fri May 14 13:44:18 2021 +0000 build_fv3.sh with ATM commit dfc8aa9a2cf5370fff38520d2a28f3960be3b583 Merge: bf5d11063 95e0dffea Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed May 12 20:11:44 2021 +0000 Merge remote-tracking branch 'upstream/develop' into merra2 commit eff8a1258aa70c061fe69697388f8914935726ee Merge: b1ad0b963 95e0dffea Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 12 19:15:17 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit 95e0dffea435af17be9150fcd0c842763768b45f Merge: fc727f405 dd4d18790 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 12 14:51:10 2021 -0400 Merge pull request #323 from NOAA-EMC/sync/operations_v16.0.9 Bring operations branch v16.0.9 changes into develop commit dd4d1879093516a7950c9e0e59f6e44e462199f6 Merge: fc727f405 68b9157bd Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 10 16:40:13 2021 +0000 Merge remote-tracking branch 'origin/operations' into sync/operations_v16.0.9 * origin/operations: bugfix for not removing last point from list in wave post pnt jobs Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) Refs: #309 commit 8def77afd4a9f1cd6cdca42c956bc7ebf675a58d Merge: c6e2a96e8 d46e8cf49 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 10 11:45:02 2021 -0400 Merge pull request #322 from JessicaMeixner-NOAA/hpcstackww3 Updates for ww3 pre and post exec builds for hpc-stack commit d46e8cf49aff0dbf72e457f1177e10e6f50252a6 Author: Jessica Meixner <Jessica.Meixner@noaa.gov> Date: Mon May 10 15:31:56 2021 +0000 update for ww3_pre/post build: -- remove ww3 specific module files -- updated module base files to be in sync with ufs-weather-model except that jasper is a more recent version which is needed for ww3_grib -- added extra ww3 execs needed for this branch -- added ww3prepost build to build_all and partial build commit c6e2a96e86611cce00455609d9be803d580e7bc0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:30:13 2021 +0000 Change fix file linking to scan for possible subfolders in set - instead of providing subfolder names, scan for subfolders in FIX_DIR path and then create symlinks based on existing subfolders in set - will not have to keep updating list of subfolders now Refs: #164 commit aa1d1e9ca1d8521ef22e1bdb654d4a70e7b1e29e Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:27:13 2021 +0000 Change CCPP_SUITE from FV3_GFS_v16beta to FV3_GFS_v16 - newer ufs-weather-model hash supports FV3_GFS_v16 suite Refs: #164 commit a8ed770d9c1e8614c5477d0129d6eaf5fe4e2085 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:32:36 2021 +0000 Companion update to Externals.cfg for WAFS tag update to gfs_wafs.v6.0.22 Refs: #1,#321 commit 68d9b5b5ff072b1f62131a9f7495c33c14c4a850 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:28:17 2021 +0000 WAFS tag update to gfs_wafs.v6.0.22 for bug fix Refs: #1,#321 commit 68b9157bd59278dc07369d316999d3c8485ebf7c Merge: 1f5af6283 97fe99096 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 5 10:50:42 2021 -0400 Merge pull request #306 from NOAA-EMC/release/gfsv16.0.0_to_ops GFSv16.0.9 commit 1aea3ee393c99d4f76556fbbdbebc43f629558c2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:30:06 2021 +0000 Add build script and modulefiles for WW3 build - WW3 execs no longer built by FV3 build, need separate build now - add new build_ww3prepost.sh script for building WW3 execs in ufs-weather-model checkout - add modulefiles for WCOSS-Dell, Hera, and Orion Refs: #164 commit 214431a2c04f6e685e966810621fc2fae771d2f5 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:26:00 2021 +0000 Update WAFS execs to include .x - update WAFS exec names in link_fv3gfs.sh to include ".x" extension that was added with new version Refs: #164 commit eb1613764794a35d165e55423682ed592b2aaacb Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:22:06 2021 +0000 ufs-weather-model hash update for WW3 support with hpc-stack - update ufs-weather-model hash to 554aedcd63e4a7c5012570406132eaf76e249ca9 - update build_fv3.sh for new compile arguments for CCPP/WW3 build Refs: #164 commit b1ad0b96328a54112ecc13ff4b71dcc08556a8c1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 5 14:13:58 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.1 Refs: #315 commit c206e8d2606f14ee6188740f881673ff512b866b Author: Mallory Row <mallory.row@noaa.gov> Date: Mon May 3 19:16:42 2021 +0000 Fix typo in config.metp There was a typo in the grid-to-obs METviewer related config variables. The variables started with "g2g1" instead of "g2o1". Refs: #315 commit f9013decd5af75f66eda619175bacc7549f4746a Author: Brian Curtis <Brian.Curtis@noaa.gov> Date: Mon May 3 14:37:13 2021 -0400 Files to test for python3 compatibility commit 0b9607711900e0da0de3d3dc1af91cc4dc9dd04d Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 12:31:01 2021 -0400 Update v16.1 release notes with wave script fix Refs: #301 commit fda26e9010ef59f69cd378c3092bdc82e57e4ec2 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon May 3 12:08:12 2021 -0400 Update config.base.nco.static Change HOMEobsproc_prep and HOMEobsproc_network to point at NCO installation of these packages. commit f9a6dd71ef7d580d6b83f50eb53814a06a944577 Merge: 173bb4814 97fe99096 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 11:55:09 2021 -0400 Merge branch 'release/gfsv16.0.0_to_ops' into release/gfsv16.1 Include wave fixes in v16.1 Refs: #301 commit 173bb4814ed2d2bc6e3436263f55c199f8dc8721 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 11:52:42 2021 -0400 Update v16.1 release notes for wave fixes Refs: #301 commit 858f216330d7ab71137afe6331f6576fec413aee Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:19:56 2021 +0000 Update EMC_post, UFS_UTILS, EMC_gfs_wafs versions in Externals.cfg Refs: #164 commit 6ce83363726ece6dbd34719430dd44f5e63bbc3c Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:14:54 2021 +0000 Component updates for UPP, WAFS, UFS_UTILS - new tag in checkout for UFS_UTILS to use hpc/1.1.0 - new hash in checkout for UPP/EMC_post to support GTG and GTG code copy fix - new hash in checkout for WAFS/EMC_gfs_wafs to support hpc-stack - build script update for WAFS (cmake/stack) - WAFS GCIP config update to fix runtime error Refs: #164 commit 709095709ca60498d05ea0f519b494501e1ecdf2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:11:51 2021 +0000 Update util_shared to 1.3.0 on WCOSS-Dell - version changed in production for v16.0.9 footer fix Refs: #164 commit bf5d110632fc67653441e6830bfdcdddda906706 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 3 10:53:37 2021 -0400 fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 commit 97fe990968955486fe2b7f3035c9d9423cef5e3e Merge: c582db288 f0fd3d410 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 3 09:15:15 2021 -0400 Merge pull request #318 from JessicaMeixner-NOAA/v16/bugforpnt Bug fix for missing buoy in wave post point commit f0fd3d4108debaa61f000ac700fd90904f1b600b Author: jessica.meixner <Jessica.Meixner@noaa.gov> Date: Fri Apr 30 17:56:34 2021 +0000 bugfix for not removing last point from list in wave post pnt jobs commit fb47a5a0f7391f670461b00eaf324c3b0102ef1f Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Apr 28 17:50:15 2021 +0000 Update TC_tracker version in config.vrfy - new TC_tracker.v1.1.15.4 was made available by Jiayi Peng - new version supports hpc-stack on supported platforms - installed locally on WCOSS-Dells, Hera, and Orion Refs: #164 commit 587ac0c914430d5b887327d7c566c452d2eace62 Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed Apr 28 10:36:49 2021 -0400 changes added in link_fv3gfs for fix_aer commit 48690cd07ceeb90c6808346a04a31a6166505c86 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed Apr 28 14:00:46 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.0 commit 1d0e0c29979101b451f1fda265af3f9a716bb9de Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Apr 27 19:33:09 2021 +0000 Reverting resource related changes - will commit resource adjustments separately Refs: #164 commit 101905ce4d92a544d353700b0acdc137aa61b088 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue Apr 27 14:15:59 2021 -0400 changed fix dir for link_fv3gfs commit 3271bac5b2072bfa2c0c0d229f050b647cd28925 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Tue Apr 27 10:08:54 2021 -0400 Update Externals.cfg and release notes for v16.1 Updated Externals.cfg GSI tag to gfsda.v16.1.0. Added sections in the release notes to explicitly say no changes to parm/config and scripts. Refs: #301 commit 31389bc23b89b1713712da17c8f226b649286b40 Merge: b1e924cd4 c582db288 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Tue Apr 27 08:31:41 2021 -0400 Merge branch 'release/gfsv16.0.0_to_ops' into release/gfsv16.1 This update brings in the wave foot fix for GFSv16.0.9. Refs: #301 commit b1e924cd44eba056443cb2a6789b1dc8040a02e1 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Tue Apr 27 07:31:44 2021 -0400 Change GSI tag to gfsda.v16.1.0 The GSI tag has been updated for the v16.1 implementation. This implementation turns on commercial RO data from GeoOptics. See release notes docs/Release_Notes.gfs.v16.1.0.txt in the global-workflow and release notes doc/Release_Notes.gfsda.v16.1.0.txt in the GSI for details. Refs: #301 commit 3142a8219c74b7b33a2bee1aed4ed7acd34ed0dc Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon Apr 26 16:59:43 2021 -0400 Add Release Notes for GFSv16.1 Added the file docs/Release_Notes.gfs.v16.1.0.txt to release branch release/gfsv16.1. Refs: #301 commit 7cd6e0e3000a47b39fa0c7e75ad66150e96385d8 Author: Mallory Row <mallory.row@noaa.gov> Date: Fri Apr 23 14:44:03 2021 +0000 Fix setting of 'SDATE_GFS' for free forecast XML In the workflow XML for free forecasts there is no SDATE_GFS variable. The 'SDATE_GFS' variable was changed to be set to the value of 'SDATE'. Refs: #315 commit d34b99d4e3d369b784fd9d2c639a0bddd1bbfc0c Author: Mallory Row <mallory.row@noaa.gov> Date: Fri Apr 23 12:59:51 2021 +0000 Clean up and add new settings in metp.sh SDATE_GFS was added into the script preamble following the addition of the variable being added as a rocoto exported environment variable for metp tasks. Config.vrfy was removed from the list of relevant configs to source. Variables CDATEm1 and PDYm1 were removed and replaced with VDATE. VDATE is the verification date to be done by the metp tasks based on VRFYBACK_HRS set in config.metp. Lines were added to catch the exit status of VERIFGLOBAL_SH and to exit if not succesfully run so it can be caught by rocoto. Refs: #315 commit 998f1a454427dedd46bb20b36e381bedbdf3e349 Author: Mallory Row <mallory.row@noaa.gov> Date: Fri Apr 23 12:49:38 2021 +0000 Revamp of config.metp Following the EMC_verif-global configuration remake, config.metp has been revamped to support the new configuration settings. Refs: #315 commit 6a01ae405202b8984fe8efa73573d7fdba2b74d2 Author: Mallory Row <mallory.row@noaa.gov> Date: Thu Apr 22 17:17:14 2021 +0000 Add 'SDATE_GFS' rocoto env var for metp tasks The connector script between EMC_verif-global and global-workflow run_verif_global_in_global_workflow.sh (housed in EMC_verif-global) contains a new feature that checks the maximum forecast hour for verification is the hour's initialization date is equal to or after the first GFS cycle initialization. If the date is before, the maximum forecast hour is adjusted to the maximum hour relative to the forecast verification date and the first GFS cycle initialization. This feature was added to cut down on METplus calls being done on data that don't exist. Refs: #315 commit dfec5816add3c56721360a418ec9f3459cfd4d8c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 15:27:56 2021 +0000 Update UFS_UTILS hash to 9d9dd23e37a51fcc5ff6b7499b834c85ab32e5f3 Refs: #164 commit be564bb85eeefbb1699992e0ed4f0705e4e2ee24 Author: anning.cheng <anning.cheng@noaa.gov> Date: Thu Apr 22 11:22:02 2021 -0400 changes on build_fv3.sh and symlinks to optical data files instead of cp commit 15c6619c6e211eb67ca6aa5c995e4a3bf4cf586f Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 14:03:46 2021 +0000 Adjust C768 fcst thread value for reduced node usage - change C768 nth_fv3_gfs value from 7 to 2 Refs: #164 commit ece41632a76e697184a46bb2a428c35ccdf08305 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Apr 22 13:58:22 2021 +0000 Add separate gfs resource variables to fcst in config.resources Refs: #164 commit 00c18b5e341d601fd83da2f9df2ac928e8dcf7c8 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 13:44:13 2021 +0000 Update FIX_DIR paths in link_fv3gfs.sh - change platform FIX_DIR paths from fix_nco_gfsv16 set to developmental fix set for v17+ Refs: #164 commit b6c392c7569ed909d6b0b27c0f6a4f828b7acdfd Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 13:40:25 2021 +0000 Set DO_WAVE=NO in config.base - set default DO_WAVE setting to NO in config.base.emc.dyn - turn off waves until hpc-stack for WW3 execs build is ready Refs: #164 commit 2b703d335b8e3e97c9764bd60d87188ed11938fd Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 13:17:28 2021 +0000 Set WAFS checkout to be optional with -o flag - add checkout_wafs to -o flag settings Refs: #164 commit 305bf5e0fb3c665cf71f10023feed1a121be329b Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 13:01:04 2021 +0000 Update Externals.cfg to match checkout.sh versions Refs: #164 commit 3cc02d507df48e2b9f99163d737123e5b5c716c0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Apr 22 12:52:46 2021 +0000 Update GLDAS and UFS_UTILS checkouts - update GLDAS checkout t…

Add updates for GSL to run new HFIP models on Jet commit 1a1a524433b2dba903680515218eea694e9c8ada Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Jun 17 06:28:07 2022 +0000 Updates for running on Jet - update environment file, env/JET.env - update module_base.jet file to use hpc-stack libraries - update jet files under modulefiles/ - create GSL and EMC versions of vrfy.sh; create link to GSL version - update paths on Jet in config.vrfy - update variables in post XML files in gfs_post.fd_gsl directory - delete ens_tracker.v1.1.15.2 directory - add ens_tracker.v1.1.15.4 directory (with Dave Huber's modifications for jet) commit e86bdf12053801cad1a07d47f8630b9e9a7c005e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri May 27 16:47:48 2022 +0000 Restore setup experiment script, ffl127.sh commit 92b4376121e8e9b08659487e574c077005c2b9d5 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu May 26 00:06:39 2022 +0000 Updates for GSL - change settings for shal_cnv and imfshalcnv for FV3_GFS_v17_p8_mynn suite in config.fcst - added new experiment setup scripts commit 8a7e0250832b39df39c16b1bcf01477b51048b22 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed May 25 10:44:51 2022 +0000 Updates for GSL - set imp_physics=8 default in config.base - modified if statement for setting imfdeepcnv/imfshalcnv in config.fcst commit 0681b9f8c2838b2861b68f13efd47e6a745d5059 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed May 25 00:16:30 2022 +0000 Updates for GSL - update UFS to NOAA-GSL:gsl/develop 23May22 branch, -7b0be42, in checkout.sh - add Build_gsi=false to build_all.sh - remove FV3_GFS_v16_RRTMGP suite from build_ufs.sh - add FV3_GFS_v17_p8,FV3_GFS_v17_p8_gf,FV3_GFS_v17_p8_mynn suites to build_ufs.sh - add sorc/ufs_model.fd_gsl directory for new SDFs (FV3_v17_p8_gf, FV3_v17_p8_mynn) commit 7313f5edd7806320736b35183969c35838465c7d Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon May 23 19:36:04 2022 +0000 Merged NOAA-EMC/develop 30Mar22 branch into gslv16_dev Squashed commit of the following: commit cabf437044cb937caf7a7830068fd9e413c5921f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Mar 30 21:28:50 2022 -0400 Update model and settings for Prototype P8b (#681) Updates model and setting defaults for prototype 8b. The UFS version is updated to a recent version of UFS (tag Prototype-P8b). As part of this, the print_esmf option is removed from the model configure file and replaced with a new setting in nems.configure. We have not made this option user-configurable at this point, but that may come in the future. The default CCPP suites have been updated for all modes to either FV3_GFS_v17_p8 or FV3_GFS_v17_coupled_p8. This involves changing the microphysics to Thompson and changes the gravity wave drag version (knob_ugwp_version) to 0. This change breaks cycled mode for the time being. A future PR will revert the defaults to ones that allow cycled to run along with a more robust system for changing settings. Tiled fix files are now used for all modes instead of just coupled. Cellular automata now defaults on ON. There are also other miscellaneous settings that have had their defaults changed. Fixes #641, #687 commit e3f707cb9c05b45e9d4019679e406f54008279a5 Author: XuLi-NOAA <55100838+XuLi-NOAA@users.noreply.github.com> Date: Thu Mar 24 05:43:31 2022 -0400 Modify eobs for EnKF thinning In the Hybrid EnKF GSI, the thinning box size, dmesh, is different for the full resolution analysis and EnKF respectively. There are set in GSI scripts for the full resolution analysis, and reset in global workflow in config.eobs. Only two thinning box sizes, dmesh(1) & dmesh(2), are defined in GSI scripts before, recently, two more, dmesh(3) & dmesh(4) are added. Accordingly, these two need to be added in config.eobs as well. Specifically, add dmesh(3)=225.0,demsh(4)=100.0 to config.eobs. Fixes #595 commit c32eea459af3177cee28e151b43fe5e12bdfc412 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 22 11:18:10 2022 -0400 Update ocean resolution for C48 (#651) The ocean resolution for C48 was set as 1-deg, but the fractional grid fix files available at C48 are for a 4-deg ocean grid. The ocean resolution is now set to this value when FV3 is C48. Also commented out a currently redundant block setting OCNRES in config.ocn. The one in ecfs has to stay as it recalculates the ocean resolution based on the EnKF resolution. Fixes #650 commit d758e8b227fca7b5a3320adc43c29ba492c3bfe9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Mar 10 05:54:49 2022 -0500 Add single forecast GOCART support (#659) Adds support for running single coupled free forecasts with GOCART aerosols. Support for continuous aerosol fields from cycle to cycle will be added in a future PR. To turn on aerosols, there is a new --aerosols option for setup_expt.py. The option takes no arguments. When it is used, aerosols will be turned on by setting DO_AERO="YES" in config.base. GOCART output files are placed in the chem directory in COM. There is a new tarball archived, chem.tar, that contains the GOCART output. Partially addresses #516 Fixes #403 commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d11 e08f55583 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb39 e08f55583 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f1 b2879fe9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature branch for testing Refs: #178 commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:41:32 2021 +0000 Correct if-statement syntax in config.init Refs: #178 commit 005d33d7b100b279e0db5290824c3e7acabfa4ba Merge: 5ec376bab e09a398f1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 15:23:05 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit b2879fe9f90def631047f533db2144858d827023 Merge: 68b9157bd a8ed770d9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 10:07:05 2021 -0400 Merge pull request #326 from NOAA-EMC/release/gfsv16.1.1 GFSv16.1.1 commit e09a398f1cedc7252219e75bf0b319d2601bc8df Merge: e3fcfebc1 6bad810bc Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri May 21 09:58:49 2021 -0400 Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade EMC_verif-global v2.0.0 major release updates commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a Author: Mallory Row <mallory.row@noaa.gov> Date: Fri May 21 13:55:13 2021 +0000 Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit 9cf615d11b096ea4843f4e5938a6a65f3500df49 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 20 20:10:18 2021 +0000 Modulefile updates for testing with waves on - updated ww3 and base modulefiles to add modules and update some - added new: pio/2.5.2i, fms/2020.04.03 - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6 Refs: #164 commit b155ff37040658703168268d4e58fe4e6b45a50d Author: Mallory Row <mallory.row@noaa.gov> Date: Thu May 20 15:00:04 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit cae62e3f47e245e70fcf3721fb4c022ea11c059f Merge: 8def77afd e3fcfebc1 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 19 19:45:05 2021 +0000 Sync merge with develop and WW3 build updates - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack - WW3 build updates: revert back to separate module files for build; address modulefile reorganization in separate issue - remove CCPP option with system build, doing CCPP by default now Refs: #164 commit 5ec376bababd935e4f3b15c4754105f5bd750657 Merge: 6b6b9ed39 e3fcfebc1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed May 19 18:24:31 2021 +0000 Merge remote-tracking branch 'origin/develop' into issue178 * origin/develop: change fv3gfs checkout head fixed a compilation error, NEMs/exe existing, in hera build_fv3.sh with ATM fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 bugfix for not removing last point from list in wave post pnt jobs changes added in link_fv3gfs for fix_aer changed fix dir for link_fv3gfs changes on build_fv3.sh and symlinks to optical data files instead of cp Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination updated config.fcst testing merra2 workflow in hera update merra2 before a new pull request Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions udate config.base.emc.dyn high resolution MERRA2 data used fixed a bug related to orion added merra2 input and update diag_table merra2 workflow for orion Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) commit 4641c5d206a95e0e66276fa86d46ecd580213fd5 Merge: eff8a1258 e3fcfebc1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 19 14:51:19 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit e3fcfebc1ff9c9f9ceda7b775de0c34117de6459 Merge: 95e0dffea fa5d1e2ba Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 19 10:02:19 2021 -0400 Merge pull request #254 from AnningCheng-NOAA/merra2 Addition of support for MERRA2 commit fa5d1e2ba242a08e26cb7bac8c68b700a83d1d60 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue May 18 10:41:16 2021 -0400 change fv3gfs checkout head commit 283c4a044847bbadd0cef46e14dde4de97abe986 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 17 15:56:56 2021 -0400 fixed a compilation error, NEMs/exe existing, in hera commit 6b574160f94329754677e7f4541ab07c44185bb0 Author: anning.cheng <anning.cheng@noaa.gov> Date: Fri May 14 13:44:18 2021 +0000 build_fv3.sh with ATM commit dfc8aa9a2cf5370fff38520d2a28f3960be3b583 Merge: bf5d11063 95e0dffea Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed May 12 20:11:44 2021 +0000 Merge remote-tracking branch 'upstream/develop' into merra2 commit eff8a1258aa70c061fe69697388f8914935726ee Merge: b1ad0b963 95e0dffea Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 12 19:15:17 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit 95e0dffea435af17be9150fcd0c842763768b45f Merge: fc727f405 dd4d18790 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 12 14:51:10 2021 -0400 Merge pull request #323 from NOAA-EMC/sync/operations_v16.0.9 Bring operations branch v16.0.9 changes into develop commit dd4d1879093516a7950c9e0e59f6e44e462199f6 Merge: fc727f405 68b9157bd Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 10 16:40:13 2021 +0000 Merge remote-tracking branch 'origin/operations' into sync/operations_v16.0.9 * origin/operations: bugfix for not removing last point from list in wave post pnt jobs Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) Refs: #309 commit 8def77afd4a9f1cd6cdca42c956bc7ebf675a58d Merge: c6e2a96e8 d46e8cf49 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 10 11:45:02 2021 -0400 Merge pull request #322 from JessicaMeixner-NOAA/hpcstackww3 Updates for ww3 pre and post exec builds for hpc-stack commit d46e8cf49aff0dbf72e457f1177e10e6f50252a6 Author: Jessica Meixner <Jessica.Meixner@noaa.gov> Date: Mon May 10 15:31:56 2021 +0000 update for ww3_pre/post build: -- remove ww3 specific module files -- updated module base files to be in sync with ufs-weather-model except that jasper is a more recent version which is needed for ww3_grib -- added extra ww3 execs needed for this branch -- added ww3prepost build to build_all and partial build commit c6e2a96e86611cce00455609d9be803d580e7bc0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:30:13 2021 +0000 Change fix file linking to scan for possible subfolders in set - instead of providing subfolder names, scan for subfolders in FIX_DIR path and then create symlinks based on existing subfolders in set - will not have to keep updating list of subfolders now Refs: #164 commit aa1d1e9ca1d8521ef22e1bdb654d4a70e7b1e29e Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:27:13 2021 +0000 Change CCPP_SUITE from FV3_GFS_v16beta to FV3_GFS_v16 - newer ufs-weather-model hash supports FV3_GFS_v16 suite Refs: #164 commit a8ed770d9c1e8614c5477d0129d6eaf5fe4e2085 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:32:36 2021 +0000 Companion update to Externals.cfg for WAFS tag update to gfs_wafs.v6.0.22 Refs: #1,#321 commit 68d9b5b5ff072b1f62131a9f7495c33c14c4a850 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:28:17 2021 +0000 WAFS tag update to gfs_wafs.v6.0.22 for bug fix Refs: #1,#321 commit 68b9157bd59278dc07369d316999d3c8485ebf7c Merge: 1f5af6283 97fe99096 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 5 10:50:42 2021 -0400 Merge pull request #306 from NOAA-EMC/release/gfsv16.0.0_to_ops GFSv16.0.9 commit 1aea3ee393c99d4f76556fbbdbebc43f629558c2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:30:06 2021 +0000 Add build script and modulefiles for WW3 build - WW3 execs no longer built by FV3 build, need separate build now - add new build_ww3prepost.sh script for building WW3 execs in ufs-weather-model checkout - add modulefiles for WCOSS-Dell, Hera, and Orion Refs: #164 commit 214431a2c04f6e685e966810621fc2fae771d2f5 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:26:00 2021 +0000 Update WAFS execs to include .x - update WAFS exec names in link_fv3gfs.sh to include ".x" extension that was added with new version Refs: #164 commit eb1613764794a35d165e55423682ed592b2aaacb Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:22:06 2021 +0000 ufs-weather-model hash update for WW3 support with hpc-stack - update ufs-weather-model hash to 554aedcd63e4a7c5012570406132eaf76e249ca9 - update build_fv3.sh for new compile arguments for CCPP/WW3 build Refs: #164 commit b1ad0b96328a54112ecc13ff4b71dcc08556a8c1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 5 14:13:58 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.1 Refs: #315 commit c206e8d2606f14ee6188740f881673ff512b866b Author: Mallory Row <mallory.row@noaa.gov> Date: Mon May 3 19:16:42 2021 +0000 Fix typo in config.metp There was a typo in the grid-to-obs METviewer related config variables. The variables started with "g2g1" instead of "g2o1". Refs: #315 commit f9013decd5af75f66eda619175bacc7549f4746a Author: Brian Curtis <Brian.Curtis@noaa.gov> Date: Mon May 3 14:37:13 2021 -0400 Files to test for python3 compatibility commit 0b9607711900e0da0de3d3dc1af91cc4dc9dd04d Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 12:31:01 2021 -0400 Update v16.1 release notes with wave script fix Refs: #301 commit fda26e9010ef59f69cd378c3092bdc82e57e4ec2 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon May 3 12:08:12 2021 -0400 Update config.base.nco.static Change HOMEobsproc_prep and HOMEobsproc_network to point at NCO installation of these packages. commit f9a6dd71ef7d580d6b83f50eb53814a06a944577 Merge: 173bb4814 97fe99096 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 11:55:09 2021 -0400 Merge branch 'release/gfsv16.0.0_to_ops' into release/gfsv16.1 Include wave fixes in v16.1 Refs: #301 commit 173bb4814ed2d2bc6e3436263f55c199f8dc8721 Author: catherine.thomas <catherine.thomas@noaa.gov> Date: Mon May 3 11:52:42 2021 -0400 Update v16.1 release notes for wave fixes Refs: #301 commit 858f216330d7ab71137afe6331f6576fec413aee Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:19:56 2021 +0000 Update EMC_post, UFS_UTILS, EMC_gfs_wafs versions in Externals.cfg Refs: #164 commit 6ce83363726ece6dbd34719430dd44f5e63bbc3c Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:14:54 2021 +0000 Component updates for UPP, WAFS, UFS_UTILS - new tag in checkout for UFS_UTILS to use hpc/1.1.0 - new hash in checkout for UPP/EMC_post to support GTG and GTG code copy fix - new hash in checkout for WAFS/EMC_gfs_wafs to support hpc-stack - build script update for WAFS (cmake/stack) - WAFS GCIP config update to fix runtime error Refs: #164 commit 709095709ca60498d05ea0f519b494501e1ecdf2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 3 15:11:51 2021 +0000 Update util_shared to 1.3.0 on WCOSS-Dell - version changed in production for v16.0.9 footer fix Refs: #164 commit bf5d110632fc67653441e6830bfdcdddda906706 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 3 10:53:37 2021 -0400 fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 commit 97fe990968955486fe2b7f3035c9d9423cef5e3e Merge: c582db288 f0fd3d410 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 3 09:15:15 2021 -0400 Merge pull request #318 from JessicaMeixner-NOAA/v16/bugforpnt Bug fix for missing buoy in wave post point commit f0fd3d4108debaa61f000ac700fd90904f1b600b Author: jessica.meixner <Jessica.Meixner@noaa.gov> Date: Fri Apr 30 17:56:34 2021 +0000 bugfix for not removing last point from list in wave post pnt jobs commit fb47a5a0f7391f670461b00eaf324c3b0102ef1f Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Apr 28 17:50:15 2021 +0000 Update TC_tracker version in config.vrfy - new TC_tracker.v1.1.15.4 was made available by Jiayi Peng - new version supports hpc-stack on supported platforms - installed locally on WCOSS-Dells, Hera, and Orion Refs: #164 commit 587ac0c914430d5b887327d7c566c452d2eace62 Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed Apr 28 10:36:49 2021 -0400 changes added in link_fv3gfs for fix_aer commit 48690cd07ceeb90c6808346a04a31a6166505c86 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed Apr 28 14:00:46 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.0 commit 1d0e0c29979101b451f1…

Squashed commit of the following: commit dbd9fa93ced07f39accf7ff4eec2859f0ed5d35f Author: ChunxiZhang-NOAA <49283036+ChunxiZhang-NOAA@users.noreply.github.com> Date: Mon May 30 21:50:56 2022 -0400 Updated SDFs and namelist settings for P8c (#795) Updates the model version in preparation for prototype 8c, along with commensurate setting updates. Some CCPP suites are removed from the UFS build as they are no longer available. Also updates the coupled initial conditions, and there is a simultaneous update to fixed orography files. Refs: #736 commit 05accc1c72b1311ae9689bef5e7a1291dc12a96a Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon May 23 17:36:51 2022 -0400 Correct incorrect increment prefix variable (#805) One instance of the increment prefix variable in `ush/forecast_postdet.sh` used `PREFIX_INC` instead of the `PREFIX_ATMINC` used elsewhere. Fixes #804 commit ac7cb1000d5c1d31babd36f4c3e17f643f30fd4d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun May 22 16:50:30 2022 -0400 Remove separate UPP clone (#803) Now that UPP is cloned within UFS, there is no need to create an independent clone in global-workflow. Scripts are updated to use the UPP within UFS. In addition to removing redundancy, this will avoid version mismatch issues when UFS and global-workflow checkout different versions. The upp directory is now linked from within UFS to sorc as upp.fd (instead of the gfs_post.fd the clone was placed in). Additionally, the build script is renamed to build_upp.sh. Fixes #770 Moots #797 commit 58728fb2c689c11335f4bf8ac371e18070c6fbd2 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 20 10:14:58 2022 -0400 Fix build script options (#801) There was an issue where if build_all.sh was called with only options that are not used by partial_build.sh, partial_build.sh would see those options because $@ was not overwritten. The script have been updated to consume those options so they are no longer present if $@ isn't overwritten in the new script call. Also fixed the getopts statement in partial_build.sh so we handle errors instead of bash (bash would report the wrong script if the script is sourced) Fixes #800 commit fa12db279cf829b861d08c06e3e3534a335e9fd7 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 18 01:04:32 2022 -0400 Refactor some build scripts (#794) Refactors the build_ufs script to allow the build of any UFS app to support future expansion of global-workflow capability. The default should be sufficient for most users, as S2SWA can be used for ATM, ATMA, S2S, and S2SW as well. The new format of the command is now: ``` build_ufs.sh [-a UFS_app][-v] -a UFS_app: Specify the UFS application to build. The default if none is provided is S2SWA -v: Turn on verbose mode (BUILD_VERBOSE) ``` build_all.sh is similarly refactored to include the same options. Also, a new `-c build_config` option is added to specify an alternative list of programs to build. ``` build_all.sh [-a UFS_app][-c build_config][-h][-v] -a UFS_app: Build a specific UFS app instead of the default -c build_config: Selectively build based on the provided config instead of the default config -h: Print usage message and exit -v: Run all scripts in verbose mode ``` partial_build.sh is also updated to take the new `-c` option to specify a build config. ``` partial_build.sh [-c config_file][-h][-v] -c config_file: Selectively build based on the provided config. The default if none is specified is gfs_build.cfg -h: Print usage message and exit -v: Run in verbose mode ``` In addition to the above, build_all and partial_build had their indentation redone and their usage/help statement updated/added. Also, the build configuration file was renamed to from fv3gfs_build.cfg to gfs_build.cfg. Fixes #745 Fixes #751 commit 2abee02765a3bae48f2b4e6a900400d6731eda06 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 18 01:02:57 2022 -0400 Add continuous aerosols support (#693) Adds support for continuous aerosols when running with GOCART (using the forecast aerosol tracers from the previous cycle as initial tracer fields). This adds a new task to the workflow mesh in forecast-only mode. The new task does not run in the first cycle, though it will appear in rocotostat/rocotoviewer. In subsequent cycles, the task will launch as soon as the needed restart files from the previous cycle are available and gfs_init has completed. There is currently no mechanism to have aerosol_init run for the first cycle (for instance, continuing from a previous experiment); users would have to run the scripts off-line to add aerosols to the initial conditions. To support the introduction of the necessary python scripts, a new python environment is added to provide necessary libraries. This virtual environment is temporarily being housed in personal space, but an issue has been opened with hpc-stack to add it to the standard stack installations. The introduction of miniconda also caused the conversion of all of the rocoto entry scripts (the ones rocoto calls to run the job) to bash. Most of them had been in korne. To make sure the needed restart files are produced, config.fcst now makes sure the forecast cadence is included in the list of restart times. This may need more testing to ensure it works properly with other restart lists. As part of this, STEP_GFS was updated to properly determine the step from gfs_cyc instead of being a set value. Closes #366 Fixes #516 Fixes #630 commit 69b39ee5af8cfbb5cbf5cf62c92d01958b697652 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu May 12 12:18:50 2022 -0400 Add --init to GSI submodule command (#781) Needed to obtain libsrc submodule during checkout and allows the GSI to build correctly since this GSI hash still needs the libsrc submodule during build. Refs: #780 commit b09f92c21028ea37e4663ce4c304935a2dc45b33 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Thu May 12 08:20:16 2022 -0400 Update field_table to be consistent with UFS (#778) Changes the fixed surface value of hydrometeor number concentrations and sub-grid TKE to 0. Also renames the field table. Both changes are consistent with changes made in UFS. Fixes #676 commit d72a62d6c0ab2e9f53ca3e6133148f29982f9d32 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Thu May 12 08:15:23 2022 -0400 Remove special MOD_PATH from build scripts (#775) We always use pre-installed libraries and special MOD_PATHs are no longer necessary, so these are removed from build scripts. MOD_PATH. This also moots MOD_PATHs that were hard-coded to Hera locations in some scripts. The MOD_PATH in build_ufs.sh remains as it is still needed and is a relative path into the UFS repo. Fixes #298 commit 2adf123814a2f29e9cca54a11fbb2807b3f6cf1b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 4 12:31:20 2022 -0400 Revert g2tmpl back to 1.10.0 (#773) Resolves bug with mismatch between hpc-ips and g2tmpl versions on the WCOSS-Dells. Also revert back to 1.10.0 on Hera and Orion to be consistent. Refs: #772 commit b90f4e99bc42f9a8afbeaa9479e674fb75e096ea Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Tue May 3 09:45:19 2022 -0400 Remove git submodule update for upp checkout (#768) UPP no longer has a CMakeModules submodule, so the submodule update is removed from the checkout script. Fixes: #767 commit ad2b14d9b1ed0fe89fe59bfb96cc03630e8457de Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Tue May 3 09:44:57 2022 -0400 Remove duplicate file linking for Thompson MP (#765) Files for Thompson MP were being copied twice by the link script: once by checking imp_physics, then again checking the CCPP Suite. This is now reduced to one check. Fixes: #675 commit a9fc0033b908aefb42d5b2d191c65af5cb7660c4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Apr 28 15:17:22 2022 -0400 Remove unneeded/outdated modulefiles (#762) Remove unneeded modulefiles for WCOSS-Cray and GSI monitoring. commit 3333dee304b6b53d3d716c60d0c87ad06d629c1c Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Thu Apr 28 14:35:57 2022 -0400 Remove prepbufr_pre-qc from archive lists (#753) The prepbuft_pre-qc file does not need to be archived, so it no longer is. Fixes #361 commit 88b1b1591d3201709f5f981908aaf7890d3021bd Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Apr 26 20:40:41 2022 -0400 Convert module files from Tcl to Lua (#756) Converts all module files from Tcl format to Lua. As a side effect, this change enforces using the files as modules rather than improperly sourcing them instead of loading. Fixes #670 commit ca80aeb86cb221263611605ba23858448bce0bad Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Apr 25 06:23:06 2022 -0400 Ensure hourly files when GLDAS is on (#740) GLDAS requires hourly output, so make sure FHOUT is 1 when GLDAS is on. Fixes #695 commit 9d00239088651b73a9667b70bd6247b34e35046f Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Tue Apr 19 21:22:22 2022 -0400 Update cyclone tracker to handle return code correctly #642 Updates the cyclone tracker call to correctly exit with an error code if the tracker script reports one. Fixes #507 commit 33d3dd14d6df8109274dde4606bb7a50e4638fa2 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Apr 19 21:18:56 2022 -0400 Update ww3 pre and post exe build to use cmake (#731) Updates the WW3 pre/post build system to use cmake. Fixes #688 commit 39facec1e03a404f84fd05b8739cd8e4010a0779 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Apr 12 11:36:30 2022 -0400 Add WCOSS2 GFSv16.2 operational def files into develop (#717) Add WCOSS2 operational GFS def files. Refs: #399 commit 0a85223e48a1a8dcced163791d8e7ae5a42a4fab Author: Xianwu Xue - NOAA <48287866+XianwuXue-NOAA@users.noreply.github.com> Date: Tue Apr 12 11:34:17 2022 -0400 Initialize "err" to avoid potential task fail (#715) If not initialize err, and change "set -x" to "set -xue", then the waveinit task will fail with error message: "line 234: err: unbound variable" On branch bugfix/issue_714 Changes to be committed: modified: scripts/exgfs_wave_init.sh Refs: #714 commit fc6e1c3316397432d2da218b3c4fc0ea1fe70644 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Apr 5 11:07:21 2022 -0400 config.base should not exist in the repository unless it is in ops. template only exists in the repo, the experiment directory should not contain the templated config.base.emc.dyn (#707) commit cabf437044cb937caf7a7830068fd9e413c5921f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Mar 30 21:28:50 2022 -0400 Update model and settings for Prototype P8b (#681) Updates model and setting defaults for prototype 8b. The UFS version is updated to a recent version of UFS (tag Prototype-P8b). As part of this, the print_esmf option is removed from the model configure file and replaced with a new setting in nems.configure. We have not made this option user-configurable at this point, but that may come in the future. The default CCPP suites have been updated for all modes to either FV3_GFS_v17_p8 or FV3_GFS_v17_coupled_p8. This involves changing the microphysics to Thompson and changes the gravity wave drag version (knob_ugwp_version) to 0. This change breaks cycled mode for the time being. A future PR will revert the defaults to ones that allow cycled to run along with a more robust system for changing settings. Tiled fix files are now used for all modes instead of just coupled. Cellular automata now defaults on ON. There are also other miscellaneous settings that have had their defaults changed. Fixes #641, #687 commit e3f707cb9c05b45e9d4019679e406f54008279a5 Author: XuLi-NOAA <55100838+XuLi-NOAA@users.noreply.github.com> Date: Thu Mar 24 05:43:31 2022 -0400 Modify eobs for EnKF thinning In the Hybrid EnKF GSI, the thinning box size, dmesh, is different for the full resolution analysis and EnKF respectively. There are set in GSI scripts for the full resolution analysis, and reset in global workflow in config.eobs. Only two thinning box sizes, dmesh(1) & dmesh(2), are defined in GSI scripts before, recently, two more, dmesh(3) & dmesh(4) are added. Accordingly, these two need to be added in config.eobs as well. Specifically, add dmesh(3)=225.0,demsh(4)=100.0 to config.eobs. Fixes #595 commit c32eea459af3177cee28e151b43fe5e12bdfc412 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 22 11:18:10 2022 -0400 Update ocean resolution for C48 (#651) The ocean resolution for C48 was set as 1-deg, but the fractional grid fix files available at C48 are for a 4-deg ocean grid. The ocean resolution is now set to this value when FV3 is C48. Also commented out a currently redundant block setting OCNRES in config.ocn. The one in ecfs has to stay as it recalculates the ocean resolution based on the EnKF resolution. Fixes #650 commit d758e8b227fca7b5a3320adc43c29ba492c3bfe9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Mar 10 05:54:49 2022 -0500 Add single forecast GOCART support (#659) Adds support for running single coupled free forecasts with GOCART aerosols. Support for continuous aerosol fields from cycle to cycle will be added in a future PR. To turn on aerosols, there is a new --aerosols option for setup_expt.py. The option takes no arguments. When it is used, aerosols will be turned on by setting DO_AERO="YES" in config.base. GOCART output files are placed in the chem directory in COM. There is a new tarball archived, chem.tar, that contains the GOCART output. Partially addresses #516 Fixes #403 commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 2021 +0000 Remove old compile command from build_fv3.sh Refs: #178 commit b36414e4ce49579c5db1829fab46e1a4ef302569 Merge: 9cf615d11 e08f55583 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 15 18:36:55 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack Refs: #164 commit 65ff48e049a651e74be8be121163c20957bf1c44 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:37:24 2021 +0000 Add v16 pgb anl pull to getic script Refs: #178 commit 37e7c2e0806678c93a11bae682f48da172940fd6 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:59 2021 +0000 Add OPS_RES variable to init script Refs: #178 commit db18627960d2def7bbfee30994f4be6586babe1c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 18:36:10 2021 +0000 Increase init job walltime to 30 mins from 15 mins Refs: #178 commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 10 15:43:27 2021 +0000 Update/fix pull of v14/v15 pgrb2 anl files in getic job Refs: #178 commit 18970c716d79922fa02b86165996bb47fb42d3fa Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 9 12:04:01 2021 -0500 Disconnect archive job in workflow from HPSS access check - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script Refs: #178 commit b52d2f0b82e0e376905c64daa593362396f8da1b Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:06:30 2021 -0500 Update UFS_UTILS checkout to ufs_utils_1_4_0 tag - new ufs_utils_1_4_0 tag includes updates to support this branch - From tag release notes: - Update the GDAS initialization utility to ingest GFS v16 data. - Update to process either the GFS or GDAS CDUMPs. Refs: #178 commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163 Author: kate.friedman <kate.friedman@noaa.gov> Date: Tue Jun 8 13:05:08 2021 -0500 Adjust comments in getic job script Refs: #178 commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:57:32 2021 +0000 Adjust getic/init job scripts - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs - remove duplicate pgb file pull from init job Refs: #178 commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 8 15:56:46 2021 +0000 Add cmake module load to Hera block in machine-setup.sh Refs: #178 commit fe448ff29aedca6a40a748ee47ae001b1639188c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 19:32:15 2021 +0000 Set DO_WAVE to NO - turning off waves by default in config.base Refs: #178 commit bfb0a33305a46d87f62c4a5c8bd7799a60362678 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:13:08 2021 -0500 Remove RUN_CCPP option, force CCPP now - remove RUN_CCPP case option from build_all.sh - remove RUN_CCPP option in build_fv3.sh, force CCPP build now - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now Refs: #178 commit 771782f109de15f9f0214bcceb852b51bb4b0e02 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 3 13:09:42 2021 -0500 Replace Orion checks with hpssarch checks for getic job - add hpssarch variable to setup_workflow_fcstonly.py - replace Orion checks with hpssarch=YES checks Refs: #178 commit e2ac5872ca482eb335bc6294e00594dc3a806718 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:23:35 2021 +0000 Update WCOSS-Dell section of machine-setup.sh - needed cmake module loaded for building - added cmake module load and prereq stack loads Refs: #178 commit f0afb91bae738413539ee2f1fdc63b79e93b3e52 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 14:22:43 2021 +0000 Change BDATE to GDATE in getic.sh Refs: #178 commit 69ac287062512b929a5193ebc86e4c7fcbbb1917 Merge: e62cefb39 e08f55583 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 2 10:17:52 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit e62cefb3943a87a90fd40234f08845534df818a1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:50:28 2021 +0000 Correct gdas operational tarball name in getic job script Refs: #178 commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 16:44:37 2021 +0000 getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting - add OPS_RES variable to define current operational resolution; use variable where needed now - updated getic job script to use OPS_RES variable in if-block check - updated getic job script with new operational tarballs to pull for warm starting high res runs Refs: #178 commit 499f217f92b5bb0fad9e71de221937d9973046ce Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue Jun 1 15:49:41 2021 +0000 Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile Refs: #178 commit e08f5558372d43d88890ca639e70ab923071361b Merge: e09a398f1 b2879fe9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 26 12:27:40 2021 -0400 Merge pull request #327 from NOAA-EMC/operations Operations updates for GFSv16.1.1 commit 824ff7254fba04a0b3726316d300f9fa6282c937 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:42:25 2021 +0000 Change UFS_UTILS version to feature branch for testing Refs: #178 commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Tue May 25 20:41:32 2021 +0000 Correct if-statement syntax in config.init Refs: #178 commit 005d33d7b100b279e0db5290824c3e7acabfa4ba Merge: 5ec376bab e09a398f1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 15:23:05 2021 -0400 Merge branch 'NOAA-EMC:develop' into issue178 commit b2879fe9f90def631047f533db2144858d827023 Merge: 68b9157bd a8ed770d9 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 24 10:07:05 2021 -0400 Merge pull request #326 from NOAA-EMC/release/gfsv16.1.1 GFSv16.1.1 commit e09a398f1cedc7252219e75bf0b319d2601bc8df Merge: e3fcfebc1 6bad810bc Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri May 21 09:58:49 2021 -0400 Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade EMC_verif-global v2.0.0 major release updates commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a Author: Mallory Row <mallory.row@noaa.gov> Date: Fri May 21 13:55:13 2021 +0000 Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit 9cf615d11b096ea4843f4e5938a6a65f3500df49 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 20 20:10:18 2021 +0000 Modulefile updates for testing with waves on - updated ww3 and base modulefiles to add modules and update some - added new: pio/2.5.2i, fms/2020.04.03 - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6 Refs: #164 commit b155ff37040658703168268d4e58fe4e6b45a50d Author: Mallory Row <mallory.row@noaa.gov> Date: Thu May 20 15:00:04 2021 +0000 Update EMC_verif-global tag to verif_global_v2.0.2 Refs: #315 commit cae62e3f47e245e70fcf3721fb4c022ea11c059f Merge: 8def77afd e3fcfebc1 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 19 19:45:05 2021 +0000 Sync merge with develop and WW3 build updates - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack - WW3 build updates: revert back to separate module files for build; address modulefile reorganization in separate issue - remove CCPP option with system build, doing CCPP by default now Refs: #164 commit 5ec376bababd935e4f3b15c4754105f5bd750657 Merge: 6b6b9ed39 e3fcfebc1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed May 19 18:24:31 2021 +0000 Merge remote-tracking branch 'origin/develop' into issue178 * origin/develop: change fv3gfs checkout head fixed a compilation error, NEMs/exe existing, in hera build_fv3.sh with ATM fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16 bugfix for not removing last point from list in wave post pnt jobs changes added in link_fv3gfs for fix_aer changed fix dir for link_fv3gfs changes on build_fv3.sh and symlinks to optical data files instead of cp Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination updated config.fcst testing merra2 workflow in hera update merra2 before a new pull request Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions udate config.base.emc.dyn high resolution MERRA2 data used fixed a bug related to orion added merra2 input and update diag_table merra2 workflow for orion Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) commit 4641c5d206a95e0e66276fa86d46ecd580213fd5 Merge: eff8a1258 e3fcfebc1 Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 19 14:51:19 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit e3fcfebc1ff9c9f9ceda7b775de0c34117de6459 Merge: 95e0dffea fa5d1e2ba Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 19 10:02:19 2021 -0400 Merge pull request #254 from AnningCheng-NOAA/merra2 Addition of support for MERRA2 commit fa5d1e2ba242a08e26cb7bac8c68b700a83d1d60 Author: anning.cheng <anning.cheng@noaa.gov> Date: Tue May 18 10:41:16 2021 -0400 change fv3gfs checkout head commit 283c4a044847bbadd0cef46e14dde4de97abe986 Author: anning.cheng <anning.cheng@noaa.gov> Date: Mon May 17 15:56:56 2021 -0400 fixed a compilation error, NEMs/exe existing, in hera commit 6b574160f94329754677e7f4541ab07c44185bb0 Author: anning.cheng <anning.cheng@noaa.gov> Date: Fri May 14 13:44:18 2021 +0000 build_fv3.sh with ATM commit dfc8aa9a2cf5370fff38520d2a28f3960be3b583 Merge: bf5d11063 95e0dffea Author: anning.cheng <anning.cheng@noaa.gov> Date: Wed May 12 20:11:44 2021 +0000 Merge remote-tracking branch 'upstream/develop' into merra2 commit eff8a1258aa70c061fe69697388f8914935726ee Merge: b1ad0b963 95e0dffea Author: Mallory Row <mallory.row@noaa.gov> Date: Wed May 12 19:15:17 2021 +0000 Merge branch 'develop' into feature/EMC_verif-global_upgrade commit 95e0dffea435af17be9150fcd0c842763768b45f Merge: fc727f405 dd4d18790 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 12 14:51:10 2021 -0400 Merge pull request #323 from NOAA-EMC/sync/operations_v16.0.9 Bring operations branch v16.0.9 changes into develop commit dd4d1879093516a7950c9e0e59f6e44e462199f6 Merge: fc727f405 68b9157bd Author: kate.friedman <kate.friedman@noaa.gov> Date: Mon May 10 16:40:13 2021 +0000 Merge remote-tracking branch 'origin/operations' into sync/operations_v16.0.9 * origin/operations: bugfix for not removing last point from list in wave post pnt jobs Update util_shared module version to 1.3.0 for wave footer fix Revert addition of ecflow trigger for wavepostbndpntbll job update ufs-weather-model tag to GFS.v16.0.16 add ecflow updates for new wave bndpntbll job Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8 Back out updates to add config.resources.nco.static WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes fix for missing wave boundary cbull and bull files Fix cycle date in bull and cbull wave files Reverting transfer parm file changes committed at 39bab45 Component tag updates for nwprod/gfsv16.0.7 Updated transfer parm files for gdas, enkf, and gfs dissemination Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions Clean up commments Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes ) Refs: #309 commit 8def77afd4a9f1cd6cdca42c956bc7ebf675a58d Merge: c6e2a96e8 d46e8cf49 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon May 10 11:45:02 2021 -0400 Merge pull request #322 from JessicaMeixner-NOAA/hpcstackww3 Updates for ww3 pre and post exec builds for hpc-stack commit d46e8cf49aff0dbf72e457f1177e10e6f50252a6 Author: Jessica Meixner <Jessica.Meixner@noaa.gov> Date: Mon May 10 15:31:56 2021 +0000 update for ww3_pre/post build: -- remove ww3 specific module files -- updated module base files to be in sync with ufs-weather-model except that jasper is a more recent version which is needed for ww3_grib -- added extra ww3 execs needed for this branch -- added ww3prepost build to build_all and partial build commit c6e2a96e86611cce00455609d9be803d580e7bc0 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:30:13 2021 +0000 Change fix file linking to scan for possible subfolders in set - instead of providing subfolder names, scan for subfolders in FIX_DIR path and then create symlinks based on existing subfolders in set - will not have to keep updating list of subfolders now Refs: #164 commit aa1d1e9ca1d8521ef22e1bdb654d4a70e7b1e29e Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Mon May 10 14:27:13 2021 +0000 Change CCPP_SUITE from FV3_GFS_v16beta to FV3_GFS_v16 - newer ufs-weather-model hash supports FV3_GFS_v16 suite Refs: #164 commit a8ed770d9c1e8614c5477d0129d6eaf5fe4e2085 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:32:36 2021 +0000 Companion update to Externals.cfg for WAFS tag update to gfs_wafs.v6.0.22 Refs: #1,#321 commit 68d9b5b5ff072b1f62131a9f7495c33c14c4a850 Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu May 6 19:28:17 2021 +0000 WAFS tag update to gfs_wafs.v6.0.22 for bug fix Refs: #1,#321 commit 68b9157bd59278dc07369d316999d3c8485ebf7c Merge: 1f5af6283 97fe99096 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 5 10:50:42 2021 -0400 Merge pull request #306 from NOAA-EMC/release/gfsv16.0.0_to_ops GFSv16.0.9 commit 1aea3ee393c99d4f76556fbbdbebc43f629558c2 Author: kate.friedman <kate.friedman@noaa.gov> Date: Wed May 5 14:30:06 2021 +0000 Add build script and modulefiles for WW3 build - WW3 execs no longer built by FV3 build, need separate build now - add new build_ww…

- merged in gfsv17p8_hfip branch - removed HFIP experiment directories for rt_v17p8_mynn and rt_v17_p8_gfonly - removed realtime experiment directories rt_ufscam_l127_hera and rt_ufscam_l127_jet Squashed commit of the following: commit f63227f238ea0f85154b4b75f085bcdd177bc89b Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Nov 17 00:24:12 2022 +0000 Corrected syntax error in Externals.cfg commit 0abbbd0bfcfeb698eeb2ce3d0ee009a1fc812abf Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Sun Sep 18 23:48:42 2022 +0000 update INFO file commit 561c194cb4be6cb90013c6768d399efef2183d93 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Sun Sep 18 23:44:04 2022 +0000 Delete old experiment directory, v17_p8_gf Change settings for suites FV3_GFS_v17_p8_gf_mynn and FV3_GFS_v17_p8_mynn sedi_semi=.false. (dt_inner will then become 75) decfl=8 commit 7e190d844929fd160db5f2db101a244e21de8c5c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Sep 15 23:50:27 2022 +0000 Changed dependencies for chkpost and vrfy tasks -- add gfspost dependency for chkpost task -- add non-zero post grib2 files to dependency for vrfy task commit d28969d337356310cacb304bd1a87f49f4a6a8a9 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Sep 14 23:46:58 2022 +0000 Updates to realtime XML files - added chkpost task to workflow * if post job fails and creates a zero-length file but returns SUCCESFUL state, chkpost task will rerun that forecast hour again - changed dependency for vrfy task to look for all non-zero post grib2 files commit bac474164019b922867cf6c2a9f68ad6e77992eb Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Sep 14 23:43:20 2022 +0000 Corrected syntax errors in parsing_namelist_FV3.sh - fix missing / from gfs_physics_nml - remove "" from FV3_GFS_v17_p8_*mynn in CCPP_SUITE case statement commit c23a9961edd13429c671d79b2c4c02f6aaad6213 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Aug 30 01:11:43 2022 +0000 Add realtime XML files for hfipPlots and ncl tasks commit 2d2fe9c323ca3deaa07f47970568c8c03e88a4f9 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Aug 30 01:10:31 2022 +0000 Updates for experiment directories - make paths consistent and use /home/rtfim/GFSv17p8_HFIP instead of /lfs1 or /lfs4 paths - add ATCFNAME as environment variable to arch task - make ICSDIR consistent and point to /lfs1 path - call jobs/rocoto/vrfy_gsl.sh for gfsvrfy task - add dependency for gfsvrfy task if running without gfspost task - add /lfs4 specific xml files for history commit 70ed9cab451fb5a968dc53c6ed66457014a71a8c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Mon Aug 29 18:38:48 2022 +0000 Updates for realtime experiments Update default config files in parm/config - turn in-line post off [WRITE_DOPOST=.false.] - turn off parallel netcdf if running on jet - increase post memory to 50G Rename rt_v17p8_gf experiment directory to rt_v17p8_gfonly Update experiment directories - move to /lfs1 filesystem from /lfs4 - update config.fcst to handle v17_p8_gf_mynn suite - update XML files to use 50G for memory_post - add gfsvrfy dependency to check size of syndat_tcvitals.2022 Update jet_xml_dir and xml directories - add XML files for hfipPlots and ncl tasks which use reservations - add non-realtime XML files for hfipPlots and ncl tasks - append PSLOT to task/job names for remap and ncl tasks - reimplement time dependency of 48h for nclzip task - run hfipPlots only for g2 cycles - switch to 144h from 168h commit 106fbada5e117bb52a2e617aec990d2ef37076aa Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Aug 26 18:13:30 2022 +0000 Update ufs_utils to ufs_utils_1_8_0 [26Aug22 commit, #1001] commit 366edada59f47cba098ff43c2d3316c78de6a929 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Sat Aug 20 00:57:12 2022 +0000 Remove files under ufs_model.fd_gsl that are already in the gsl/develop repository commit 5dc80e326149e3e283df9330b4272221d7983c3d Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Sat Aug 20 00:38:43 2022 +0000 Additional changes to config.fcst for FV3_GFS_v17_p8_gf_mynn suite Added effective date to INFO file commit 41c756f15bd492fe6aaa9d01cc1f7e5004d4097b Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Aug 19 21:56:54 2022 +0000 Update to HFIP2022-08-17 gsl/develop tag, b42ca73 - add FV3_GFS_v17_p8_gf_mynn suite - updates to GFS-MYNN configuration - update to GF and sgscloud_radpre - add regression test for p8+gf+mynn - add bl_mynn* namelist parameters for p8+gf+mynn - use aerosol-aware Thompson * ltaerosol=.true. * field_table_thompson_aero_tke - set do_gsl_drag_tofd = .false. commit 48fab18a9e82395f6febafa8fa8593880782615b Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Aug 10 17:12:58 2022 +0000 Added corrections for post task - added nam_micro_lookup.dat to link_workflow.sh - corrected typos in link_workflow.sh and .gitignore - missing from 10Jun22 initial commit [#771] - corrected in 27Jun22 commit [#851] and 08Jul22 commit [#895] commit 434a1f02e890c81cd16f3d6a929f4be1b4b6eb9a Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Sat Jul 23 01:39:17 2022 +0000 Updates for GSL - changed if-statement for netcdf files in GSL archive script to look for a single file (atmf000 netcdf file) instead of multiple files since it now produces errors when running as bash script - added GSL archive script for archiving netcdf files only - changed getic script to look for atm file instead of sfc file in if-statements since atm file is much larger than sfc file - comment out if-statement to check if 0p25 grib2 file already exists in post.sh so post job will run if resubmitted when walltime is exceeded - change config.base.emc.dyn link to point to JET version # Please enter the commit message for your changes. Lines starting commit 29bc7b7eeaa8765238af7e6131d41f9c0ebb2b1b Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Sat Jul 23 01:19:19 2022 +0000 Add HFIP experiment directories - rt_v17_p8_gf - rt_v17_p8_mynn - v17_p8_gf Add NCL graphics directories - jet_xml_dir - xml Delete gsl_v5 experiment directory commit 5f58523d4c5be051b4177350f1f9f1f3146f086a Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Jul 1 17:16:38 2022 +0000 Squashed commit of the following: commit 2bde13a6bec1d81375cdc04f1c67f06176de5ba6 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Jul 1 17:05:59 2022 +0000 Remove GFS_SCNV entries from GFS_v7_p8_gf suite definition file commit 97515c6866308788c21d98ed80779668e58949b1 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Jul 1 17:04:30 2022 +0000 Update version of ufs_utils.fd to be consistent with what we have been using in our realtime runs, which uses ESMF 8.2.0 library commit bb8cb4a729a8021eee6747d6b93e067dca42ab71 Merge: a1b7d599 845dea70 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Jul 1 16:57:46 2022 +0000 Merge branch '30may_commit' of https://github.com/jkhender/global-workflow into 30may_commit commit 845dea70d482e8980d440ecaeba6bba89c433d5f Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Fri Jul 1 10:33:39 2022 -0400 Fix settings of dt_inner and lheatstrg (#883) For Thompson microphysics, currently dt_inner is set to half of physics timestep. It should be set to the same as the physics timestep if semi-Lag sedimentation is applied to rain and graupel. Canopy heat storage is incorrectly turned off for NOAH LSM, and on for NOAH-MP LSM. This setting needs to be reversed. Fixes #884 commit 4d45b6b9d133a5542955bee4ecf57a400bdaa012 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Jun 30 16:46:18 2022 +0000 Moved GSL-modified post parm files under ufs_model.fd_gsl/FV3/upp/parm commit 03399b0155f3d2c590fd016dcff13716835521ff Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Jun 30 07:02:38 2022 +0000 Merge in Walter's additional commits for UPP Remove gfs_post.fd_gsl/ush/fv3gfs_downstream_nems.sh Squashed commit of the following: commit aa5c78301b914fb5ab717ec5e74333acb7e587e9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jun 10 03:29:16 2022 -0400 Move remaining global post scripts over from UPP (#771) Several scripts currently located under NOAA-EMC/UPP are only used for global, so they have been moved within global-workflow so they can be managed by the global-workflow team. Scripts are just copied from the current tip of UPP develop, other than some changes to standardize style and indentation. Also coming over are four parm files that are used to produce GFS products. As a result, we are no longer linking the entire upp parm directory; instead we are creating individual links for the files we use that still reside in upp. Fixes #630 Fixes #769 commit 8a0a35b707f1d677bcea310030bb54aeeee59c73 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jun 7 01:35:15 2022 -0400 Consolidate post scripts to eliminate coupled mode of link script (#766) The two scripts that had modified versions for the coupled model have been joined with changes to the original scripts, eliminating the need for a special coupled mode for the link script. As part of this, those two scripts are no longer copied from UPP and are now part of the global-workflow repository. Fixes: #679 Fixes: #746 Refs: #270 commit 5e776021e28b1a8c87f0f29d4a606531545f3ad3 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Jun 30 05:09:49 2022 +0000 Modify parsing_namelists_FV3.sh - added namelist parameters for GFSv17_p8_MYNN - set default value for lheatstrg to .false. commit a18aa5cade877d457b5e01033b84e7bd46cd691e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Jun 30 05:06:11 2022 +0000 Add WGRIB2 and CRTM_FIX variables to modulefiles/module_base.jet.lua Load module ncl in modulefiles/module_base.jet.lua commit a01f4fc545f2fdd4b2e82863a02c4f3d7d4208ef Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Jun 24 02:03:37 2022 +0000 Modify srun command to print out memory information Request 60G of memory for init task on Jet commit b538350a481467fa218050074d17b862b40d2e89 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Jun 23 01:22:05 2022 +0000 Updates for running on Jet - corrected typos in module_base.jet.lua - change DO_VRFY to "YES" for jet - create machine-specific files for GSL forecast-only Python workflow scripts to set paths for each machine - pass in ATCFNAME variable for vrfy task on Jet commit 8ff6446102c411e1e344eb6ff925e49aff000b36 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Jun 23 00:32:47 2022 +0000 Add sedi_semi and decfl namelist parameters to config.fcst commit 681e4d4704986d242dba43dd1c87059bea6c3db5 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Wed Jun 22 21:59:05 2022 +0000 Change default workflow_utils.py script to GSL version commit cd802762e1ba30e49c53cb5b37059ea416a1161a Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Jun 21 22:47:52 2022 +0000 Update UFS to NOAA-GSL:gsl/develop 14Jun22 branch, 576b58e, in checkout.sh commit c47265f1f4407e25a11c771fe128bb058457669c Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Sat Jun 18 00:38:19 2022 +0000 Updates for GSL - add Jet changes to JGFS_ATMOS_CYCLONE_TRACKER - change GSL scripts to bash - have vrfy.sh script link to GSL version - delete files leftover from merge commit 68a10c55428cf5ddb42af56ad23163e307125b52 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Fri Jun 17 09:28:52 2022 +0000 Merged NOAA-EMC/develop 30May22 branch into gslv16_dev Squashed commit of the following: commit dbd9fa93ced07f39accf7ff4eec2859f0ed5d35f Author: ChunxiZhang-NOAA <49283036+ChunxiZhang-NOAA@users.noreply.github.com> Date: Mon May 30 21:50:56 2022 -0400 Updated SDFs and namelist settings for P8c (#795) Updates the model version in preparation for prototype 8c, along with commensurate setting updates. Some CCPP suites are removed from the UFS build as they are no longer available. Also updates the coupled initial conditions, and there is a simultaneous update to fixed orography files. Refs: #736 commit 05accc1c72b1311ae9689bef5e7a1291dc12a96a Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon May 23 17:36:51 2022 -0400 Correct incorrect increment prefix variable (#805) One instance of the increment prefix variable in `ush/forecast_postdet.sh` used `PREFIX_INC` instead of the `PREFIX_ATMINC` used elsewhere. Fixes #804 commit ac7cb1000d5c1d31babd36f4c3e17f643f30fd4d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun May 22 16:50:30 2022 -0400 Remove separate UPP clone (#803) Now that UPP is cloned within UFS, there is no need to create an independent clone in global-workflow. Scripts are updated to use the UPP within UFS. In addition to removing redundancy, this will avoid version mismatch issues when UFS and global-workflow checkout different versions. The upp directory is now linked from within UFS to sorc as upp.fd (instead of the gfs_post.fd the clone was placed in). Additionally, the build script is renamed to build_upp.sh. Fixes #770 Moots #797 commit 58728fb2c689c11335f4bf8ac371e18070c6fbd2 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 20 10:14:58 2022 -0400 Fix build script options (#801) There was an issue where if build_all.sh was called with only options that are not used by partial_build.sh, partial_build.sh would see those options because $@ was not overwritten. The script have been updated to consume those options so they are no longer present if $@ isn't overwritten in the new script call. Also fixed the getopts statement in partial_build.sh so we handle errors instead of bash (bash would report the wrong script if the script is sourced) Fixes #800 commit fa12db279cf829b861d08c06e3e3534a335e9fd7 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 18 01:04:32 2022 -0400 Refactor some build scripts (#794) Refactors the build_ufs script to allow the build of any UFS app to support future expansion of global-workflow capability. The default should be sufficient for most users, as S2SWA can be used for ATM, ATMA, S2S, and S2SW as well. The new format of the command is now: ``` build_ufs.sh [-a UFS_app][-v] -a UFS_app: Specify the UFS application to build. The default if none is provided is S2SWA -v: Turn on verbose mode (BUILD_VERBOSE) ``` build_all.sh is similarly refactored to include the same options. Also, a new `-c build_config` option is added to specify an alternative list of programs to build. ``` build_all.sh [-a UFS_app][-c build_config][-h][-v] -a UFS_app: Build a specific UFS app instead of the default -c build_config: Selectively build based on the provided config instead of the default config -h: Print usage message and exit -v: Run all scripts in verbose mode ``` partial_build.sh is also updated to take the new `-c` option to specify a build config. ``` partial_build.sh [-c config_file][-h][-v] -c config_file: Selectively build based on the provided config. The default if none is specified is gfs_build.cfg -h: Print usage message and exit -v: Run in verbose mode ``` In addition to the above, build_all and partial_build had their indentation redone and their usage/help statement updated/added. Also, the build configuration file was renamed to from fv3gfs_build.cfg to gfs_build.cfg. Fixes #745 Fixes #751 commit 2abee02765a3bae48f2b4e6a900400d6731eda06 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 18 01:02:57 2022 -0400 Add continuous aerosols support (#693) Adds support for continuous aerosols when running with GOCART (using the forecast aerosol tracers from the previous cycle as initial tracer fields). This adds a new task to the workflow mesh in forecast-only mode. The new task does not run in the first cycle, though it will appear in rocotostat/rocotoviewer. In subsequent cycles, the task will launch as soon as the needed restart files from the previous cycle are available and gfs_init has completed. There is currently no mechanism to have aerosol_init run for the first cycle (for instance, continuing from a previous experiment); users would have to run the scripts off-line to add aerosols to the initial conditions. To support the introduction of the necessary python scripts, a new python environment is added to provide necessary libraries. This virtual environment is temporarily being housed in personal space, but an issue has been opened with hpc-stack to add it to the standard stack installations. The introduction of miniconda also caused the conversion of all of the rocoto entry scripts (the ones rocoto calls to run the job) to bash. Most of them had been in korne. To make sure the needed restart files are produced, config.fcst now makes sure the forecast cadence is included in the list of restart times. This may need more testing to ensure it works properly with other restart lists. As part of this, STEP_GFS was updated to properly determine the step from gfs_cyc instead of being a set value. Closes #366 Fixes #516 Fixes #630 commit 69b39ee5af8cfbb5cbf5cf62c92d01958b697652 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu May 12 12:18:50 2022 -0400 Add --init to GSI submodule command (#781) Needed to obtain libsrc submodule during checkout and allows the GSI to build correctly since this GSI hash still needs the libsrc submodule during build. Refs: #780 commit b09f92c21028ea37e4663ce4c304935a2dc45b33 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Thu May 12 08:20:16 2022 -0400 Update field_table to be consistent with UFS (#778) Changes the fixed surface value of hydrometeor number concentrations and sub-grid TKE to 0. Also renames the field table. Both changes are consistent with changes made in UFS. Fixes #676 commit d72a62d6c0ab2e9f53ca3e6133148f29982f9d32 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Thu May 12 08:15:23 2022 -0400 Remove special MOD_PATH from build scripts (#775) We always use pre-installed libraries and special MOD_PATHs are no longer necessary, so these are removed from build scripts. MOD_PATH. This also moots MOD_PATHs that were hard-coded to Hera locations in some scripts. The MOD_PATH in build_ufs.sh remains as it is still needed and is a relative path into the UFS repo. Fixes #298 commit 2adf123814a2f29e9cca54a11fbb2807b3f6cf1b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 4 12:31:20 2022 -0400 Revert g2tmpl back to 1.10.0 (#773) Resolves bug with mismatch between hpc-ips and g2tmpl versions on the WCOSS-Dells. Also revert back to 1.10.0 on Hera and Orion to be consistent. Refs: #772 commit b90f4e99bc42f9a8afbeaa9479e674fb75e096ea Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Tue May 3 09:45:19 2022 -0400 Remove git submodule update for upp checkout (#768) UPP no longer has a CMakeModules submodule, so the submodule update is removed from the checkout script. Fixes: #767 commit ad2b14d9b1ed0fe89fe59bfb96cc03630e8457de Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Tue May 3 09:44:57 2022 -0400 Remove duplicate file linking for Thompson MP (#765) Files for Thompson MP were being copied twice by the link script: once by checking imp_physics, then again checking the CCPP Suite. This is now reduced to one check. Fixes: #675 commit a9fc0033b908aefb42d5b2d191c65af5cb7660c4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Apr 28 15:17:22 2022 -0400 Remove unneeded/outdated modulefiles (#762) Remove unneeded modulefiles for WCOSS-Cray and GSI monitoring. commit 3333dee304b6b53d3d716c60d0c87ad06d629c1c Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Thu Apr 28 14:35:57 2022 -0400 Remove prepbufr_pre-qc from archive lists (#753) The prepbuft_pre-qc file does not need to be archived, so it no longer is. Fixes #361 commit 88b1b1591d3201709f5f981908aaf7890d3021bd Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Apr 26 20:40:41 2022 -0400 Convert module files from Tcl to Lua (#756) Converts all module files from Tcl format to Lua. As a side effect, this change enforces using the files as modules rather than improperly sourcing them instead of loading. Fixes #670 commit ca80aeb86cb221263611605ba23858448bce0bad Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Apr 25 06:23:06 2022 -0400 Ensure hourly files when GLDAS is on (#740) GLDAS requires hourly output, so make sure FHOUT is 1 when GLDAS is on. Fixes #695 commit 9d00239088651b73a9667b70bd6247b34e35046f Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Tue Apr 19 21:22:22 2022 -0400 Update cyclone tracker to handle return code correctly #642 Updates the cyclone tracker call to correctly exit with an error code if the tracker script reports one. Fixes #507 commit 33d3dd14d6df8109274dde4606bb7a50e4638fa2 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Apr 19 21:18:56 2022 -0400 Update ww3 pre and post exe build to use cmake (#731) Updates the WW3 pre/post build system to use cmake. Fixes #688 commit 39facec1e03a404f84fd05b8739cd8e4010a0779 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Apr 12 11:36:30 2022 -0400 Add WCOSS2 GFSv16.2 operational def files into develop (#717) Add WCOSS2 operational GFS def files. Refs: #399 commit 0a85223e48a1a8dcced163791d8e7ae5a42a4fab Author: Xianwu Xue - NOAA <48287866+XianwuXue-NOAA@users.noreply.github.com> Date: Tue Apr 12 11:34:17 2022 -0400 Initialize "err" to avoid potential task fail (#715) If not initialize err, and change "set -x" to "set -xue", then the waveinit task will fail with error message: "line 234: err: unbound variable" On branch bugfix/issue_714 Changes to be committed: modified: scripts/exgfs_wave_init.sh Refs: #714 commit fc6e1c3316397432d2da218b3c4fc0ea1fe70644 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Apr 5 11:07:21 2022 -0400 config.base should not exist in the repository unless it is in ops. template only exists in the repo, the experiment directory should not contain the templated config.base.emc.dyn (#707) commit cabf437044cb937caf7a7830068fd9e413c5921f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Mar 30 21:28:50 2022 -0400 Update model and settings for Prototype P8b (#681) Updates model and setting defaults for prototype 8b. The UFS version is updated to a recent version of UFS (tag Prototype-P8b). As part of this, the print_esmf option is removed from the model configure file and replaced with a new setting in nems.configure. We have not made this option user-configurable at this point, but that may come in the future. The default CCPP suites have been updated for all modes to either FV3_GFS_v17_p8 or FV3_GFS_v17_coupled_p8. This involves changing the microphysics to Thompson and changes the gravity wave drag version (knob_ugwp_version) to 0. This change breaks cycled mode for the time being. A future PR will revert the defaults to ones that allow cycled to run along with a more robust system for changing settings. Tiled fix files are now used for all modes instead of just coupled. Cellular automata now defaults on ON. There are also other miscellaneous settings that have had their defaults changed. Fixes #641, #687 commit e3f707cb9c05b45e9d4019679e406f54008279a5 Author: XuLi-NOAA <55100838+XuLi-NOAA@users.noreply.github.com> Date: Thu Mar 24 05:43:31 2022 -0400 Modify eobs for EnKF thinning In the Hybrid EnKF GSI, the thinning box size, dmesh, is different for the full resolution analysis and EnKF respectively. There are set in GSI scripts for the full resolution analysis, and reset in global workflow in config.eobs. Only two thinning box sizes, dmesh(1) & dmesh(2), are defined in GSI scripts before, recently, two more, dmesh(3) & dmesh(4) are added. Accordingly, these two need to be added in config.eobs as well. Specifically, add dmesh(3)=225.0,demsh(4)=100.0 to config.eobs. Fixes #595 commit c32eea459af3177cee28e151b43fe5e12bdfc412 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 22 11:18:10 2022 -0400 Update ocean resolution for C48 (#651) The ocean resolution for C48 was set as 1-deg, but the fractional grid fix files available at C48 are for a 4-deg ocean grid. The ocean resolution is now set to this value when FV3 is C48. Also commented out a currently redundant block setting OCNRES in config.ocn. The one in ecfs has to stay as it recalculates the ocean resolution based on the EnKF resolution. Fixes #650 commit d758e8b227fca7b5a3320adc43c29ba492c3bfe9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Mar 10 05:54:49 2022 -0500 Add single forecast GOCART support (#659) Adds support for running single coupled free forecasts with GOCART aerosols. Support for continuous aerosol fields from cycle to cycle will be added in a future PR. To turn on aerosols, there is a new --aerosols option for setup_expt.py. The option takes no arguments. When it is used, aerosols will be turned on by setting DO_AERO="YES" in config.base. GOCART output files are placed in the chem directory in COM. There is a new tarball archived, chem.tar, that contains the GOCART output. Partially addresses #516 Fixes #403 commit a0e23e254c7c881b20d66c1c53cd36de509e6d69 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Mar 1 10:50:39 2022 -0500 Specify memory for init job (#669) The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed. Fixes #631 commit 6874e8939211fdc07143450bfd1b6a2863172e10 Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com> Date: Fri Feb 25 16:39:45 2022 -0500 Cleanup of utils directory (#660) Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo. Fixes #618 commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 24 22:49:45 2022 -0500 Fix bug with partition_batch on WCOSS (#668) partition_batch was not being defined for WCOSS machines, but was being used in a substitution for config.base. Fixes #667 commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 21 02:10:00 2022 -0500 Split output filetype variable into atm and sfc (#602) The determination of the FV3 output filetype was a bit unwieldy as it contained two different settings (one for the atmosphere and one for the surface) that were not necessarily changed at the same time. They were also being determined in a different location than other settings based on the model resolution. Now the old OUTPUT_FILETYPES variable has been split into two different variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi- nation was also moved into the config.fv3 file, where other resolution- dependent computational settings are set. This has resulted in some functional change on WCOSS Dell, as the EnKF was using different chunking settings and never used parallel output for the surface likely because wasn't being run at a low enough resolu- tion to consider it. However, there is no reason to believe the two forecast modes should have different chunk or output settings. So, I've used the EnKF chunking settings and the free forecast switchover point for the surface output mode. The new filetype settings are now also divorced from the OUTPUT_FILE setting. However, that setting will soon be unnecessary as nemsio is removed from the code as an option (see Issue #601). Fixes #600 Refs #601 commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Feb 17 15:55:24 2022 -0500 Correct MODE comparisons for forecast only (#658) When the setup_expt scripts were combined, the forecast mode became a mandatory argument. The value of this option is then directly used for the MODE variable, but the argument name (forecast-only) does not match what was previously used for MODE in the forecast-only script (free) and some scripts were still testing against the old value instead of the new one. Those comparisons have now been updated to use the new MODE name. Fixes #657 commit f8867d3f0b1f3b5d238dced412996c56e30d31a1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Feb 10 20:23:54 2022 -0500 Add LOCALARCH option (#628) Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR. Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO). Fixes #624. commit 2950c7b97f99341caa738526138022987f665627 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Feb 10 18:07:43 2022 -0500 Turn on fractional grid by default for uncoupled forecasts (#638) Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true. Fixes #571 commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Feb 9 17:02:39 2022 -0500 Specify warm start as .true. or .false. (#644) Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`. Fixes #643 commit e537f0cecabc8e16e26b14e606558de906b19e3f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 23:33:21 2022 -0500 Archive TC tracking logs if produced (#627) The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track. Fixes #625. commit 32f93becde5ffa07c162252b95417845f2ab5159 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:59:37 2022 -0500 Fix separate threading for GFS and GDAS forecasts. (#621) Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs. Fixes #610 commit 9bb09a92c55d4534feca5d521fbbd1c664730317 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Feb 8 20:58:05 2022 -0500 Updated the RadMon and OznMon links. #596 (#597) commit 97ebc4d4e6483b135468d85cd9ed974f88955914 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 3 02:56:34 2022 -0500 Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537) `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name. The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`. ``` ❯ python3 setup_expt.py -h usage: setup_expt.py [-h] {cycled,forecast-only} ... Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link initial condition files from $ICSDIR to $COMROT positional arguments: {cycled,forecast-only} cycled arguments for cycled mode forecast-only arguments for forecast-only mode optional arguments: -h, --help show this help message and exit ``` Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively. ``` ❯ python3 setup_expt.py forecast-only -h feature/unify-setups usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--app {ATM,ATMW,S2S,S2SW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --app {ATM,ATMW,S2S,S2SW} UFS application ``` ``` ❯ python3 setup_expt.py cycled -h feature/unify-setups usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}] [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}] optional arguments: -h, --help show this help message and exit --pslot PSLOT parallel experiment name --resdet RESDET resolution of the deterministic model forecast --comrot COMROT full path to COMROT --expdir EXPDIR full path to EXPDIR --idate IDATE starting date of experiment, initial conditions must exist! --edate EDATE end date experiment --icsdir ICSDIR full path to initial condition directory --configdir CONFIGDIR full path to directory containing the config files --cdump CDUMP CDUMP to start the experiment --gfs_cyc {0,1,2,4} GFS cycles to run --start {warm,cold} restart mode: warm or cold --resens RESENS resolution of the ensemble model forecast --nens NENS number of ensemble members --app {ATM,ATMW} UFS application ``` Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications. The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing. The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source. The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation. There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's. Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged. commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:19:43 2022 -0500 Stop archiving gfsarch.log as it is being written (#581) The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group. Fixes: #558 commit 1b300dbf98eccdf03117b3795a2d8da3310a6126 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 2 11:18:55 2022 -0500 Fix build on non-WCOSS2 machines (#612) The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions. Also updates the UFS_UTILS repository to its new location under UFS instead of EMC. Fixes #476, #561 commit d3028b9d8268028226f9c27800fcd6655e9e4bb8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jan 19 14:29:51 2022 -0500 Fix setting of OUTPUT_FILETYPES (#589) The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine. Fixes #588 commit 13421b01a07e5d1cca32ee7579a4094d8209b072 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:16:29 2022 -0500 Update PR template commit 322a61a61238e8486cb42d7d26282b2728d0c32f Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 12:13:33 2022 -0500 Move PR template MD file. Update issue templates commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 11:32:51 2022 -0500 rename pull_request_template.md commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 19 10:34:54 2022 -0500 make changes to the templates commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 19 10:08:45 2022 -0500 Fix lfrac entry in diag table (#570) Land fraction was listed in the wrong module, keeping it from being written to output. Refs: #562 commit e2657adbdadaac7089591390428324c6aec260a9 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 17:04:04 2022 -0500 Update NCO_bug_report.md commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 16:59:18 2022 -0500 Update bug report issue template commit 2fab8b4213645b79b3fea8127e7d4ab21044188e Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 18 15:13:53 2022 -0500 Add templates for Github (#560) Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included. commit 03be05309b184421c473f1b43082b766b114fd46 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:02:02 2022 -0500 Fix toggle for building workflow_utils (#580) The fv3gfs_build.cfg did not have a space between the periods and the setting for workflow_utils, which means the setting was ignored and the default of yes was always used. Fixes: #577 commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Jan 18 10:01:24 2022 -0500 Remove redundant toggle for gldas build (#579) The build cfg files controlling which components are built and the partial_build.sh script all have two instances trying to set the value for gldas. This means one of the settings did nothing when changed. Fixes: #578 commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Jan 14 01:05:59 2022 -0500 Update config missed in last GSI update (#569) When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489). Refs: PR #530 commit 33308ea3b477db17a5db455a4c4887e3d5cbc711 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu Jan 6 00:44:43 2022 -0500 Updates for P8a (#538) Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype. Updates include: Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml ) Updates to CA namelists Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2 Closes #525 commit ae7092405e7552f76674b33fc81cb3973a68ad4e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 3 17:28:47 2022 -0500 Reordered CDUMP_LIST Refs #541 (#542) commit 033b1d8ef29b7c829e8131758135b372ae61de26 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Sun Dec 19 22:18:48 2021 -0500 Update GSI version to 2021 Dec 14 (#530) commit b187e2aa15bfd7600c49627fd4c2d02915b50abe Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Thu Dec 16 22:15:45 2021 -0500 Replace all backticks for command substitution (#526) All instances where backticks are used for command substitution are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: #397 commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Dec 10 15:35:00 2021 -0500 Add coupled support and update UFS (#500) Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon. This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously. Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed. Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum: ``` ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc ``` A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested. When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file. Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location. There are new options available for the checkout.sh, build_all, and link_fv3 scripts: - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out. - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg. - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files. ### To run in coupled mode with prototype settings/inputs 1. Clone as usual 2. Run checkout.sh 3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary) 4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled` 5. Run setup_expt_fcstonly.py using the --app option S2SW 6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW 7. Run setup_workflow_fcstonly.py as usual 8. Setup rocoto to run your experiment ### Technical udpates Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on. The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination. Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm. The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs. The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/ The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh. Error checking was added to the build_ww3prepost.sh script. The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517). rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use. For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0). Co-authored-by: jikuang <jikuang@umd.edu> Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: JessicaMeixner-NOAA <Jessica.Meixner@noaa.gov> Co-authored-by: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> commit 8abe1dfa8d613f9398cd86564046b53235f62749 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Dec 8 16:36:52 2021 -0500 Fix resource assignment issue found in analysis job running global_cycle (#467) Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere. commit fdffeaaf013f638ac43ad421981e48fabf7a7070 Author: malloryprow <mallory.row@noaa.gov> Date: Thu Nov 18 14:17:02 2021 -0500 Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508) * Update gfsmetp and gfsarch dependencies * Update EMC_verif-global tag to verif_global_v2.8.0 Refs: #437, #472 commit 108abc589b746b2ba585d18a6b6587e5a0d89f39 Merge: f6f1bb702 e5cd63693 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Nov 16 10:11:39 2021 -0500 Merge pull request #497 from NOAA-EMC/feature/shebang Update ush/ script files with "python3" in shebang commit e5cd636930b0e36ae9b2b25697cda317a2df996d Author: jikuang <jikuang@umd.edu> Date: Fri Nov 12 11:50:53 2021 -0600 update the following files with "python3" in shebang commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724 Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Wed Nov 10 10:08:42 2021 -0500 Add flag to launcher command to prepend task number to lines in stdout/err (#493) Modified env file settings for launcher variable to prepend task number label with "-l" flag. commit 096fc1fb76ee01aff7908b91adc9851da9235cad Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Nov 9 08:47:22 2021 -0500 Update NSSTBUFR file logic in prep job (#469) Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh. Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow. NSSTBUFR is created with different DTYPS_nsst before 2020102200. commit 84194a735b46c907656fe2b2cca3ca97799396f0 Merge: a39cb11ef 0740b5b6c Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Oct 27 11:52:55 2021 -0400 Merge pull request #474 from NOAA-EMC/feature/setx2 Hide module load commands commit 0740b5b6c622d64b770c73aa47d9789494d94a99 Author: jikuang <jikuang@umd.edu> Date: Tue Oct 26 13:19:07 2021 -0500 wrap module load commands with set +x commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Sep 29 09:36:31 2021 -0400 Update EMC_verif-global tag to verif_global_v2.5.2 (#450) New tag provides the following updates since the verif_global_v2.2.1 tag: - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards) - Added capability to produce fit-to-obs plots - Added support for Jet - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids - Hot fix for new METviewer AWS host name - Hot fix for reorganizing precipitation verification input files Refs: #438 commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30 Author: JianKuang-UMD <51758200+JianKuang-UMD@users.noreply.github.com> Date: Tue Sep 28 09:53:16 2021 -0400 Remove firstcyc job (#440) The need for the firstcyc job has gone away, removing redundant job. commit 1ca27148d776eedf96636a845feb95881cfaa138 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Sep 9 11:53:11 2021 -0400 Update repository name for EMC_post component to UPP (#441) - the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433 commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Aug 23 11:22:26 2021 -0400 Add rstprod support to Orion (#421) - Update EMC_verif-global tag to verif_global_v2.2.1 - Turn on rstprod support by default on Orion - Change default DMPDIR path on Orion to new rstprod-supported GDA Refs: #347 commit 20c331dd9678834b980ccc932b6235a8266d4a88 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Aug 19 13:01:07 2021 -0400 Update obsproc package versions for TAC2BUFR implementation (#423) Update obsproc package versions for TAC2BUFR implementation: - obsproc_prep v5.5.0 - obsproc_global v3.4.2 - new packages installed on WCOSS-Dell, Hera, Jet, Orion Refs: #341 commit 7f0f7400520b031e2428238a9741d4d8bfb8207a Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 18 12:41:09 2021 -0400 Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414) Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs Refs: #401 commit 9233d965cd19a94ee649b4ee8c117bb587b78923 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 12:48:12 2021 -0400 Update workflow_utils build modules and remove ncio module hack (#412) Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline. Refs: #407 commit df26e953792913669698ba64b414b3be5184f43d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Aug 17 11:15:38 2021 -0400 UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410) * Update UFS_UTILS tag to ufs_utils_1_6_0 * Update HPSS path for real-time GFSv16 pre-implementation parallels Refs: #400 commit 34427f560c729ee3b7cc91ff357b3ad908a7486a Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Date: Mon Aug 9 15:47:27 2021 -0400 Free-forecast mode support on Jet (#394) Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported. commit 8c777ad04bce0555bed9f6666b808515b0a3766d Merge: ce66c74bb fc48af56d Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jul 20 15:53:45 2021 -0400 Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3 Convert setup scripts to python3 commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 20:48:05 2021 +0000 Missed a set of raw_input(), in py3 they are just input() commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:59:54 2021 +0000 revert rocoto_viewer as its being worked on elsewhere commit 37f25384c29f6697be5c851868ce98d8b6c31207 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 19:27:32 2021 +0000 Fixes from testing commit c0716f41f2446fec9a441b285d9033f73345c5d4 Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 10:28:06 2021 -0400 Merge w/upstream and update those changes to py3 commit cf8758f84418c236fb45913912491a1c27b2829f Merge: f9013decd ce66c74bb Author: Brian Curtis <brian.curtis@noaa.gov> Date: Mon Jul 19 09:21:25 2021 -0400 fix merge conflict in workflow_fcstonly commit ce66c74bbc43e997bae66a2c2035f2412d3f602b Merge: 96347ea52 7a166da9f Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jul 14 16:18:55 2021 -0400 Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres Correct wrong settings for high-res warm-start free-forecast commit 7a166da9f20a59729be39fff953bfe367987f046 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:19:45 2021 +0000 Reduce C768 npe_wav_gfs from ops 440 to dev 140 Refs: #353 commit b34c581c3b19ecdcdb4eff463e855597e5c08d80 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jul 14 19:15:31 2021 +0000 Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step - remove default value for start (EXP_WARM_START) - if user provides start flag then use it for EXP_WARM_START - if user doesn't provide start flag then make a decision for them based on resolution - if start=None and res=768 then start=warm - if start=None and res!=768 then start=cold Refs: #353 commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Thu Jun 24 16:38:25 2021 +0000 Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768 - have free-forecast setup_expt script check if resolution is operational resolution (C768) and if so, set EXP_WARM_START=.true. - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting - the --start argument still works but new check will override if res=768 - users can still change config.base setting as needed for special scenarios Refs: #353 commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 21:21:51 2021 +0000 Revert EXP_WARM_START if-block addition in config.getic - need to determine better way to set EXP_WARM_START Refs: #353 commit 1c03067ca570295b65f967467ef2329fb7999578 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:33:18 2021 +0000 Revert config.base EXP_WARM_START check change Refs: #353 commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:12:27 2021 +0000 Add checks for EXP_WARM_START in config.base and config.getic - add OPS_RES variable to both config.base.emc.dyn and config.getic - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops) - check in config.base helps with later IAU checks - help catch when user doesn't set EXP_WARM_START=true when running v16 C768 Refs: #353 commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:10:17 2021 +0000 Add cd to ROTDIR when pulling ops warm starts - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR Refs: #353 commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 23 19:06:42 2021 +0000 Reduce C768 resource settings to fit node limits - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job - bring C768 settings in config.fv3 down to 148 nodes (on Hera) - tested new settings in free-forecast mode on Hera Refs: #353 commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c Merge: cfca8bb2c 5c042e087 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Jun 23 11:13:06 2021 -0400 Merge pull request #316 from NOAA-EMC/feature/hpc-stack GFS components update for hpc-stack support commit 5c042e087c02cb82fe24ce666e477791f5e2417e Merge: b36414e4c cfca8bb2c Author: kate.friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 19:33:03 2021 +0000 Merge remote-tracking branch 'origin/develop' into feature/hpc-stack commit cfca8bb2ca0dc0105b905c536f346002408db771 Merge: e08f55583 fba8cef5b Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jun 17 14:40:18 2021 -0400 Merge pull request #342 from KateFriedman-NOAA/issue178 Free-forecast integration with chgres_cube and resolve know mode bugs commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:57:14 2021 +0000 Remove wave restart pull in getic script Refs: #178 commit 921838feb9f6fd3fc3c69579c677ffdd7175a103 Author: Kate.Friedman <Kate.Friedman@noaa.gov> Date: Wed Jun 16 13:18:35 20…

KateFriedman-NOAA added the maintenance Regular updates and maintenance work label Aug 26, 2021

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This was referenced Sep 9, 2021

Update repository name for EMC_post component to UPP in develop branch #441

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Update repository name for EMC_post component to UPP in operations branch #442

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KateFriedman-NOAA added a commit that referenced this issue Sep 9, 2021

Update repository name for EMC_post component to UPP (#441)

1ca2714

- the "EMC_post" repository was renamed to "UPP" on September 6th 2021 - update repository url in checkout script and Externals.cfg Refs: #433

KateFriedman-NOAA assigned WalterKolczynski-NOAA Sep 21, 2021

KateFriedman-NOAA closed this as completed Oct 12, 2021

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Update post repository name from "EMC_post" to "UPP" #433

Update post repository name from "EMC_post" to "UPP" #433

KateFriedman-NOAA commented Aug 26, 2021 •

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KateFriedman-NOAA commented Oct 12, 2021

Update post repository name from "EMC_post" to "UPP" #433

Update post repository name from "EMC_post" to "UPP" #433

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