Convert archive jobs to proper j-jobs #1115
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Include script, JJob, and utility for GDAS, ENKFGDAS, and GFS archive jobs Detailed information can be found in github issue NOAA-EMC#1051 NOAA-EMC#1051
Move JJob and scripts into HOMEgfs level
…into feature/ecf-archive
…into feature/ecf-archive
![github-advanced-security[bot]](https://github.com/avatars/in/57789?s=60&v=4){kind=small}
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shellcheck found more than 10 potential problems in the proposed changes. Check the Files changed tab for more details.
aerorahul
reviewed
Nov 14, 2022
jobs/JENKFGDAS_ARCHIVE
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| export EARCINC_CYC=${ARCH_CYC} | ||
| export EARCICS_CYC=$((ARCH_CYC-assim_freq)) | ||
| if [ ${EARCICS_CYC} -lt 0 ]; then | ||
| export EARCICS_CYC=$((EARCICS_CYC+24)) | ||
| fi |
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Please move these to exgdas_enkf_earc.sh and drop the export
jobs/JENKFGDAS_ARCHIVE
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| # EnKF update in GFS, GDAS or both | ||
| export CDUMP_ENKF=$(echo ${EUPD_CYC:-"gdas"} | tr a-z A-Z) | ||
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| export ARCH_LIST="${ROTDIR}/enkf${CDUMP}.${PDY}/${cyc}/${COMPONENT}/earc${ENSGRP}" |
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This belongs to exgdas_enkf_earc.sh and is there.
scripts/exgdas_enkf_earc.sh
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| ############################################################### | ||
| ## Abstract: | ||
| ## Ensemble archive driver script | ||
| ## RUN_ENVIR : runtime environment (emc | nco) | ||
| ## HOMEgfs : /full/path/to/workflow | ||
| ## EXPDIR : /full/path/to/config/files | ||
| ## CDATE : current analysis date (YYYYMMDDHH) | ||
| ## PDY : current date (YYYYMMDD) | ||
| ## cyc : current cycle (HH) | ||
| ## CDUMP : cycle name (gdas / gfs) | ||
| ## ENSGRP : ensemble sub-group to archive (0, 1, 2, ...) | ||
| ############################################################### |
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jobs/JENKFGDAS_ARCHIVE
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| ############################# | ||
| export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config} | ||
| configs="base earc" | ||
| config_path=${EXPDIR:-${NWROOT}/gfs.${gfs_ver}/parm/config} |
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Suggested change
| config_path=${EXPDIR:-${NWROOT}/gfs.${gfs_ver}/parm/config} | |
| config_path=${EXPDIR:-${PACKAGEROOT}/gfs.${gfs_ver}/parm/config} |
jobs/JGLOBAL_ARCHIVE
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| ############################################# | ||
| # Source workflow level common utilities | ||
| ############################################# | ||
| #### This utility is under development as of 20221020 | ||
| #### will not use it at this time | ||
| #### source "${HOMEgfs}/ush/file_utils.sh" |
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Please delete.
These are being sourced and used in exglobal_archive.sh
jobs/JGLOBAL_ARCHIVE
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| export ARCHINC_CYC=$ARCH_CYC | ||
| export ARCHICS_CYC=$((ARCH_CYC-assim_freq)) | ||
| if [ $ARCHICS_CYC -lt 0 ]; then | ||
| ARCHICS_CYC=$((ARCHICS_CYC+24)) | ||
| fi | ||
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| # CURRENT CYCLE | ||
| export APREFIX="${CDUMP}.t${cyc}z." | ||
| export ASUFFIX=${ASUFFIX:-$SUFFIX} | ||
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| if [ $ASUFFIX = ".nc" ]; then | ||
| format="netcdf" | ||
| else | ||
| format="nemsio" | ||
| fi |
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Please move these to exglobal_archive.sh and drop the export
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@aerorahul, recommended changes have been made. |
aerorahul
approved these changes
Nov 14, 2022
WalterKolczynski-NOAA
requested changes
Nov 14, 2022
WalterKolczynski-NOAA
approved these changes
Nov 14, 2022
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Tested in Cactus with C192C96 cycled run. Job completed. |
Please make sure you also test coupled, since it creates a different set of archive files. Coupled isn't fully working on WCOSS2 yet, so you'll have to use an RDHPCS machine. |
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@WalterKolczynski-NOAA Some of the shellcheck suggestions are likely out of scope from this PR e.g. |
Since this is shifting code around, just leave them. We'll take care of them later. |
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The C384 ATM fcst only test on Hera completed. The Hera space is too low for ATMW cycled test. Will proceed that test on wcoss. |
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C768C384 ATMW couple cycled test executed on wcoss2. All jobs completed as expected. |
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Still needs a full coupled S2SWA test. It will have to be run on an RDHPCS machine because it won't work on WCOSS2 yet. Workflow will automatically get the (C384) ICs for you. Use 2013040100. |
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Full coupled S2SWA fcst only test on Orion is done with gfsarch job status completed. |
WalterKolczynski-NOAA
changed the title
KateFriedman-NOAA
added a commit
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Jan 30, 2023
* 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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Description
This PR is to update the archive jobs using arc.sh, j-job, ex-script approach similar style to the package format.
Fixes #1051
Refs: #720
How Has This Been Tested?
C192C96 cycled run tested on Cactus