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Fix file promotion and updated versioned FIX_DIR paths in workflow #966

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36 tasks done
KateFriedman-NOAA opened this issue Aug 10, 2022 · 8 comments · Fixed by #1009
Closed
36 tasks done

Fix file promotion and updated versioned FIX_DIR paths in workflow #966

KateFriedman-NOAA opened this issue Aug 10, 2022 · 8 comments · Fixed by #1009
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feature New feature or request maintenance Regular updates and maintenance work

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@KateFriedman-NOAA
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KateFriedman-NOAA commented Aug 10, 2022

Description

This issue will document the promotion of fix_NEW to fix and the associated workflow linking updates to the newly restructured and versioned fix file sets on supported platforms. The initial promotion tasks will happen over a two day period and then the workflow updates will occur.

Checklist

August 10th (promotion day 1)

  • rename fix to fix_20210923 (Hera)
  • rename fix to fix_20210923 (WCOSS2 Cactus)
  • rename fix to fix_20210923 (WCOSS2 Dogwood)
  • rename fix to fix_20210923 (Orion)
  • rename fix to fix_20210923 (Jet)
  • copy new fix in to replace fix (Hera)
  • rsync new fix from Hera in to replace fix on WCOSS2 Cactus
  • rsync new fix from Hera in to replace fix on WCOSS2 Dogwood
  • rsync new fix from Hera in to replace fix on Orion
  • rsync new fix from Hera in to replace fix on Jet
  • copy test version of fix_NEW (fix_NEW_test) into global space for sanity testing on Hera
  • perform sanity tests on fix_NEW_test on Hera

August 11th (promotion day 2)

  • rename fix_NEW to fix_NEW_20220726 (Hera)
  • rename fix_NEW to fix_NEW_20220726 (WCOSS2 Cactus)
  • rename fix_NEW to fix_NEW_20220726 (WCOSS2 Dogwood)
  • rename fix_NEW to fix_NEW_20220726 (Orion)
  • rename fix_NEW to fix_NEW_20220726 (Jet)
  • create new fix_NEW with symlinks to updated fix (Hera)
  • create new fix_NEW with symlinks to updated fix (WCOSS2 Cactus)
  • create new fix_NEW with symlinks to updated fix (WCOSS2 Dogwood)
  • create new fix_NEW with symlinks to updated fix (Orion)
  • create new fix_NEW with symlinks to updated fix (Jet)

August 19th (cleanup)

  • delete fix_NEW_20220726 (Hera)
  • delete fix_NEW_20220726 (WCOSS2 Cactus)
  • delete fix_NEW_20220726 (WCOSS2 Dogwood)
  • delete fix_NEW_20220726 (Orion)
  • delete fix_NEW_20220726 (Jet)

August 26th (cleanup)

  • delete fix_20210923 (Hera)
  • delete fix_20210923 (WCOSS2 Cactus)
  • delete fix_20210923 (WCOSS2 Dogwood)
  • delete fix_20210923 (Orion)
  • delete fix_20210923 (Jet)

Workflow updates

@KateFriedman-NOAA KateFriedman-NOAA added feature New feature or request maintenance Regular updates and maintenance work labels Aug 10, 2022
KateFriedman-NOAA added a commit that referenced this issue Aug 25, 2022
- Source new fix.ver file to get fix subfolder version values for setting up fix folder symlinks.
- Change "fix_NEW" to "fix" for FIX_DIR paths: use newly reorganized and versioning fix set.
- Remove "fix_" from /fix folder symlink names.
- Update /fix folder symlink creation to use version variables from fix.ver.
- Update GSI and GDAS fix symlinks.

Refs: #966
KateFriedman-NOAA added a commit that referenced this issue Aug 25, 2022
- Change FV3JEDI_FIX in related configs to change the path subfolder from
"fix_jedi" to "gdas".

Refs: #966
KateFriedman-NOAA added a commit that referenced this issue Aug 25, 2022
- Remove "fix_" text from fix file paths in several configs.

Refs: #966
KateFriedman-NOAA added a commit that referenced this issue Aug 25, 2022
- Update /scripts and /ush scripts to remove the "fix_" text
from fix subfolder paths.

Refs: #966
@KateFriedman-NOAA
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Ran control (with fix_NEW) and test (using updated fix paths) on Orion (both atmos-only and coupled). The test output matches the control run.

atmos-only run spot checking:

Orion-login-1[39] /work/noaa/stmp/kfriedma/comrot/fixveratmos$ cmp ../devctrlatmos/gdas.20220101/18/atmos/gdas.t18z.master.grb2f009 gdas.20220101/18/atmos/gdas.t18z.master.grb2f009
Orion-login-1[40] /work/noaa/stmp/kfriedma/comrot/fixveratmos$ cmp ../devctrlatmos/gdas.20220101/18/atmos/gdas.t18z.sfluxgrbf009.grib2 gdas.20220101/18/atmos/gdas.t18z.sfluxgrbf009.grib2
Orion-login-1[42] /work/noaa/stmp/kfriedma/comrot/fixveratmos$ cmp ../devctrlatmos/gdas.20220102/00/atmos/gdas.t00z.master.grb2f009 gdas.20220102/00/atmos/gdas.t00z.master.grb2f009
Orion-login-1[43] /work/noaa/stmp/kfriedma/comrot/fixveratmos$ cmp ../devctrlatmos/gdas.20220102/00/atmos/gdas.t00z.sfluxgrbf009.grib2 gdas.20220102/00/atmos/gdas.t00z.sfluxgrbf009.grib2
Orion-login-1[50] /work/noaa/stmp/kfriedma/comrot/fixveratmos$ nccmp -dgB ../devctrlatmos/gdas.20220102/00/atmos/gdas.t00z.sfcf009.nc gdas.20220102/00/atmos/gdas.t00z.sfcf009.nc
Orion-login-1[52] /work/noaa/stmp/kfriedma/comrot/fixveratmos$ nccmp -dgB ../devctrlatmos/gfs.20220102/00/atmos/gfs.t00z.sfcf024.nc gfs.20220102/00/atmos/gfs.t00z.sfcf024.nc
Orion-login-1[53] /work/noaa/stmp/kfriedma/comrot/fixveratmos$ nccmp -dgB ../devctrlatmos/gfs.20220102/00/atmos/gfs.t00z.atmf024.nc gfs.20220102/00/atmos/gfs.t00z.atmf024.nc
Orion-login-1[54] /work/noaa/stmp/kfriedma/comrot/fixveratmos$

@KateFriedman-NOAA
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Ran test/diff_ROTDIR.sh on coupled control and test using updated fix file set. Everything came back as identical/matching between the runs.

@KateFriedman-NOAA
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@GeorgeGayno-NOAA Below are the UFS_UTILS files I had to modify for the updated fix subfolders (see clone on Orion):

Orion-login-1[151] /work/noaa/global/kfriedma/git/feature-fix-versioning/sorc/ufs_utils.fd$ git log -1
commit a2b0817028e91aca4233c2d4198d14049bd6abbd
Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com>
Date:   Wed Jun 1 14:34:01 2022 -0400

    Update documentation for SRW App (#656)

    Update the doxygen and 'readthedocs' documentation. Update the
    varmap file 'readme' file. Supports v2.0 of the SRW Application.

    Fixes #643.
Orion-login-1[150] /work/noaa/global/kfriedma/git/feature-fix-versioning/sorc/ufs_utils.fd$ git status
# HEAD detached at a2b0817
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#       modified:   fix/link_fixdirs.sh
#       modified:   scripts/exemcsfc_global_sfc_prep.sh
#       modified:   ush/emcsfc_ice_blend.sh
#       modified:   ush/emcsfc_snow.sh
#       modified:   ush/fv3gfs_driver_grid.sh
#       modified:   ush/global_cycle.sh
#       modified:   ush/global_cycle_driver.sh
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       fix/am
#       fix/orog
#       fix/sfc_climo
no changes added to commit (use "git add" and/or "git commit -a")

We'll need you to make these same changes in UFS_UTILS develop and then we'll update the UFS_UTILS version as the related global-workflow changes go in. I have another issue (#974) that competes with this work a bit. May need to coordinate when we commit these fix changes for after we update to the newer UFS_UTILS tag. Not 100% sure at the moment.

@GeorgeGayno-NOAA
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@GeorgeGayno-NOAA Below are the UFS_UTILS files I had to modify for the updated fix subfolders (see clone on Orion):

Orion-login-1[151] /work/noaa/global/kfriedma/git/feature-fix-versioning/sorc/ufs_utils.fd$ git log -1
commit a2b0817028e91aca4233c2d4198d14049bd6abbd
Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com>
Date:   Wed Jun 1 14:34:01 2022 -0400

    Update documentation for SRW App (#656)

    Update the doxygen and 'readthedocs' documentation. Update the
    varmap file 'readme' file. Supports v2.0 of the SRW Application.

    Fixes #643.
Orion-login-1[150] /work/noaa/global/kfriedma/git/feature-fix-versioning/sorc/ufs_utils.fd$ git status
# HEAD detached at a2b0817
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#       modified:   fix/link_fixdirs.sh
#       modified:   scripts/exemcsfc_global_sfc_prep.sh
#       modified:   ush/emcsfc_ice_blend.sh
#       modified:   ush/emcsfc_snow.sh
#       modified:   ush/fv3gfs_driver_grid.sh
#       modified:   ush/global_cycle.sh
#       modified:   ush/global_cycle_driver.sh
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       fix/am
#       fix/orog
#       fix/sfc_climo
no changes added to commit (use "git add" and/or "git commit -a")

We'll need you to make these same changes in UFS_UTILS develop and then we'll update the UFS_UTILS version as the related global-workflow changes go in. I have another issue (#974) that competes with this work a bit. May need to coordinate when we commit these fix changes for after we update to the newer UFS_UTILS tag. Not 100% sure at the moment.

Just opened an issue to track this: ufs-community/UFS_UTILS#687

@KateFriedman-NOAA
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Just opened an issue to track this: ufs-community/UFS_UTILS#687

Awesome, thanks @GeorgeGayno-NOAA !

@WalterKolczynski-NOAA
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Just a note here to make sure we're on the same page: link_fixdirs should probably take in the versions just like we do for modulefiles. Not sure if Kate's current changes do that, but the final solution should.

KateFriedman-NOAA added a commit that referenced this issue Aug 25, 2022
- Create a new version folder to hold version files.
- Create a new fix.ver to hold fix file versions.

Refs: #966
@KateFriedman-NOAA
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Great point @WalterKolczynski-NOAA , thanks!

@GeorgeGayno-NOAA Please see the link script changes I made in my g-w branch here: fdd640f

I also created a fix.ver file to hold the subfolder versions, which link_workflow.sh uses when creating the symlinks under fix:
https://github.com/NOAA-EMC/global-workflow/blob/feature/fix-versioning/versions/fix.ver

I updated my changes to my UFS_UTILS copy to show what the symlinks should now be based on the contents of fix.ver:

Orion-login-1[19] /work/noaa/global/kfriedma/git/feature-fix-versioning/sorc/ufs_utils.fd/fix$ pwd
/work/noaa/global/kfriedma/git/feature-fix-versioning/sorc/ufs_utils.fd/fix
Orion-login-1[20] /work/noaa/global/kfriedma/git/feature-fix-versioning/sorc/ufs_utils.fd/fix$ ll
total 4
lrwxrwxrwx 1 kfriedma global   41 Aug 25 16:03 am -> /work/noaa/global/glopara/fix/am/20220805/
-rwxr-xr-x 1 kfriedma global 1699 Aug 25 14:33 link_fixdirs.sh*
lrwxrwxrwx 1 kfriedma global   43 Aug 25 16:04 orog -> /work/noaa/global/glopara/fix/orog/20220805/
lrwxrwxrwx 1 kfriedma global   48 Aug 25 16:04 sfc_climo -> /work/noaa/global/glopara/fix/sfc_climo/20220805/

WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/UFS_UTILS that referenced this issue Aug 29, 2022
Global workflow recently updated their fix directory structure to incorporate
versioning using dates within the directory tree. Additionally, some files were
moved and directories renamed (including removing all the 'fix_' prefixes of
subdirectories). This commit updates the fix paths in UFS utils to match the
new directory structure, and also take version numbers for each of the fix
component directories, similar to how versions are used for modulefiles.)

Fixes ufs-community#687
Refs: NOAA-EMC/global-workflow#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/UFS_UTILS that referenced this issue Aug 29, 2022
Global workflow recently updated their fix directory structure to incorporate
versioning using dates within the directory tree. Additionally, some files were
moved and directories renamed (including removing all the 'fix_' prefixes of
subdirectories). This commit updates the fix paths in UFS utils to match the
new directory structure, and also take version numbers for each of the fix
component directories, similar to how versions are used for modulefiles.)

Fixes ufs-community#687
Refs: NOAA-EMC/global-workflow#966
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Aug 31, 2022
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Aug 31, 2022
- Source new fix.ver file to get fix subfolder version values for setting up fix folder symlinks.
- Change "fix_NEW" to "fix" for FIX_DIR paths: use newly reorganized and versioning fix set.
- Remove "fix_" from /fix folder symlink names.
- Update /fix folder symlink creation to use version variables from fix.ver.
- Update GSI and GDAS fix symlinks.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Aug 31, 2022
- Change FV3JEDI_FIX in related configs to change the path subfolder from
"fix_jedi" to "gdas".

Refs: NOAA-EMC#966
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Aug 31, 2022
- Remove "fix_" text from fix file paths in several configs.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Aug 31, 2022
- Update /scripts and /ush scripts to remove the "fix_" text
from fix subfolder paths.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Aug 31, 2022
- Create a new version folder to hold version files.
- Create a new fix.ver to hold fix file versions.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/UFS_UTILS that referenced this issue Sep 6, 2022
Global workflow recently updated their fix directory structure to incorporate
versioning using dates within the directory tree. Additionally, some files were
moved and directories renamed (including removing all the 'fix_' prefixes of
subdirectories). This commit updates the fix paths in UFS utils to match the
new directory structure, and also take version numbers for each of the fix
component directories, similar to how versions are used for modulefiles.)

Fixes ufs-community#687
Refs: NOAA-EMC/global-workflow#966
@KateFriedman-NOAA
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@WalterKolczynski-NOAA fyi, the following changes will need to be made to the GLDAS scripts for this issue:

diff --git a/jobs/JGDAS_ATMOS_GLDAS b/jobs/JGDAS_ATMOS_GLDAS
index a75e814..caa1684 100755
--- a/jobs/JGDAS_ATMOS_GLDAS
+++ b/jobs/JGDAS_ATMOS_GLDAS
@@ -74,7 +74,7 @@ export COMPONENT=${COMPONENT:-atmos}
 ##############################################
 export gldas_ver=${gldas_ver:-v2.3.0}
 export HOMEgldas=${HOMEgldas:-$HOMEgfs}
-export FIXgldas=${FIXgldas:-$HOMEgldas/fix/fix_gldas}
+export FIXgldas=${FIXgldas:-$HOMEgldas/fix/gldas}
 export PARMgldas=${PARMgldas:-$HOMEgldas/parm/gldas}
 export EXECgldas=${EXECgldas:-$HOMEgldas/exec}
 export USHgldas=${USHgldas:-$HOMEgldas/ush}

diff --git a/scripts/exgdas_atmos_gldas.sh b/scripts/exgdas_atmos_gldas.sh
index ad14fc6..7697712 100755
--- a/scripts/exgdas_atmos_gldas.sh
+++ b/scripts/exgdas_atmos_gldas.sh
@@ -61,7 +61,7 @@ export nlat=$((2*res))
 export nlon=$((4*res))

 export FIXgldas=${FIXgldas:-$HOMEgfs/fix}
-export topodir=${topodir:-$HOMEgfs/fix/fix_fv3_gmted2010/$CASE/}
+export topodir=${topodir:-$HOMEgfs/fix/orog/$CASE/}

WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/UFS_UTILS that referenced this issue Sep 17, 2022
Global workflow recently updated their fix directory structure to incorporate
versioning using dates within the directory tree. Additionally, some files were
moved and directories renamed (including removing all the 'fix_' prefixes of
subdirectories). This commit updates the fix paths in UFS utils to match the
new directory structure, and also take version numbers for each of the fix
component directories, similar to how versions are used for modulefiles.)

Fixes ufs-community#687
Refs: NOAA-EMC/global-workflow#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 20, 2022
An earlier change had inadvertently stopped checking out GSI Monitor,
GSI Utils, and GLDAS when GDAS is used instead of GSI.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 20, 2022
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 20, 2022
First wave of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 23, 2022
Second wave of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 23, 2022
Wave 3 of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 23, 2022
Wave 4 of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 24, 2022
The last merge from develop introduced a minor syntax error in the
link script due to a bad conflict resolution. The issue is now
corrected.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 26, 2022
GLDAS scripts were recent moved into the workflow repo and need to
be updated for the new fix structure like other components.

Refs: NOAA-EMC#622, NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 27, 2022
Moved the setting of FIXDIR higher so it errors on an unknown machine
sooner. Also removed redundant version file load.

Refs: NOAA-EMC#966
@KateFriedman-NOAA KateFriedman-NOAA linked a pull request Sep 28, 2022 that will close this issue
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
- Source new fix.ver file to get fix subfolder version values for setting up fix folder symlinks.
- Change "fix_NEW" to "fix" for FIX_DIR paths: use newly reorganized and versioning fix set.
- Remove "fix_" from /fix folder symlink names.
- Update /fix folder symlink creation to use version variables from fix.ver.
- Update GSI and GDAS fix symlinks.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
- Change FV3JEDI_FIX in related configs to change the path subfolder from
"fix_jedi" to "gdas".

Refs: NOAA-EMC#966
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
- Remove "fix_" text from fix file paths in several configs.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
- Update /scripts and /ush scripts to remove the "fix_" text
from fix subfolder paths.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA pushed a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
- Create a new version folder to hold version files.
- Create a new fix.ver to hold fix file versions.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
An earlier change had inadvertently stopped checking out GSI Monitor,
GSI Utils, and GLDAS when GDAS is used instead of GSI.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
First wave of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
Second wave of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
Wave 3 of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
Wave 4 of linter fixes for removing gfs-utils code/fix reorg.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
The last merge from develop introduced a minor syntax error in the
link script due to a bad conflict resolution. The issue is now
corrected.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
GLDAS scripts were recent moved into the workflow repo and need to
be updated for the new fix structure like other components.

Refs: NOAA-EMC#622, NOAA-EMC#966
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Oct 4, 2022
Moved the setting of FIXDIR higher so it errors on an unknown machine
sooner. Also removed redundant version file load.

Refs: NOAA-EMC#966
WalterKolczynski-NOAA added a commit that referenced this issue Oct 4, 2022
Removes all of the code and scripts that were moved to the new [gfs-utils repo](https://github.com/NOAA-EMC/gfs-utils) and adjusts workflow scripts to build and use them from the new location.

Some of the build scripts had unnecessary calls to machine-setup that are removed because the lower-level script already has the same functionality.

This PR also includes updates to use the new fix organization. This includes the addition of a fix versions file, updates to the link script, and some changes in the fix directories used by scripts to account for files that have been relocated. The versions file sets the version number for each component of fix, so that fix can be more easily maintained and documented. The initial versions are all the same, and correspond to the old fix_NEW directory (other than some directories have been renamed or reorganized). Except gdas, which has already had a new set of fix files added. The fix update also required an update to UFS-Utils.

Finally, the link script has been updated to match the syntax of the rest of the build system ([checkout.sh](sorc/checkout.sh) and [build_all.sh](sorc/build_all.sh)). [link_workflow.sh](sorc/link_workflow.sh) now detects the machine automatically instead of requiring an argument, and dev mode, which used to be set using `emc` as an argument, is now assumed. To run in ops mode (copy instead of link), the `-o` option is used. The full syntax is now simply:
```
./link_workflow.sh [-o]

Options:
  -o: Run in operations (NCO) mode (copy instead of link)
```

Fixes #356
Fixes #966
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