MOM5 WOMBAT Fix without Dependency Update #17

CodeGat · 2024-07-09T01:31:35Z

In this PR:

Revert the Dependency Update (and old WOMBAT update)
Update the version of MOM5 to the WOMBAT fix version
Update versions of spack-packages/spack-config to avoid hdf5 bug
Removed versions.schema.json as schema is stored in ACCESS-NRI/schema
Update modulefile to only autoload: run rather than direct

References closed #16
Closes #7

…e8" and "Update MOM5 to include ice-ocean BGC coupling bug fix (#12)" This reverts commit 1d521f0, reversing changes made to 92ae023. This also reverts commit 2cf4904.

…k-config 2024.07.05

…, updated formatting, made compiler version/target required

…cies)

github-actions · 2024-07-09T01:32:25Z

🚀 Deploying access-om2-bgc 2024.07.0 as prerelease pr17-7

Details and usage instructions

This access-om2-bgc model will be deployed as:

2024.07.0 as a Release (when merged).
pr17-7 as a Prerelease (during this PR).

This Prerelease is accessible on Gadi using:

module use /g/data/vk83/prerelease/modules/access-models/
module load access-om2-bgc/pr17-7

where the binaries shall be on your $PATH.
This Prerelease is also accessible on Gadi via /g/data/vk83/prerelease/apps/spack/0.21/spack in the access-om2-bgc-pr17-7 environment.

🛠️ Using: spack-packages `2024.07.08`, spack-config `2024.07.05`

Details

It will be deployed using:

access-nri/spack-packages version 2024.07.08
access-nri/spack-config version 2024.07.05

If this is not what was expected, commit changes to config/versions.json.

dougiesquire · 2024-07-09T04:29:58Z

In the table below:

Exp 1 uses release-1deg_jra55_ryf_bgc modified to run for 1 year at a time;
Exp 2 uses the same configuration but the executable paths are changed to those built in prerelease pr17-7.

I ran three years of each. The experiments were run at the same time on Gadi. Times in the table are from the PAYU_WALLTIME field in job.yaml.

	Exp 1	Exp 2
`output000`	1533.65 s	1539.95 s
`output001`	1538.13 s	1542.18 s
`output002`	1535.69 s	1544.85 s
average	1535.82 s	1542.33 s

< 0.5% difference, so I'd say there's no obvious difference in performance 🚀

Below is the (selective) output of a diff between the two experiments:

$ git diff -- orig pr17-7
diff --git a/orig/config.yaml b/pr17-7/config.yaml
index a971d90..2c4028e 100644
--- a/orig/config.yaml
+++ b/pr17-7/config.yaml
@@ -31,7 +31,7 @@ input:
 submodels:
     - name: atmosphere
       model: yatm
-      exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/libaccessom2-git.2023.10.26=2023.10.26-ltfg7jcn6t4cefotvj3kjnyu5nru26xo/bin/yatm.exe
+      exe: /g/data/vk83/prerelease/apps/spack/0.22/release/linux-rocky8-x86_64/intel-19.0.5.281/libaccessom2-git.2023.10.26_2023.10.26-xarvbgn4yf4mxy5hxixm4gfbp7rbzsfh/bin/yatm.exe
       input:
           - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/rmp_jrar_to_cict_CONSERV.nc
           - /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data
@@ -39,7 +39,7 @@ submodels:

     - name: ocean
       model: mom
-      exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2023.11.09=2023.11.09-64l5azdtcoxhrgb5ynn2vued5lmjvn33/bin/fms_ACCESS-OM-BGC.x
+      exe: /g/data/vk83/prerelease/apps/spack/0.22/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2024.06.27_2024.06.27-q6bpwu526xql2gm6dbpnvf36yvnfxynj/bin/fms_ACCESS-OM-BGC.x
       input:
           - /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/bgc_param.nc
           - /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/co2_iaf.nc
@@ -64,7 +64,7 @@ submodels:

     - name: ice
       model: cice5
-      exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/cice5-git.2023.10.19=2023.10.19-v3zncpqjj2gyseudbwiudolcjq3k3leo/bin/cice_auscom_360x300_24x1_24p.exe
+      exe: /g/data/vk83/prerelease/apps/spack/0.22/release/linux-rocky8-x86_64/intel-19.0.5.281/cice5-git.2023.10.19_2023.10.19-4tttbvaxg4afg3hjcrfaah6qngp43e5e/bin/cice_auscom_360x300_24x1_24p.exe
       input:
           - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions_biogeochemistry/global.1deg/2022.02.24/i2o.nc
           - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions_biogeochemistry/global.1deg/2022.02.24/o2i.nc
@@ -81,7 +81,7 @@ collate:
   mem: 30GB
   ncpus: 4
   queue: normal
-  exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2023.11.09=2023.11.09-64l5azdtcoxhrgb5ynn2vued5lmjvn33/bin/mppnccombine.spack
+  exe: /g/data/vk83/prerelease/apps/spack/0.22/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2024.06.27_2024.06.27-q6bpwu526xql2gm6dbpnvf36yvnfxynj/bin/mppnccombine.spack

 manifest:
   reproduce:
diff --git a/orig/manifests/exe.yaml b/pr17-7/manifests/exe.yaml
index fec7972..5eaa111 100644
--- a/orig/manifests/exe.yaml
+++ b/pr17-7/manifests/exe.yaml
@@ -2,17 +2,17 @@ format: yamanifest
 version: 1.0
 ---
 work/atmosphere/yatm.exe:
-  fullpath: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/libaccessom2-git.2023.10.26=2023.10.26-ltfg7jcn6t4cefotvj3kjnyu5nru26xo/bin/yatm.exe
+  fullpath: /g/data/vk83/prerelease/apps/spack/0.22/release/linux-rocky8-x86_64/intel-19.0.5.281/libaccessom2-git.2023.10.26_2023.10.26-xarvbgn4yf4mxy5hxixm4gfbp7rbzsfh/bin/yatm.exe
   hashes:
-    binhash: 4e8b4ef76e971c4af3b26cfac632e160
-    md5: 5baa1d417fe6708fc30cbeaa57d82f96
+    binhash: 6aafa395ec59173dbb8448525f2aca9c
+    md5: 563868717c8ba3926c0c41176a6c52d4
 work/ice/cice_auscom_360x300_24x1_24p.exe:
-  fullpath: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/cice5-git.2023.10.19=2023.10.19-v3zncpqjj2gyseudbwiudolcjq3k3leo/bin/cice_auscom_360x300_24x1_24p.exe
+  fullpath: /g/data/vk83/prerelease/apps/spack/0.22/release/linux-rocky8-x86_64/intel-19.0.5.281/cice5-git.2023.10.19_2023.10.19-4tttbvaxg4afg3hjcrfaah6qngp43e5e/bin/cice_auscom_360x300_24x1_24p.exe
   hashes:
-    binhash: 3a65f67d21152e77034da28c22a94c66
-    md5: 37866455b057c85c3ea50c0ef0ea840b
+    binhash: f5e63ad5892304804c32f7aed199af68
+    md5: d5aa57088c227207a5efb6096f73fcbd
 work/ocean/fms_ACCESS-OM-BGC.x:
-  fullpath: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2023.11.09=2023.11.09-64l5azdtcoxhrgb5ynn2vued5lmjvn33/bin/fms_ACCESS-OM-BGC.x
+  fullpath: /g/data/vk83/prerelease/apps/spack/0.22/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2024.06.27_2024.06.27-q6bpwu526xql2gm6dbpnvf36yvnfxynj/bin/fms_ACCESS-OM-BGC.x
   hashes:
-    binhash: 45352e33876da49ca042014a9f6686e5
-    md5: a909552e85690be692ad3ec94016181b
+    binhash: 745a82031b7e5cda6b117bfab1358105
+    md5: 6d08c6e48dbc294e32c3d48f64399581
diff --git a/orig/manifests/input.yaml b/pr17-7/manifests/input.yaml
index 6f6eab3..81471ce 100644
--- a/orig/manifests/input.yaml
+++ b/pr17-7/manifests/input.yaml
@@ -155,7 +155,7 @@ work/ocean/INPUT/csiro_bgc.res.nc:
 work/ocean/INPUT/csiro_bgc_sediment.res.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/csiro_bgc_sediment.res.nc
   hashes:
-    binhash: 5dcf7a15477f488cd7d2f85a1d39a176
+    binhash: fff3375ad2ae36b7d0521dd67912a9fd
     md5: 12488f7cf8f9c2f714c0ff2dbbb33a9b
 work/ocean/INPUT/dust.nc:
   fullpath: /g/data/vk83/experiments/inputs/access-om2/ocean/biogeochemistry/global.1deg/2022.02.24/dust.nc

dougiesquire

LGTM

For reference, this is the diff from the 2024.03.0 release.

CodeGat added 7 commits July 5, 2024 15:45

Revert both "Merge pull request #11 from ACCESS-NRI/dougiesquire/issu…

1987f64

…e8" and "Update MOM5 to include ice-ocean BGC coupling bug fix (#12)" This reverts commit 1d521f0, reversing changes made to 92ae023. This also reverts commit 2cf4904.

Deleted versions.schema.json, updated spack-packages 2024.07.03, spac…

7b2d443

…k-config 2024.07.05

Updated mom5 2024.06.27 (wombat fix), updated model version 2024.07.0…

e1dcce7

…, updated formatting, made compiler version/target required

versions.json: Added required field 'spack'

eeeba46

versions.json: spack-packages 2024.07.06 (abgc runs type for dependen…

5e1575d

…cies)

spack.yaml: Added comments, rebuilding using ACCESS-NRI/spack@42e3100

e54e31a

versions.json: Update spack-packages 2024.07.08

75dd3ed

CodeGat added type:release priority:high labels Jul 9, 2024

CodeGat requested a review from dougiesquire July 9, 2024 01:31

CodeGat self-assigned this Jul 9, 2024

CodeGat temporarily deployed to Gadi Prerelease July 9, 2024 01:32 — with GitHub Actions Inactive

dougiesquire approved these changes Jul 9, 2024

View reviewed changes

CodeGat merged commit dcd452b into main Jul 9, 2024
12 checks passed

CodeGat deployed to Gadi Prerelease July 9, 2024 04:43 — with GitHub Actions Active

CodeGat deleted the 7-mom5-wombat-fix branch July 9, 2024 05:50

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

MOM5 WOMBAT Fix without Dependency Update #17

MOM5 WOMBAT Fix without Dependency Update #17

CodeGat commented Jul 9, 2024

github-actions bot commented Jul 9, 2024

dougiesquire commented Jul 9, 2024 •

edited

Loading

dougiesquire left a comment

MOM5 WOMBAT Fix without Dependency Update #17

MOM5 WOMBAT Fix without Dependency Update #17

Conversation

CodeGat commented Jul 9, 2024

github-actions bot commented Jul 9, 2024

dougiesquire commented Jul 9, 2024 • edited Loading

dougiesquire left a comment

Choose a reason for hiding this comment

dougiesquire commented Jul 9, 2024 •

edited

Loading