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Link staged GSI fix files instead of cloning them from gerrit #1132

Merged
merged 4 commits into from
Nov 30, 2022
Merged

Link staged GSI fix files instead of cloning them from gerrit #1132

merged 4 commits into from
Nov 30, 2022

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aerorahul
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@aerorahul aerorahul commented Nov 22, 2022 •
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Description
This PR links staged fix files for GSI instead of cloning them from gerrit as part of the GSI checkout process.

Fixes #1128

This may need minor updates on how the CM's stage the GSI fix files.

How Has This Been Tested?
Testing will have to wait until files are in place in the glopara space.

  • Clone and link tests on Hera, Orion, WCOSS2

Dependencies

GSI fix files in the glopara space on all machines

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

WalterKolczynski-NOAA
WalterKolczynski-NOAA previously requested changes Nov 22, 2022
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@WalterKolczynski-NOAA WalterKolczynski-NOAA left a comment

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Changes look fine so far, other than the need for a fix gsi version number. Barring complaints from @KateFriedman-NOAA or GSI team, I see no problem staging it alongside the other fix directories.

sorc/link_workflow.sh Outdated Show resolved Hide resolved
@WalterKolczynski-NOAA
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Please update the title and description though so we know what this PR does without having to look at the issue (especially once it becomes a commit in the log).

@aerorahul
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Please update the title and description though so we know what this PR does without having to look at the issue (especially once it becomes a commit in the log).

done.

@aerorahul aerorahul changed the title Fixes #1128 Link staged GSI fix files instead of cloning them from gerrit Nov 28, 2022
@aerorahul aerorahul marked this pull request as ready for review November 28, 2022 19:20
@aerorahul aerorahul dismissed WalterKolczynski-NOAA’s stale review November 28, 2022 19:21

requesting review after making changes.

@KateFriedman-NOAA
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Approved pending testing from @RussTreadon-NOAA on using the Hera set and then me rsyncing them to the other platforms.

@RussTreadon-NOAA
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@KateFriedman-NOAA , the Hera queue is backed up. 11 of 19 GSI regression tests have run with acceptable behavior. The remaining GSI regression tests should complete overnight. Please move forward with this PR is you prefer to merge today.

@KateFriedman-NOAA KateFriedman-NOAA mentioned this pull request Nov 28, 2022
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@RussTreadon-NOAA
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All 19 GSI regression tests successfully ran to completion on Hera using /scratch1/NCEPDEV/global/glopara/fix/gsi/20221128 for fixgsi.

RussTreadon-NOAA
RussTreadon-NOAA reviewed Nov 29, 2022
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sorc/link_workflow.sh
@@ -91,6 +91,7 @@ for dir in aer \
cpl \
datm \
gldas \
gsi \
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How do we handle the case that a developer does NOT want to use the staged GSI fix files? This question actually applies to all the staged fix files. One answer is that we assume the developer knows what (s)he wants to do and manually makes the required changes.

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Since all that is being done is creating symlinks, it is a simple matter to replace one of them with a location of your choice manually afterwards.

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Agreed. It is simple to replace one link with another. Does the g-w wiki capture this detail? Not everyone understands what these scripts do or how they work.

RussTreadon-NOAA
RussTreadon-NOAA reviewed Nov 29, 2022
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sorc/link_workflow.sh
@@ -163,15 +165,6 @@ if [[ -d "${script_dir}/gfs_wafs.fd" ]]; then
fi


#------------------------------
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Same question as above. What happens when a developer does NOT want to use staged GSI fix files? It may be too cumbersome to have the checkout and link script cover all possibilities. Perhaps it is sufficient to update the g-w wiki to explain options.

RussTreadon-NOAA
RussTreadon-NOAA approved these changes Nov 29, 2022
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Changes look good. Three comments added. Resolving the comments is not a prerequisite to approving this PR.

@KateFriedman-NOAA KateFriedman-NOAA merged commit 4e3335b into NOAA-EMC:develop Nov 30, 2022
@aerorahul aerorahul deleted the feature/gsi_fix_local branch November 30, 2022 19:11
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

@RussTreadon-NOAA RussTreadon-NOAA RussTreadon-NOAA approved these changes

@KateFriedman-NOAA KateFriedman-NOAA KateFriedman-NOAA approved these changes

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Stage GSI fix files in global/glopara space and disable recursive clone of GSI
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@aerorahul @WalterKolczynski-NOAA @KateFriedman-NOAA @RussTreadon-NOAA