Update operational workflow to work with GSI develop branch #3068

ADCollard · 2024-11-05T17:02:47Z

Update operational workflow to work with GSI develop branch. This mostly involves changing the links to elements that have been moved out of the GSI repository since GFSv16.3. The ultimate aim is to be able to cycle with v16 workflow but using a version of GSI close to develop. This will not reproduce operations.

Resolves #3045

Type of change

Bug fix (fixes something broken)
New feature (adds functionality)
Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

Is this a breaking change (a change in existing functionality)? YES
Does this change require a documentation update? NO
Does this change require an update to any of the following submodules? YES
- GSI

How has this been tested?

Testing is limited to WCOSS2. Initialised full resolution cycling experiment. Will compare to operational performance.

Checklist

…bal-workflow into dev/gfs.v16.GSIdev

emilyhcliu · 2024-11-05T22:22:36Z

@ADCollard I see that most file changes are due to the changes in the .gitignore.
These changes make sense. I see that the CRTM is still crtm 2.4.1.
I am checking out the branch to build.
Two questions.

Will this global-workflow branch build GSI from the GSI develop?
Do you want me to run tests with this global-workflow branch?

ADCollard · 2024-11-05T23:10:58Z

@ADCollard I see that most file changes are due to the changes in the .gitignore. These changes make sense. I see that the CRTM is still crtm 2.4.1. I am checking out the branch to build. Two questions.

Will this global-workflow branch build GSI from the GSI develop?

Do you want me to run tests with this global-workflow branch?

@emilyhcliu Yes, the idea is that this is a v16 workflow that will checkout the develop version of GSI (eventually it will be a specific tag).

I am mostly looking for feedback on whether this is the right way to do this. I have also started a real time parallel on WCOSS2 (this will only run on WCOSS2), but right now the machine is unavailable, so it might be easiest just to look at those results.

Yes, the CRTM version is 2.4.0.1 which is the current operational version. I don't think we have time to move to CRTM v3.0 for GFSv16.4, but that would be addressed via a different issue anyway.

Thanks for looking at this!

KateFriedman-NOAA

We can't bring in most v17 script updates and need to stick closer to the v16 versions for this update. Please see my comments and let me know if I can assist at all. Thanks @ADCollard !

KateFriedman-NOAA · 2024-11-05T18:06:22Z

jobs/JGDAS_ATMOS_VERFOZN

+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"


This looks like the script in develop for GFSv17 since it has the preamble and jjob_header scripts in here. Those scripts won't exist in v16 so we need the version of this script as it is in v16 (or somewhere between).

KateFriedman-NOAA · 2024-11-05T18:07:27Z

jobs/JGDAS_ATMOS_VERFRAD

+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"


Same comment as above, need to use the v16 versions with any needed changes for GSI develop.

KateFriedman-NOAA · 2024-11-05T18:08:03Z

jobs/JGDAS_ATMOS_VMINMON

+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"


Same comment as above, need to use the v16 versions with any needed changes for GSI develop.

KateFriedman-NOAA · 2024-11-06T14:19:43Z

jobs/JGFS_ATMOS_VMINMON

+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"


Same comment as above, need to use the v16 versions with any needed changes for GSI develop.

KateFriedman-NOAA · 2024-11-06T14:24:22Z

scripts/exgdas_atmos_verfozn.sh

@@ -0,0 +1,91 @@
+#! /usr/bin/env bash
+
+source "$HOMEgfs/ush/preamble.sh"


Same comment as above. Can't use preamble but thankfully it looks like this script hasn't changed much between v16 and v17 so you can likely keep most of the v17 version:

[kfriedma@hercules-login-2 scripts]$ pwd /work/noaa/global/kfriedma/git_hercules/dev-gfs.v16.GSIdev/scripts [kfriedma@hercules-login-2 scripts]$ diff ../../release-gfs.v16.3.21/scripts/exgdas_atmos_verfozn.sh exgdas_atmos_verfozn.sh 1c1 < #/bin/sh --- > #! /usr/bin/env bash 3c3 < set -ax --- > source "$HOMEgfs/ush/preamble.sh" 12,13d11 < export scr=exgdas_vrfyozn.sh < 73c71 < count=`ls diag* | grep ".nc4" | wc -l` --- > count=$(ls diag* | grep ".nc4" | wc -l) 76,77c74,75 < for filenc4 in `ls diag*nc4.gz`; do < file=`echo $filenc4 | cut -d'.' -f1-2`.gz --- > for filenc4 in $(ls diag*nc4.gz); do > file=$(echo $filenc4 | cut -d'.' -f1-2).gz 92,98d89 < < if [[ "$VERBOSE" = "YES" ]]; then < echo "end exgdas_vrfyozn.sh, exit value = ${err}" < fi < < < set +x

KateFriedman-NOAA · 2024-11-06T14:33:28Z

sorc/link_fv3gfs.sh

+#-----------------------------------
+#--add gfs_wafs link if checked out
+if [ -d ${pwd}/gfs_wafs.fd ]; then
+#-----------------------------------
+ cd ${pwd}/../jobs               ||exit 8
+     $LINK ../sorc/gfs_wafs.fd/jobs/*                         .
+ cd ${pwd}/../parm               ||exit 8
+     [[ -d wafs ]] && rm -rf wafs
+    $LINK ../sorc/gfs_wafs.fd/parm/wafs                      wafs
+ cd ${pwd}/../scripts            ||exit 8
+    $LINK ../sorc/gfs_wafs.fd/scripts/*                      .
+ cd ${pwd}/../ush                ||exit 8
+    $LINK ../sorc/gfs_wafs.fd/ush/*                          .
+ cd ${pwd}/../fix                ||exit 8
+    [[ -d wafs ]] && rm -rf wafs
+    $LINK ../sorc/gfs_wafs.fd/fix/*                          .
+fi


This WAFS block shouldn't be getting added. Need to recheck the sync with the release/gfs.v16.3.21 branch and/or remove this block in your branch. The release/gfs.v16.4 branch will need to get synced with the prior release branches again anyway but let's remove this block now.

KateFriedman-NOAA · 2024-11-06T14:34:02Z

sorc/link_fv3gfs.sh

+# The following are now explicitly in the global-workflow repository
+#    $LINK ../sorc/gsi.fd/ush/gsi_utils.py        .
+#    $LINK ../sorc/gsi.fd/ush/calcanl_gfs.py      .
+#    $LINK ../sorc/gsi.fd/ush/calcinc_gfs.py      .
+#    $LINK ../sorc/gsi.fd/ush/getncdimlen         .


Good to know, let's remove these lines now.

KateFriedman-NOAA · 2024-11-06T14:36:09Z

ush/jjob_header.sh

@@ -0,0 +1,115 @@
+#! /usr/bin/env bash


Please remove this script from your branch. This won't go into the GFS with v16 and still needs sign off from NCO for v17.

KateFriedman-NOAA · 2024-11-06T14:36:31Z

ush/preamble.sh

@@ -0,0 +1,92 @@
+#! /usr/bin/env bash


Please remove this from your branch. This won't go into the GFS with v16 and still needs sign off from NCO for v17.

KateFriedman-NOAA · 2024-11-06T14:37:04Z

ush/rstprod.sh

@@ -0,0 +1,19 @@
+#! /usr/bin/env bash
+
+source "$HOMEgfs/ush/preamble.sh"


If we definitely need this script from the v17 package then remove the preamble line.

ADCollard · 2024-11-06T15:23:19Z

We can't bring in most v17 script updates and need to stick closer to the v16 versions for this update. Please see my comments and let me know if I can assist at all. Thanks @ADCollard !

@KateFriedman-NOAA Thank you for this review. This is exactly the type of feedback I was looking for.

Just so I am clear on this, why are the preamble.sh and jjob_header.sh scripts forbidden in v16? I will attempt to make these scripts look closer to v17, but I want to be sure if there is something particularly problematic with these.

ADCollard added 26 commits August 20, 2024 21:19

Add GSI script files into workflow scripts directory

9a61cb0

Check out GSI develop

b3ce334

Check out GSI develop

6d1ab29

Add Enkf scripts and jobs

bc683d8

Turn off some links

0792e7b

Add former gsi.fd scripts to ush

dbc2d37

Add external gsi_utils

3ddc2a7

Update some links

dde6c68

Update gsi_utils version number and add ncdiag

644a64f

Use an earlier version of gsi_utils

57a11cd

Remove use_qsatensmean ref. GSI#602

e07187b

Slight change to version of GSI_utils

93abb69

Another version number change

f1c5459

Fix some links

38fe6cf

Merge branch 'dev/gfs.v16.GSIdev' of https://github.com/ADCollard/glo…

e3a7817

…bal-workflow into dev/gfs.v16.GSIdev

Another link fix

66745c4

Merge tag 'gfs.v16.3.19' into dev/gfs.v16.GSIdev

3a8d928

Fix small bug in archive and change default ANAVINFO

b7cee3b

Turn on optconv option - see GSI NOAA-EMC#375

5b1297e

Restore observation monitoring capability

399cac0

More radmon updates

52431ae

Add monitor scripts from global-workflow #f159d39

e70b340

Fix info messages

03d6877

Slightly earlier tag for GSI-Monitor

11c5163

Merge branch 'dev/gfs.v16.GSIdev' of https://github.com/ADCollard/glo…

4a57689

…bal-workflow into dev/gfs.v16.GSIdev

Fix conflicts

65cc531

ADCollard requested review from KateFriedman-NOAA, emilyhcliu and aerorahul November 5, 2024 17:03

ADCollard self-assigned this Nov 5, 2024

ADCollard added the production update Processing update in production label Nov 5, 2024

ADCollard marked this pull request as draft November 5, 2024 17:04

KateFriedman-NOAA requested changes Nov 6, 2024

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Update operational workflow to work with GSI develop branch #3068

Update operational workflow to work with GSI develop branch #3068

ADCollard commented Nov 5, 2024

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ADCollard commented Nov 6, 2024

		source "${HOMEgfs}/ush/preamble.sh"
		source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"

		@@ -0,0 +1,91 @@
		#! /usr/bin/env bash

		source "$HOMEgfs/ush/preamble.sh"

		@@ -0,0 +1,19 @@
		#! /usr/bin/env bash

		source "$HOMEgfs/ush/preamble.sh"

Update operational workflow to work with GSI develop branch #3068

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Update operational workflow to work with GSI develop branch #3068

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ADCollard commented Nov 5, 2024

Type of change

Change characteristics

How has this been tested?

Checklist

emilyhcliu commented Nov 5, 2024

ADCollard commented Nov 5, 2024

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ADCollard commented Nov 6, 2024