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Update UFS-DA atmospheric prep script to be consistent with GDASApp update #1265

Merged
merged 4 commits into from
Jan 25, 2023
Merged

Update UFS-DA atmospheric prep script to be consistent with GDASApp update #1265

merged 4 commits into from
Jan 25, 2023

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RussTreadon-NOAA
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@RussTreadon-NOAA RussTreadon-NOAA commented Jan 21, 2023 •
edited by WalterKolczynski-NOAA
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Description
GDASApp PR #278 restores the ability of run_jedi_exe.py to execute UFS-DA applications, specifically fv3jedi_var.x. Included in PR #278 is the removal of entry ufsda.stage from ush/ufsda/__init__.py. Scripts which simply import ufsda must now specify the functions to from ufsda.stage.

g-w issue #1262 documents the addition of the ufsda.stage line to scripts/exgdas_global_atmos_analysis_prep.py. This change is required for g-w to successfully stage files used by the var and ensemble UFS-DA applications.

Fixes #1262

NOTE: This PR depends upon the merger of GDASApp PR #278 into GDASApp develop followed by updating the GDASApp hash in g-w Externals.cfg and sorc/checkout.sh

Type of change

  • Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

  • Clone and Build g-w on Orion and Hera
  • Execute GDASApp ctests test_gdasapp_atm_jjob_var and test_gdasapp_atm_jjob_ens

Checklist

  • My code follows the style guidelines of this project
  • I have performed a self-review of my own code
  • New and existing tests pass with my changes

@RussTreadon-NOAA RussTreadon-NOAA mentioned this pull request Jan 21, 2023
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@RussTreadon-NOAA RussTreadon-NOAA self-assigned this Jan 21, 2023
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GDASApp built from GDASApp PR 278 within local clone of RussTreadon-NOAA:feature/ufsda_stage on both Orion and Hera. GDASApp ctests executed on both machines. All ctests pass including test_gdasapp_atm_jjob_var* and test_gdasapp_atm_jjob_ens*.

The g-w changes in this PR only impact atmospheric UFS DA. GSI based DA is not altered by this PR.

@RussTreadon-NOAA
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GDASApp PR #278 has been opened for review. g-w tests using RussTreadon-NOAA:feature/ufsda_stage confirm that the combination of GDASApp PR #278 and g-w PR #1265 produce the desired behavior.

Once GDASApp PR #278 is approved and merged into GDASApp develop, the GDASApp hash in Externals.cfg and sorc/checkout.sh will be updated in this PR.

@RussTreadon-NOAA
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GDASApp PR #278 was merged into GDASApp develop at f7c23af. Given this, the GDASApp hash in Externals.cfg and sorc/checkout.sh have been updated to the new head of GDASApp develop. Done at 0744e22.

This PR is now ready for review.

@RussTreadon-NOAA RussTreadon-NOAA marked this pull request as ready for review January 24, 2023 14:07
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@WalterKolczynski-NOAA and @CoryMartin-NOAA , do you have time to review this PR? Three files are changed:

  1. scripts/exgdas_global_atmos_analysis_prep.sh - add line to import the ufsda functions used by the script. This change is required due to the merger of GDASApp PR #278 into GDASApp develop at f7c23af.
  2. Externals.cfg - update GDASApp hash to head of GDASApp develop, f7c23af
  3. sorc/checkout.sh - same change as Externals.cfg

aerorahul
aerorahul approved these changes Jan 24, 2023
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looks ok to me.

@RussTreadon-NOAA
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looks ok to me.

Thank you @aerorahul!

CoryMartin-NOAA
CoryMartin-NOAA approved these changes Jan 24, 2023
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Looks good, thanks @RussTreadon-NOAA

@WalterKolczynski-NOAA WalterKolczynski-NOAA merged commit fb54bb6 into NOAA-EMC:develop Jan 25, 2023
@RussTreadon-NOAA RussTreadon-NOAA deleted the feature/ufsda_stage branch January 25, 2023 20:42
KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this pull request Jan 30, 2023
@KateFriedman-NOAA
Merge branch 'develop' into feature/version-files
e81ed7c 
* develop:
  Correct issue in linking final restart files (NOAA-EMC#1285)
  Remove execute permissions from config files (NOAA-EMC#1281)
  Make needed updates to run forecast from GEFS (NOAA-EMC#1203)
  Remove unnecessary variables which reference to nemsio (NOAA-EMC#1259)
  Create analysis files for early-cycle EnKF by default (NOAA-EMC#1237)
  Don't wipe $DATA before running ocean bmat (NOAA-EMC#1280)
  More marine DA j-jobs (NOAA-EMC#1270)
  Update UFS-DA atmospheric prep script to be consistent with GDASApp update (NOAA-EMC#1265)
  Add new jjob for ocean analysis bmat (NOAA-EMC#1239)
  Retire ecf/versions in develop (NOAA-EMC#1267)
  Deploy documentation to RTD (NOAA-EMC#1264)
  Temporarily disable failing pytest (NOAA-EMC#1263)
  Remove incorrect/misleading comments in config.base (NOAA-EMC#1261)
  Add initial Sphinx documentation (NOAA-EMC#1258)
  Remove nemsio support (NOAA-EMC#1255)
  Increase wallclock for diag jobs (NOAA-EMC#1216)
  Use correct resources for GFS gempak (NOAA-EMC#1214)
  Abstract common j-job tasks (NOAA-EMC#1230)
  Add missing mkgfsawps.x link (NOAA-EMC#1218)
  Fix post sounding job (NOAA-EMC#1212)
  Revert "Use fracoro data for all new UFS applications (NOAA-EMC#1182)" (NOAA-EMC#1240)
  Use fracoro data for all new UFS applications (NOAA-EMC#1182)
  Revert "Merge GFS v16.3 operational GSI changes into develop branch. (NOAA-EMC#1158)" (NOAA-EMC#1238)
  Add more user defined parameters for the marine DA (NOAA-EMC#1235)
  Update pytests action version and run sequentially (NOAA-EMC#1236)
  Add utility to compare Fortran namelists (NOAA-EMC#1234)
  Updates for pygw (NOAA-EMC#1231)
  Merge GFS v16.3 operational GSI changes into develop branch. (NOAA-EMC#1158)
  Move member up in directory hierarchy (NOAA-EMC#1201)
  Enable staging ics for cycled experiments. (NOAA-EMC#1199)
  Add tests for configuration.py (NOAA-EMC#1192)
  Replace ocnanal_${CDATE}} with ${RUN}ocnanal_${cyc} (NOAA-EMC#1191)
  define NET and RUN in the Rocoto XML to accurately mimic the ecf in ecflow (NOAA-EMC#1193)
  Fix checking for restart files (NOAA-EMC#1186)
  Fix 'DEBUG' option in build_ufs.sh (NOAA-EMC#1188)
  Update archive job memory request value for R&Ds (NOAA-EMC#1183)
  Reorder post so all flux files are generated when running offline (NOAA-EMC#1181)
  Stop checking for restarts on non-GFS CDUMPs (NOAA-EMC#1179)
  Add missing jobids in some pre-job scripts (NOAA-EMC#1176)
  Remove existing directory if it exists when getic runs (NOAA-EMC#1165)
  Add logging decorator, test and test for yaml_file (NOAA-EMC#1178)
  fix coding norm check in `hosts.py` (NOAA-EMC#1174)
  Fix some bugs and make other changes so ctest in GDASApp works (NOAA-EMC#1172)
  Support for the GDASApp testing in containers (NOAA-EMC#1151)
  ATM 3DVAR with and without IAU (NOAA-EMC#1113)
  Enable checking for python norms and fix violating code (NOAA-EMC#1168)
  Enforce decimal math in atmos post (NOAA-EMC#1171)
  Update marine DA j-jobs to new format (NOAA-EMC#1149)
  Add utility to manipulate files en masse  (NOAA-EMC#1166)
  add action to run pytests (NOAA-EMC#1167)
  Pin `differential-shellcheck` to `v3` tag (NOAA-EMC#1162)
  Add a task base class and basic logger (NOAA-EMC#1160)
  Recursively convert dict to AttrDict when making an AttrDict (NOAA-EMC#1154)
  move configuration.py to pygw. Use it from there.  return AttrDict after sourcing configs (NOAA-EMC#1153)
  JEDI based Marine DA tasks (NOAA-EMC#1134)
  Allow customizations based on user/configuration (NOAA-EMC#1146)
  First step towards making j-jobs consistent in use from ecflow and rocoto (NOAA-EMC#1120)
  enable APP=S2SWA on WCOSS2 (NOAA-EMC#1142)
  Fix typo in .shellcheckrc
  Remove prod_envir module load from WCOSS2 (NOAA-EMC#1138)
  Link staged GSI fix files instead of cloning them from gerrit (NOAA-EMC#1132)
  Address shellcheck warnings in env files (NOAA-EMC#1136)
  Adds group size and nmem for GEFS (NOAA-EMC#1127)
  Remove unnecessary sCDATE assignment in forecast_predet.sh (NOAA-EMC#1133)
  Convert archive jobs to proper j-jobs (NOAA-EMC#1115)
  Update C48 forecast to run with one thread (NOAA-EMC#1131)
  Improved error messages from atmos analysis (NOAA-EMC#1125)
  Update MODULEPATH for Orion (NOAA-EMC#1126)
  MPMD variable updates and fix (NOAA-EMC#1124)
  Introduce FHMAX_ENKF_GFS to extending ensemble forecast capabilities (NOAA-EMC#1122)
  Update R&D launcher commands for tasks and multi-prog (NOAA-EMC#1112)
  Correct crtm path in UFS DA atmospheric analysis scripts (NOAA-EMC#1111)
  Correct syntax in remaining sorc scripts (NOAA-EMC#1105)
  Add GSI background error covariance as an option for UFS DA variational assimilation (NOAA-EMC#1104)
  Add Early Cycle EnKF workflow (NOAA-EMC#1022)
  Correct errors with gdas and monitoring symlinks (NOAA-EMC#1101)
  Fixed gfs-utils links (NOAA-EMC#1099)
  Fix build scripts and bring into compliance (NOAA-EMC#1096)
  Feature/updates for gdas app (NOAA-EMC#1091)
  Change GLDAS USE_CFP to NO on Hera (NOAA-EMC#1094)
  Resource updates to support WCOSS2 (NOAA-EMC#1070)
  Set COMPILER in link for detect machine (NOAA-EMC#1092)
  gfs utils update (NOAA-EMC#1088)
  GFS-UTILS update for build and ush scripts (NOAA-EMC#1082)
  Update UFS version to 2022 Oct 19 (NOAA-EMC#1083)
  Use more cycledefs for task control (NOAA-EMC#1078)
  removing superfluous EFSOI-specific files from develop (NOAA-EMC#1079)
  Update UFS to Sept 9 version (NOAA-EMC#1073)
  Modify default file location for monitor data when using rocoto (NOAA-EMC#1065)
  Fix companion ocean resolution for C48 (NOAA-EMC#1066)
  Add trailing slash for gldas topo path (NOAA-EMC#1064)
  Limit number of CPU for post (NOAA-EMC#1061)
  Fix eupd trace (NOAA-EMC#1057)
  Port to S4 (NOAA-EMC#1023)
  Update to obsproc.v1.0.2 and prepobs.v1.0.1 (NOAA-EMC#1049)
  Add GDAS to the partial build list (NOAA-EMC#1050)
  Fix group number being treated as octal in gdas arch (NOAA-EMC#1053)
  Remove trace from link script (NOAA-EMC#1046)
  Update gfs-utils hash to 3a609ea (NOAA-EMC#1048)
  Fix link script usage statement (NOAA-EMC#1045)
  Replace preamble variable commands with functions (NOAA-EMC#1012)
  Implement fix reorg and remove gfs-utils code (NOAA-EMC#1009)
  Rename post scripts (NOAA-EMC#1038)
  Fix missing @ symbol with COMINsyn in config.base (NOAA-EMC#1039)
  WCOSS2 run support and script/config updates (NOAA-EMC#1030)
  Remove base_svn from Hera and Orion hosts files (NOAA-EMC#1036)
  initial commit for incoming yaml work (NOAA-EMC#1029)
  Fix radiance verification failing to find diag files (NOAA-EMC#1031)
  Supported resolutions on platforms and defaults for mode (NOAA-EMC#1026)
  Add GLDAS scripts & fix GLDAS job (NOAA-EMC#1018)
  Update GSI Monitor for radmon fix
  Correct shell linter config (NOAA-EMC#1013)
  Correct diagnostic file handling in ush/ozn_xtrct.sh (NOAA-EMC#1016)
  Add shell linter Github action for pull requests (NOAA-EMC#1007)
  Build updates for WCOSS2 (NOAA-EMC#1002)
  Update UFS_UTILS tag to `ufs_utils_1_8_0` (NOAA-EMC#1001)
  Fix preamble id (NOAA-EMC#996)
  Add missing "atmos" into job dependencies (NOAA-EMC#998)
  Bugfix in arch.sh to remove hardwired "htar" (NOAA-EMC#992)
  Add in stubs for aerosol DA tasks + bugfix for setup_expt where cycled and ATMA are used (NOAA-EMC#990)
  Add GSI monitor scripts (NOAA-EMC#969)
  Fix product generation at some fcst hrs (NOAA-EMC#988)
  Add initial config files for global aerosol DA (NOAA-EMC#986)
  Update diag table to remove wav-ocn coupling fields (NOAA-EMC#979)
  use a robust Findwgrib2.cmake to find wgrib2 built w/ native wgrib2 build (NOAA-EMC#970)
  Externals.cfg was stale and had drifted off (NOAA-EMC#965)
  Fix post comparison with zero-padded numbers (NOAA-EMC#964)
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@WalterKolczynski-NOAA WalterKolczynski-NOAA WalterKolczynski-NOAA approved these changes

@aerorahul aerorahul aerorahul approved these changes

@CoryMartin-NOAA CoryMartin-NOAA CoryMartin-NOAA approved these changes

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import specific ufsda stage functions in ufsda atm prep script
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@RussTreadon-NOAA @CoryMartin-NOAA @aerorahul @WalterKolczynski-NOAA