Remove nemsio support #1255

lgannoaa · 2023-01-19T14:52:58Z

Description
Removes remaining nemsio support from scripts. Now unnecessary variables will be removed in a follow-up PR.

Refs: #601

How Has This Been Tested?

Cycled test on WCOSS

Checklist

My code follows the style guidelines of this project
I have performed a self-review of my own code
My changes generate no new warnings

GitHub: 601

aerorahul

Changes look good to me.
I have not tested this change.
A future PR can remove the source codes that are related to nemsio and the linking of the executables.
This clean-up is greatly appreciated.

WalterKolczynski-NOAA

We can remove a lot of variables that aren't really needed anymore now that only netcdf is supported. For those that are used in namelists or filenames, you'll need to replace them with the hard-coded value.

WalterKolczynski-NOAA · 2023-01-19T18:18:24Z

parm/config/config.base.emc.dyn

+export NEMSIO_IN=".false."
+export NETCDF_IN=".true."


Should be able to get rid of these variables entirely now. Find wherever they are used and replace with hard-coded values.

WalterKolczynski-NOAA · 2023-01-19T18:23:21Z

scripts/exgdas_enkf_update.sh

+use_gfs_ncio=".true."
+use_gfs_nemsio=".false."


These should also be able to be removed now.

(1) The use_gfs_nemsio is part of the enkf.nml namelist. It should not be changed.
(2) The variable use_gfs_nemsio is only used locally.
Therefore, recommend no change here.

There is no need for these variables. So they could/should be removed.

WalterKolczynski-NOAA · 2023-01-19T18:25:27Z

scripts/exgfs_atmos_postsnd.sh

@@ -36,38 +36,20 @@ export INCREMENT=12
 export MAKEBUFR=NO
 export F00FLAG=YES
 export fformat=${OUTPUT_FILE:-netcdf}
-if [ $fformat == "netcdf" ]
- then
 export atmfm="nc"


This one too, I think.

WalterKolczynski-NOAA · 2023-01-19T18:30:38Z

ush/hpssarch_gen.sh

 SUFFIX=${SUFFIX:-".nc"}
-if [ $SUFFIX = ".nc" ]; then
-  format="netcdf"
-else
-  format="nemsio"
-fi
+format="netcdf"


These as well.

WalterKolczynski-NOAA · 2023-01-19T18:31:01Z

ush/gfs_post.sh

@@ -222,8 +222,7 @@ export LOGSCRIPT=${LOGSCRIPT:-}
 export ENDSCRIPT=${ENDSCRIPT:-}
 export GFSOUT=${GFSOUT:-gfsout}
 export CTLFILE=${CTLFILE:-${NWPROD}/parm/gfs_cntrl.parm}
-#export MODEL_OUT_FORM=${MODEL_OUT_FORM:-binarynemsiompiio}
-export OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
+export OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}


WalterKolczynski-NOAA · 2023-01-19T18:31:24Z

ush/gaussian_sfcanl.sh

+OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
+export NETCDF_OUT=".true."


WalterKolczynski-NOAA · 2023-01-19T18:31:46Z

ush/forecast_predet.sh

@@ -133,11 +133,10 @@ FV3_GFS_predet(){

  QUILTING=${QUILTING:-".true."}
  OUTPUT_GRID=${OUTPUT_GRID:-"gaussian_grid"}
-  OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
+  OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}


WalterKolczynski-NOAA · 2023-01-19T18:31:53Z

ush/forecast_predet.sh

  WRITE_NEMSIOFLIP=${WRITE_NEMSIOFLIP:-".true."}
  WRITE_FSYNCFLAG=${WRITE_FSYNCFLAG:-".true."}
-  affix="nemsio"
-  [[ "$OUTPUT_FILE" = "netcdf" ]] && affix="nc"
+  affix="nc"


WalterKolczynski-NOAA · 2023-01-19T18:32:01Z

ush/forecast_postdet.sh

  cd $DATA
-
  affix="nc"


Variable affix is used locally. Therefore, no need to modify.

The point is I want you to replace $affix with "nc" everywhere it appears. Similarly for the others.

since there is not other affix, this variable is no longer needed and should be removed as the reviewer suggests.

WalterKolczynski-NOAA · 2023-01-19T18:32:16Z

scripts/exglobal_archive.sh

-else
-   format="nemsio"
-fi
+format="netcdf"


Variable format is used locally. Therefore it should be ok not to change it.

lgannoaa · 2023-01-19T19:07:59Z

We can remove a lot of variables that aren't really needed anymore now that only netcdf is supported. For those that are used in namelists or filenames, you'll need to replace them with the hard-coded value.

@WalterKolczynski-NOAA, Would you please check again these change request? It save time and resource to make modification once for all.

WalterKolczynski-NOAA · 2023-01-19T19:20:57Z

We can remove a lot of variables that aren't really needed anymore now that only netcdf is supported. For those that are used in namelists or filenames, you'll need to replace them with the hard-coded value.

@WalterKolczynski-NOAA, Would you please check again these change request? It save time and resource to make modification once for all.

I... don't know what you're asking for here.

WalterKolczynski-NOAA · 2023-01-19T21:19:30Z

Any variables that are no longer needed for switching to nemsio should be removed, and any variables that no longer change (like affix) should be replaced with their static value. There may be more than I have spotted during review. Please examine the scripts.

aerorahul · 2023-01-19T22:02:59Z

@lgannoaa would like to address the reviewer comments in a follow-up PR.
Issue #601 will be left opened until the reviewer comments are resolved in the follow-up PR.

WalterKolczynski-NOAA

Approved with understanding the now unnecessary variables will be removed in a follow-up PR.

* 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)

lgannoaa added 2 commits January 19, 2023 14:36

Remove nemsio support

e984cf6

GitHub: 601

Remove test code for JGLOBAL_ATMOS_ANALYSIS_CALC

6844963

lgannoaa self-assigned this Jan 19, 2023

aerorahul approved these changes Jan 19, 2023

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aerorahul requested review from KateFriedman-NOAA and WalterKolczynski-NOAA January 19, 2023 16:08

WalterKolczynski-NOAA requested changes Jan 19, 2023

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WalterKolczynski-NOAA approved these changes Jan 19, 2023

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WalterKolczynski-NOAA merged commit 78509d6 into NOAA-EMC:develop Jan 19, 2023

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Remove nemsio support #1255

Remove nemsio support #1255

lgannoaa commented Jan 19, 2023 •

edited by WalterKolczynski-NOAA

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		OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
		export NETCDF_OUT=".true."

		use_gfs_ncio=".true."
		use_gfs_nemsio=".false."

Remove nemsio support #1255

Remove nemsio support #1255

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lgannoaa commented Jan 19, 2023

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lgannoaa commented Jan 19, 2023 •

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