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Neon updates #1872

Merged
merged 104 commits into from
Nov 20, 2022
Merged

Neon updates #1872

merged 104 commits into from
Nov 20, 2022

Commits on Jul 15, 2022

  1. Fix albgrd_col value in SurfaceAlbedoType

    @ka7eh
    ka7eh committed Jul 15, 2022
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Commits on Jul 19, 2022

  1. Add error checking in ParitionWoodFluxes

    @ka7eh
    ka7eh committed Jul 19, 2022
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Commits on Oct 14, 2022

  1. python updates for ESCOMP#1871

    @wwieder
    wwieder committed Oct 14, 2022
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  2. usermod changes for ESCOMP#1871

    @wwieder
    wwieder committed Oct 14, 2022
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  3. local gcs modifications

    @wwieder
    wwieder committed Oct 14, 2022
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Commits on Oct 16, 2022

  1. Merge tag 'ctsm5.1.dev112' into neon_updates 

    Rework fates test definitions and add new fates tests

This tag includes a number of updates to the fates test definitions and test list to gain more coverage:

(1) Reorder and update the fates test definitions so that fates satellite phenology mode
can be configured for cases using a compset.

(2) Add a long-term exact restart test to catch issues that may arise due to updates to
fates procedure calls during end of year simulation dates.

(3) Add a no-competition + fixed biogeography, non-satellite phenology test definition to provide
additional mode combination configuration.

(4) Update the fates externals tag to incorporate a fix a vegetation temperature exact restart
issue discovered while implementing (1) above.

(5) Truncate all testmods starting with "Fates" to mitigate running over the limits on the length
of testnames, typically when specifying custom `test_id` using `run_sys_test`.

(6) Updates the expected failures list.
    @ekluzek
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  2. modified path for uploading to GCS

    @wwieder
    wwieder committed Oct 16, 2022
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Commits on Oct 17, 2022

  1. Merge branch 'neon_updates' of github.com:wwieder/CTSM into neon_updates

    @ekluzek
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Commits on Oct 18, 2022

  1. Fix per comment 

    https://github.com/ESCOMP/CTSM/pull/1814/files#r997597612
    @ka7eh
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Commits on Oct 19, 2022

  1. Update neon_gcs_upload 

    Correct path for initial conditions
    @wwieder
    wwieder authored Oct 19, 2022
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  2. Update shell_commands 

    BARR
    @wwieder
    wwieder authored Oct 19, 2022
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  3. Update shell_commands 

    GUAN
    @wwieder
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  4. Update shell_commands 

    LAJA
    @wwieder
    wwieder authored Oct 19, 2022
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  5. Update shell_commands 

    LENO
    @wwieder
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  6. Update shell_commands 

    MLBS
    @wwieder
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  7. Update shell_commands 

    MOAB
    @wwieder
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  8. Update shell_commands 

    ONAQ
    @wwieder
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  9. Update shell_commands 

    TEAK
    @wwieder
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  10. Update shell_commands 

    TOOL
    @wwieder
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  11. Update shell_commands 

    WREF
    @wwieder
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  12. Update shell_commands 

    YELL
    @wwieder
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  13. Update neon_gcs_upload 

    removed unused code, per @ekluzek 's suggestion
    @wwieder
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Commits on Oct 21, 2022

  1. Update shell_commands 

    SJER
    @wwieder
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Commits on Oct 22, 2022

  1. trying to address cases with non-standard start/end years

    @wwieder
    wwieder committed Oct 22, 2022
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  2. resolve conflicts

    @wwieder
    wwieder committed Oct 22, 2022
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  3. Correct the syntax so the bash if statements work

    @ekluzek
    ekluzek committed Oct 22, 2022
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Commits on Oct 23, 2022

  1. additional modifications needed for usermods to work as intended

    @wwieder
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  2. correction for DATM_YR_END in ad and postAD

    @wwieder
    wwieder committed Oct 23, 2022
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Commits on Oct 25, 2022

  1. Working version of run_neon.py, I tried running shell_commands after … 

    …the case is setup, but that does not work as the read of env_run.xml would need to be done again
    @ekluzek
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Commits on Oct 26, 2022

  1. Remove some of the prints I added, and the shell_commands part I comm… 

    …ented out, and most importantly use a transient compset for the transient case
    @ekluzek
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  2. Use the compset to determine if this is a transient case or not

    @ekluzek
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  3. Have the last year for the datm data be 2022, so that it will work fo… 

    …r all cases: ad, postad, and transient. This does mean the ad and postad cases won't have this data align with the meterological forcing data, but that's probably fine
    @ekluzek
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  4. Set CLM streams to go until 2022 as well

    @ekluzek
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  5. Set the use-case by the type of compset

    @ekluzek
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Commits on Oct 27, 2022

  1. Add run_neon output directories to the git ignore

    @ekluzek
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  2. Add the neon listing to git ignore

    @ekluzek
    ekluzek committed Oct 27, 2022
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  3. Add in 2018 and 2018-PD transient use cases

    @ekluzek
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  4. CLM stream settings are now in the 2018 use cases

    @ekluzek
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Commits on Nov 2, 2022

  1. Merge remote-tracking branch 'escomp/master' into neon_updates

    @ekluzek
    ekluzek committed Nov 2, 2022
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  2. Set urbantv start and end for 2018

    @ekluzek
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  3. 2018 control needs to use future scenario data

    @ekluzek
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  4. Explicitly turn crop on for the two NEON AG sites fixing ESCOMP#1889

    @ekluzek
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Commits on Nov 3, 2022

  1. Fix a little glitch where run-length couldn't be set

    @ekluzek
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Commits on Nov 4, 2022

  1. Make sure the compset type is correct for both basecase and case clon… 

    …ing from that
    @ekluzek
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  2. Always ensure to build/run single point NEON sites with mpi-serial ra… 

    …ther than a full MPI library to save complexity
    @ekluzek
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  3. Add the header for user_nl_datm_streams, so that there are instructio… 

    …ns on usage
    @ekluzek
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  4. Don't reapply user-mod in run_neon clone, and don't set DATM_YR_END 

    The base case already has the NEON user-mods applied in it, so
we don't need to reapply in the cloned case.

Don't set DATM_YR_END, let it be set in the default user-mods
and the specific user-mods for the site. The only advantage of
setting DATM_YR_END in run_neon is if your run-length is shorter
than what's in the user-mods, and it only saves downloading
the extra files and a little bit of time to read them at
initialization. So there's no need to have logic to handle that
here.
    @ekluzek
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  5. Add mesh file for reduced Lightning dataset

    @ekluzek
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  6. Remove the PIO_REARRANGER setting, which is hopefully not needed with… 

    … the ESMF mesh file for lightning, and use of mpi-serial
    @ekluzek
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Commits on Nov 5, 2022

  1. needed so cloned cases point to correct datm input directory

    @wwieder
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  2. Add comment about needing to keep the user_mod_dirs argument in the c… 

    …lone case
    @ekluzek
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Commits on Nov 6, 2022

  1. Add run_black target to not just check with black but to run it, add … 

    …beginning of a new test for add_tag_to_filename, is currently hardwired to only work on todays date
    @ekluzek
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  2. force STOP_OPTION in transient run to nmonths

    @wwieder
    wwieder committed Nov 6, 2022
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  3. modified for last month of DATM data at CPER

    @wwieder
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  4. let usermods set start date for transient runs

    @wwieder
    wwieder committed Nov 6, 2022
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  5. modify shell comands to avoid cycling climte data for last month in t… 

    …ransient case
    @wwieder
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Commits on Nov 8, 2022

  1. Get mock working for date, and use the way date was used in utils

    @ekluzek
    ekluzek committed Nov 8, 2022
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  2. Add some more tests

    @ekluzek
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  3. Add test for domain file as well

    @ekluzek
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Commits on Nov 9, 2022

  1. Add ability of add_tag_to_filename to replace resolution for the surf… 

    …ace dataset, and add a unit test for it
    @ekluzek
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  2. Allow more characters for resolution in filename

    @ekluzek
    ekluzek committed Nov 9, 2022
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  3. Add a landunit test for the replace_res option

    @ekluzek
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  4. Add a test to loop over a list of surface dataset names

    @ekluzek
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  5. Add more complex surface dataset names and make sure works

    @ekluzek
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  6. Make sure works for a 4-digit year date string as well

    @ekluzek
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  7. Add note that 4-digit years are allowed and test for it

    @ekluzek
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  8. Replace the resolution in the surface and landuse.timeseries filenames

    @ekluzek
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  9. Change NEON surface dataset name

    @ekluzek
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  10. Add modules needed for neon_surf_wrapper

    @ekluzek
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  11. Update surface dataset names for NEON

    @ekluzek
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  12. Merge branch 'neon_updates' of github.com:wwieder/CTSM into neon_updates

    @ekluzek
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Commits on Nov 10, 2022

  1. Add python modules needed for neon_surf_wrapper to all conda requirem… 

    …ents files
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Commits on Nov 11, 2022

  1. updated path to surface datasets

    @wwieder
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  2. Replace notes about using ncar_pylib with running py_env_create

    @ekluzek
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  3. Remove the toolchain files, this work was moved over to the ctsm5.2 b… 

    …ranch, which changed the process for how surface datasets would be created
    @ekluzek
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Commits on Nov 12, 2022

  1. Add note that start option is not functional and remove the code abou… 

    …t it, but add a comment for it
    @ekluzek
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  2. Merge remote-tracking branch 'ka7eh/add-error-checking-in-PartitionWo… 

    …odFluxes' into neon_updates
    @ekluzek
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  3. Merge remote-tracking branch 'ka7eh/fix-albgrd_col-value' into neon_u… 

    …pdates
    @ekluzek
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Commits on Nov 14, 2022

  1. Update mosart to bring in direct_to_outlet fixes

    @ekluzek
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  2. Add a direction for the check_for_nans so that the direction the fiel… 

    …ds are going will be written out fixing ESCOMP#1896
    @ekluzek
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  3. Update change files

    @ekluzek
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  4. change file updates, rm old neon_s3_upload as replaced by neon_gcs_up… 

    …load version
    @ekluzek
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  5. rm old neon_s3_upload as replaced by neon_gcs_upload version

    @ekluzek
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  6. Fix for ESCOMP#1901

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Commits on Nov 16, 2022

  1. Explicitly set the NEON site to run

    @ekluzek
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  2. Move run of py_env_create to after CLM_ROOT is set and call it for al… 

    …l machines
    @ekluzek
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  3. Merge branch 'neon_updates' of github.com:wwieder/CTSM into neon_updates

    @ekluzek
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  4. Update date for change files

    @ekluzek
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  5. Merge branch 'neon_updates' of github.com:wwieder/CTSM into neon_updates

    @ekluzek
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Commits on Nov 17, 2022

  1. Fix syntax error

    @ekluzek
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  2. OK really fix the syntax for the comment

    @ekluzek
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  3. Add some checks that directories are there as expected

    @ekluzek
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  4. Add some more checking that create_newcase exists as expected and tha… 

    …t the inputdata_path directory exists if provided
    @ekluzek
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  5. Add a check that the main inputdata directory exists or not, and add … 

    …a unit test for it
    @ekluzek
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  6. Add inputdata-dir option

    @ekluzek
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  7. Add a check that using command line argument to something that doesn'… 

    …t exist aborts as expected
    @ekluzek
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  8. Run black

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  9. Set inputdata option so testing can run on both cheyenne and izumi

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    ekluzek committed Nov 17, 2022
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Commits on Nov 18, 2022

  1. Add argument for inputdata-directory

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    ekluzek committed Nov 18, 2022
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  2. Set inputdata directory so can work on izumi

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    ekluzek committed Nov 18, 2022
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  3. Make datm forcing data under the inputdata-dir so doesn't need a sepe… 

    …rate path and can work on izumi as well
    @ekluzek
    ekluzek committed Nov 18, 2022
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Commits on Nov 19, 2022

  1. Check if pandas is recent enough

    @ekluzek
    ekluzek committed Nov 19, 2022
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  2. Fix the error, which was failing in writing an empty list

    @ekluzek
    ekluzek committed Nov 19, 2022
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Commits on Nov 20, 2022

  1. Update changelog

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    ekluzek committed Nov 20, 2022
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