WCOSS2 run support and script/config updates #1030

KateFriedman-NOAA · 2022-09-22T17:37:56Z

Description

This PR includes script and run support updates for running the develop branch on WCOSS2. This PR does not include resource updates for running on WCOSS2 and does not complete the port to WCOSS2. Additional WCOSS2 develop port PRs will follow this PR.

Changes in this PR mostly address the following:

WCOSS2 port changes requested by NCO (e.g. NWPROD/NWROOT -> PACKAGEROOT) in the move of operations to WCOSS2 in the past year.
Adding WCOSS2 support in the way of creating WCOSS2.env, a wcoss2.yaml hosts file for rocoto, and config updates.
Some cleanup that was also done in the operations GFS port to WCOSS2.

More specifically, the changes in this PR are:

Create WCOSS2.env under the env folder.
Remove references/usage of jlogfile thoughout.
Change NWPROD to PACKAGEROOT throughout.
Replace NWROOT with OPSROOT where appropriate.
Env file updates (non-WCOSS2):

Update "anal" if block in HERA.env and ORION.env to add "or" for "analcalc"; needed to match similar setting in WCOSS2.env and change in jobs/JGLOBAL_ATMOS_ANALYSIS_CALC

Update JJOB scripts:

Update jobs/JGLOBAL_ATMOS_ANALYSIS_CALC to pass "analcalc" to env file instead of "anal"
Move config and env file sourcing from rocoto job scripts into JJOBs for gempak
Update the default COM* paths to utilize compath.py and the new compath.py format; includes updating COMINukmet and COMINecmwf defaults to new compath.py format
Add COMINobsproc to jobs/JGFS_ATMOS_GEMPAK_NCDC_UPAPGIF
Replace COMINgfs with COMINobsproc and replace COMINgfs_m6hrs with COMIN_m6hrs in jobs/JGLOBAL_ATMOS_EMCSFC_SFC_PREP
Update ARCHSYND, HOMENHC and TANK_TROPCY in jobs/JGLOBAL_ATMOS_TROPCY_QC_RELOC, remove HOMENHCp1
Update default APRUN commands for several downstream jobs (mpirun -> mpiexec)
Set wavempexec to wavempexec instead of launcher in jobs/JGLOBAL_WAVE_INIT
Correct list of configs to source in jobs/JGLOBAL_WAVE_POST_BNDPNTBLL to include wavepostbndpntbll instead wavepostbndpnt
Update how PDY is invoked (. PDY to . ./PDY)
Update the RUN and RUN2 variables in jobs/JGFS_ATMOS_GEMPAK_PGRB2_SPEC
Some cleanup to remove unneeded RUN_ENVIR=nco checks and some extra whitespaces.

Update rocoto job scripts:

Move config and env sourcing out of gempak rocoto job scripts (moved to JJOB scripts); also change to invoke JJOB directly and add exit $status
Update fit2obs and tracker section of jobs/rocoto/vrfy.sh
Add missing env file sourcing to jobs/rocoto/wafsgcip.sh

Update module_base.wcoss2.lua to use para version of ncdiag module (update to use official ops install later)
Updates to configs:

Whitespace cleanup in config.anal
Add export nth_echgres=$nth_echgres_gfs when CDUMP=gfs in config.analcalc
Add COMINsyn to config.base.emc.dyn
Update ROTDIR in config.base.nco.static
Change OUTPUT_FILETYPE_ variables to be "netcdf" on all machines in config.efcs
Updates to config.fv3.nco.static: remove non-WCOSS2 references, add npe_node_max=128 for WCOSS2, change C384 DELTIM to 200 (ops value), and update variables for C384/C768 to ops values
Remove GEMPAKSH=$HOMEgfs/jobs/JGFS_ATMOS_GEMPAK line in config.gempak; now invoking $HOMEgfs/jobs/JGFS_ATMOS_GEMPAK directly in the JJOB
Update COMINsyn default in config.prep and config.vrfy
Create config.resources.nco.static, copy from operations; will need updating for GFSv17 opd
Tracker updates in config.vrfy

Updates to scripts:

Updates to RUN and RUN2 variables in scripts/exgdas_atmos_nawips.sh, scripts/exgfs_atmos_goes_nawips.sh, and scripts/exgfs_atmos_nawips.sh
Replace COMINgfs with COMINobsproc in scripts/exgfs_atmos_gempak_gif_ncdc_skew_t.sh
Update APRUN in scripts/exgfs_atmos_gempak_meta.sh (mpirun -> mpiexec)

Update sorc/link_workflow.sh to also copy the appropriate versions of config.fv3 and config.resources in NCO mode.
Updates to ush scripts:

Remove references to NWPROD and replace with appropriate variables or paths.
Add echos to ush/gfs_bufr.sh to print out the specific forecast hour files for SPAs to check in case of failure. (Added by GDIT and Bo Cui)
Delete ush/global_extrkr.sh (not used anywhere anymore).

Update util source codes to build with ftn and include -g -traceback FFLAGS
Updates to setup script files:

Replace nwprod with packageroot in hosts files and setup_expt.py.
Create wcoss2.yaml host file.
Update workflow_tasks.py to set native xml tag for pbspro.

Issue #419

Type of change

New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Clone and build tests on WCOSS2, Hera, and Orion
Cycled atmos-only tests on WCOSS2, Hera, and Orion (C192C96L127 on all machines and C768C384L127 on WCOSS2)
Forecast-only coupled tests on Hera and Orion

No downstream/ops-only jobs were invoked in testing, however updates to those job scripts are included in this PR.

Checklist

My code follows the style guidelines of this project
I have performed a self-review of my own code
I have commented my code, particularly in hard-to-understand areas
My changes need updates to the documentation. I have made corresponding changes to the documentation
My changes generate no new warnings
New and existing tests pass with my changes
Any dependent changes have been merged and published

- 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

- commit GFSv16.2 WCOSS2 operational GFS defs files as of April 7th 2022 - final changes to defs files will be merged later Refs: NOAA-EMC#399

Refs: NOAA-EMC#399

…OAA-EMC#768) REF:767

- Change COMROOT/comroot back to prior path on Hera. - Add cominsyn to setup_expt.py and hosts files to set COMINsyn in config.base[.emc.dyn] on supported platforms. - When syndat is added to ops mirror to Hera change comroot to new mirror location to get syndat. Refs NOAA-EMC#419

Refs NOAA-EMC#419

- Change default for PACKAGEROOT and crtm_ver to ?. Refs NOAA-EMC#419

Refs NOAA-EMC#419

- Will make change to code makefile in new utils repo as needed. Refs NOAA-EMC#419

* develop: Fix radiance verification failing to find diag files (NOAA-EMC#1031) Supported resolutions on platforms and defaults for mode (NOAA-EMC#1026)

KateFriedman-NOAA · 2022-09-27T18:27:16Z

Sync merged with develop and resolved conflict in workflow/hosts/orion.yaml.

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