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Update UFS to Sept 9 version #1073

Merged
merged 5 commits into from
Oct 17, 2022
Merged

Update UFS to Sept 9 version #1073

merged 5 commits into from
Oct 17, 2022

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WalterKolczynski-NOAA
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@WalterKolczynski-NOAA WalterKolczynski-NOAA commented Oct 17, 2022 •
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Description
Updates the UFS version. This captures the conversion of UFS module from TCL to lua. A couple of the CICE namelist variables are no longer valid in this version, so they are removed.

Due to memory limitations on Hera and the increased memory requirements of GOCART, the number of threads is increased there when running the forecast with aerosols.

Also added a temporary block to delete any existing gocart output files. The ability to clobber files was deactivated a while ago and I got fed up with forecast jobs failing on retry.

Type of change

  • Maintenance

How Has This Been Tested?

  • Cycled test on Orion
  • Coupled test on Orion
  • ATMA test on Hera
  • Coupled test on Hera

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 generate no new warnings
  • New and existing tests pass with my changes

@WalterKolczynski-NOAA
Remove existing aerosol output
3c8f216 
Due to a change, GOCART currently will not clobber existing output files,
resulting in a model crash when attempting to rerun. So, we temporarily
remove the aerosol output until an option is introduced to allow clobber.
@WalterKolczynski-NOAA
Update UFS to Sept 9
a4a978b 
Updates the UFS model to Sept 9. Some modules are updated to match the UFS
versions.

This update is still not fully tested and additional changes may be necessary.
@WalterKolczynski-NOAA
Adjust fcst resources on Hera for aerosols
6188c35 
Hera has less memory per core than other machines. When UFS is run
with GOCART, this results in crashes due to the memory limit being
reached. To avoid this, the number of threads is increased on Hera
when running with aerosols.
aerorahul
aerorahul approved these changes Oct 17, 2022
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A couple of comments.
As long as the other reviewers are satisfied, this PR can be merged.

@WalterKolczynski-NOAA
Remove unneeded w3nco module load
2575eaa 
With the move to a w3emc that includes w3nco, the latter no longer
needs to be loaded to build WW3 pre/post.

Additionally, added the w3emc module loads for the two machines that
were not supported when this update process started.
JessicaMeixner-NOAA
JessicaMeixner-NOAA approved these changes Oct 17, 2022
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The updates match what I see here: ufs-community/ufs-weather-model@Prototype-P8...3c3548d

Thanks @WalterKolczynski-NOAA !

@WalterKolczynski-NOAA WalterKolczynski-NOAA merged commit 7fc0f26 into NOAA-EMC:develop Oct 17, 2022
@WalterKolczynski-NOAA WalterKolczynski-NOAA deleted the feature/update_ufs branch October 17, 2022 18:57
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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Reviewers

@aerorahul aerorahul aerorahul approved these changes

@JessicaMeixner-NOAA JessicaMeixner-NOAA JessicaMeixner-NOAA approved these changes

@KateFriedman-NOAA KateFriedman-NOAA Awaiting requested review from KateFriedman-NOAA

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@WalterKolczynski-NOAA @aerorahul @JessicaMeixner-NOAA