MC_8km_jra_ryf-test1-expt-4f2841fe
8km jra_ryf-test1
❌ Latest submission: Run 24 failed (payu exit status 1): probably a model crash. See the logs below. Model date reached: 1902-06-01 (2.3 model years complete).
Notebooks: Timeseries_daily_extreme_from_2D_fields, temp-salt-vs-depth-time, ❌ ocean_stats, ❌ timeseries
📋 Summary for the GitHub issue
### OM3 Monitor summary: `MC_8km_jra_ryf-test1-expt-4f2841fe`
*8km jra_ryf-test1*
- **Latest submission:** ❌ Run 24 failed (payu exit status 1): probably a model crash. (run 24, PBS job 180339684.gadi-pbs, last recorded 2026-10-02 19:27 AEST, model date 1902-06-01)
- **Model date reached:** 1902-06-01 (2.3 model years complete)
- **Average throughput:** 0.73 SYPD
- **Truncations:** 485,692 in 14 of 25 output folders
<details><summary>Last lines of the model logs</summary>
`access-om3.180339684.gadi-pbs.err` [1]
```
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
--------------------------------------------------------------------------
prterun has exited due to process rank 92 with PID 0 on node gadi-cpu-spr-0003 calling
"abort". This may have caused other processes in the application to be
terminated by signals sent by prterun (as reported here).
--------------------------------------------------------------------------
```
`access-om3.180339684.gadi-pbs.out` [2]
```
fsens = 0.000000000000000E+000
flat = 0.000000000000000E+000
evap = 0.000000000000000E+000
flwout = 0.000000000000000E+000
(abort_ice)ABORTED:
(abort_ice) error =
(diagnostic_abort)ERROR: (step_therm1) icepack_step_therm1 aborted
(abort_ice)(diagnostic_abort)ERROR: (step_therm1) icepack_step_therm1 aborted
```
</details>
| Where | Records | Output folders | Max speed (m/s) | Max CFL |
|---|---:|---|---:|---:|
| [73.3°E, 67.9°N](https://www.google.com/maps/place/67.89,73.26/@67.89,73.26,5z) | 600* | 001–005, 013–017, 023–024 | 4.0 | 0.74 |
| [144.9°W, 74.0°N](https://www.google.com/maps/place/73.98,-144.88/@73.98,-144.88,5z) | 48 | 006 | 16210000.0 | 1146000.00 |
| [135.2°W, 74.9°N](https://www.google.com/maps/place/74.90,-135.16/@74.90,-135.16,5z) | 41 | 006 | 1063.0 | 77.26 |
| [130.9°W, 73.0°N](https://www.google.com/maps/place/73.02,-130.85/@73.02,-130.85,5z) | 34 | 005 | 2099.0 | 142.80 |
| [123.7°W, 80.3°N](https://www.google.com/maps/place/80.28,-123.69/@80.28,-123.69,5z) | 29 | 006 | 2130.0 | 182.30 |
\* a PE at MOM6's 50-records-per-run cap, so the true count is higher.
**References**
1. `/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/error_logs/access-om3.180339684.gadi-pbs.err`
2. `/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/error_logs/access-om3.180339684.gadi-pbs.out`
3. Archive folder: `/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe`
4. Run directory: `/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1` (current or crashed run in `work/`)
5. Status page: https://chrisb13.github.io/access-om3-live/live/MC_8km_jra_ryf-test1-expt-4f2841fe/
*Generated automatically by the [OM3 Monitor](https://chrisb13.github.io/access-om3-live/live/) on 2026-10-19 16:38 AEDT; it may contain errors, so check against the files above.*
Run directory: current or crashed run
Read from the payu control directory /g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1.
Log files
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/access-om3.err (last lines; modified 2026-10-02 19:26 AEST)
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
--------------------------------------------------------------------------
prterun has exited due to process rank 92 with PID 0 on node gadi-cpu-spr-0003 calling
"abort". This may have caused other processes in the application to be
terminated by signals sent by prterun (as reported here).
--------------------------------------------------------------------------
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/access-om3.out (last lines; modified 2026-10-02 19:26 AEST)
swidr = 15.5648832728749
swidf = 8.53558114964105
flw = 288.161421183901
frain = 3.606367500160833E-008
fsnow = 0.000000000000000E+000
ocn states and fluxes
frzmlt = -9866.40687356572
sst = 0.234311174636105
sss = 3.20968264612705
Tf = -0.174606735949312
uocn = 9.424180033772288E-003
vocn = 1.842359842873333E-004
strtltxU= -7.410837525841108E-003
strtltyU= -9.000136240056859E-003
srf states and fluxes
Tref = 0.000000000000000E+000
Qref = 0.000000000000000E+000
Uref = 0.000000000000000E+000
fsens = 0.000000000000000E+000
flat = 0.000000000000000E+000
evap = 0.000000000000000E+000
flwout = 0.000000000000000E+000
(abort_ice)ABORTED:
(abort_ice) error =
(diagnostic_abort)ERROR: (step_therm1) icepack_step_therm1 aborted
(abort_ice)(diagnostic_abort)ERROR: (step_therm1) icepack_step_therm1 aborted
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/8km_jra_ryf_s.o180583041 (last lines; modified 2026-10-06 13:54 AEDT)
payu_jobs/25/
payu_jobs/25/collate/
payu_jobs/25/collate/180582119.gadi-pbs.json
payu_jobs/25/postscript/
payu_jobs/25/postscript/180583039.gadi-pbs.json
payu_jobs/25/sync/
payu_jobs/25/sync/180583041.gadi-pbs.json
sent 1,095,704 bytes received 312 bytes 313,147.43 bytes/sec
total size is 17,534,465 speedup is 16.00
Running command: rsync -vrltoD --safe-links /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/metadata.yaml /g/data/ol01/outputs/access-om3-8km/MC_8km_jra_ryf-test1-expt-4f2841fe/
sending incremental file list
metadata.yaml
sent 2,038 bytes received 35 bytes 4,146.00 bytes/sec
total size is 1,937 speedup is 0.93
Updating git-runlog at /g/data/ol01/outputs/access-om3-8km/MC_8km_jra_ryf-test1-expt-4f2841fe/git-runlog
payu: Found modules in /opt/Modules/v4.3.0
======================================================================================
Resource Usage on 2026-10-06 13:54:40:
Job Id: 180583041.gadi-pbs
Project: tm70
Exit Status: 0
Service Units: 0.10
NCPUs Requested: 1 CPU Time Used: 00:01:20
Memory Requested: 2.0GB Memory Used: 2.0GB
Walltime Requested: 10:00:00 Walltime Used: 00:02:52
JobFS Requested: 10.0GB JobFS Used: 0B
======================================================================================
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/8km_jra_ryf_s.e180583041 (last lines; modified 2026-10-06 13:54 AEDT)
[WARNING] Failed to get parent branch time from restart path /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/restart024: Cannot find rpointer.cpl file, which is required for date-based restart pruning
[WARNING] Ignoring restart024 from date-based restart pruning. Error: Cannot find rpointer.cpl file, which is required for date-based restart pruning
To /g/data/ol01/outputs/access-om3-8km/MC_8km_jra_ryf-test1-expt-4f2841fe/git-runlog
e586a85..97eb9e5 expt -> expt
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/8km_jra_ryf_c.o180582119 (last lines; modified 2026-10-06 13:44 AEDT)
archive path: /scratch/tm70/cyb561/access-om3/archive
Found experiment archive: /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe
------ Job submitted ------
Submitted command: qsub -N payu_postscript -W depend=afterok:180582119.gadi-pbs -v PAYU_CURRENT_OUTPUT_DIR=/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/output024,PAYU_CURRENT_RESTART_DIR=/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/restart024,PAYU_ARCHIVE_DIR=/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe,PAYU_CURRENT_RUN=24 -v PROJECT,SCRIPTS_DIR=/g/data/vk83/apps/om3-scripts -lstorage=gdata/ol01+gdata/tm70+gdata/vk83+scratch/tm70+gdata/xp65 /g/data/vk83/apps/om3-scripts/payu_config/postscript.sh
Job ID: 180583039.gadi-pbs
laboratory path: /scratch/tm70/cyb561/access-om3
binary path: /scratch/tm70/cyb561/access-om3/bin
input path: /scratch/tm70/cyb561/access-om3/input
work path: /scratch/tm70/cyb561/access-om3/work
archive path: /scratch/tm70/cyb561/access-om3/archive
Found experiment archive: /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe
Loading input manifest: manifests/input.yaml
Loading restart manifest: manifests/restart.yaml
Loading exe manifest: manifests/exe.yaml
payu: Found modules in /opt/Modules/v4.3.0
------ Job submitted ------
Submitted command: qsub -P tm70 -l walltime=10:00:00 -l ncpus=1 -l mem=2GB -l jobfs=10GB -N 8km_jra_ryf_s -l wd -j n -W depend=afterok:180583039.gadi-pbs -q copyq -l storage=gdata/tm70+scratch/tm70+gdata/vk83+gdata/ol01 -v PAYU_PATH=/containerised_envs/payu/1.3.6_1/bin,PAYU_CURRENT_RUN=25,PAYU_SYNC_RESTARTS=True,MODULESHOME=/opt/Modules/v4.3.0,MODULES_CMD=/opt/Modules/v4.3.0/libexec/modulecmd.tcl,MODULEPATH=/g/data/vk83/prerelease/modules:/g/data/vk83/modules:/etc/scl/modulefiles:/opt/Modules/modulefiles:/opt/Modules/v4.3.0/modulefiles:/apps/Modules/modulefiles -- /g/data/vk83/apps/containerised_envs/envs/payu/1.3.6_1/bin/launcher.sh /containerised_envs/payu/1.3.6_1/bin/python3.10 /containerised_envs/payu/1.3.6_1/bin/payu-sync
Job ID: 180583041.gadi-pbs
======================================================================================
Resource Usage on 2026-10-06 13:44:57:
Job Id: 180582119.gadi-pbs
Project: tm70
Exit Status: 0
Service Units: 1.23
NCPUs Requested: 4 CPU Time Used: 00:17:02
Memory Requested: 30.0GB Memory Used: 6.06GB
Walltime Requested: 04:00:00 Walltime Used: 00:06:10
JobFS Requested: 10.0GB JobFS Used: 204.22KB
======================================================================================
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/payu_postscript.o180583039 (last lines; modified 2026-10-06 13:49 AEDT)
/g/data/xp65/public/apps/med_conda/envs/analysis3-25.05/lib/python3.11/site-packages/access_nri_intake/source/utils.py:142: UserWarning: Time coordinate does not include bounds information. Guessing start and end times.
warnings.warn(
/g/data/xp65/public/apps/med_conda/envs/analysis3-25.05/lib/python3.11/site-packages/access_nri_intake/source/utils.py:142: UserWarning: Time coordinate does not include bounds information. Guessing start and end times.
warnings.warn(
/g/data/xp65/public/apps/med_conda/envs/analysis3-25.05/lib/python3.11/site-packages/access_nri_intake/source/utils.py:142: UserWarning: Time coordinate does not include bounds information. Guessing start and end times.
warnings.warn(
/g/data/xp65/public/apps/med_conda/envs/analysis3-25.05/lib/python3.11/site-packages/intake_esm/cat.py:187: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.11/migration/
data = self.dict().copy()
[32m[22mSucessfully built esm-datastore![0m
[34m[22mSaving esm-datastore to [36m[1m/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/archive[0m
Successfully wrote ESM catalog json file to: file:///g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/archive/experiment_datastore.json
[34m[22mHashing catalog to prevent unnecessary rebuilds.
This may take some time...[0m
[32m[22mCatalog sucessfully hashed![0m
[32m[22mDatastore sucessfully written to [36m[1m/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/archive/experiment_datastore.json[32m[22m!
[34m[22mPlease note that this has not added the datastore to the access-nri-intake catalog.
To add to catalog, please run '[37m[1mscaffold_catalog_entry[34m[22m' for help on how to do so.
sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.
======================================================================================
Resource Usage on 2026-10-06 13:49:49:
Job Id: 180583039.gadi-pbs
Project: tm70
Exit Status: 0
Service Units: 14.27
NCPUs Requested: 104 CPU Time Used: 03:19:25
Memory Requested: 500.0GB Memory Used: 308.32GB
Walltime Requested: 00:30:00 Walltime Used: 00:04:07
JobFS Requested: 100.0GB JobFS Used: 0B
======================================================================================
Check this on Gadi: when these logs were written, and their last lines
# WHAT THIS DOES: for each log file listed above, prints when it was last changed and its last 30
# lines, which are the lines the page shows.
# 'for' repeats the three lines below once for each file; $f is the file it is on.
# 'ls -l' lists a file with details; --time-style=long-iso writes its time as 2026-07-01 00:02.
for f in /g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/access-om3.err /g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/access-om3.out /g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/8km_jra_ryf_s.o180583041 /g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/8km_jra_ryf_s.e180583041 /g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/8km_jra_ryf_c.o180582119 /g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/payu_postscript.o180583039; do
echo "== $f" # which file this is
ls -l --time-style=long-iso "$f" # when it was last changed (the date and time are in the middle)
tail -n 30 "$f" # its last 30 lines
done
Configuration files
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/config.yaml (modified 2026-10-02 17:39 AEST)
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/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/MOM_input (modified 2026-09-18 16:05 AEST)
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/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/ice_in (modified 2026-09-18 16:05 AEST)
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/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/nuopc.runconfig (modified 2026-09-24 10:13 AEST)
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/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/nuopc.runseq (modified 2026-09-24 10:12 AEST)
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Check this on Gadi: when these files were last modified
# WHAT THIS DOES: prints when each configuration file shown above was last changed (the 'modified'
# time in each title).
R=/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1
# 'cd' goes into the control directory, where these files are
cd "$R"
# 'ls -l' lists files with details; --time-style=long-iso writes the time as 2026-07-01 00:02
ls -l --time-style=long-iso config.yaml MOM_input ice_in nuopc.runconfig nuopc.runseq
Archive folder: completed runs
Read from the payu archive folder /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe.
- Output folders: 25 (latest
output024) - Model date reached: 1902-06-01
- Runs recorded by payu: 34, of which failed: 8
Check this on Gadi: these counts
# WHAT THIS DOES: re-counts the 'Archive folder' list: how many output folders there are, which is
# the latest, how many runs payu recorded, how many of those failed, and how far the model got. The
# four lines it prints should match the page.
A=/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe
# Step 1: count the output folders (output000, output001, ...) and name the last one
ls -d "$A"/output[0-9]* | wc -l
basename "$(ls -d "$A"/output[0-9]* | tail -n 1)"
# Step 2: read payu's run records with a few lines of python, and count them
python3 - "$A" <<'EOF'
import glob, json, os, sys
# payu keeps one small file for every run: payu_jobs/<number>/run/<job>.json. Read them all.
archive = sys.argv[1] # the archive folder, handed over by the shell line above
runs = []
for path in glob.glob(archive + "/payu_jobs/*/run/*.json"):
try:
with open(path) as f:
record = json.load(f)
record["file"] = path # remember which file it came from
runs.append(record)
except (OSError, ValueError):
pass # skip a file we may not read, or that is not valid JSON
# Put the runs in order: by run number, and by start time if a run was tried more than once.
runs.sort(key=lambda r: (int(r.get("payu_current_run") or 0), r.get("timings", {}).get("payu_start_time") or ""))
# a run failed if payu's exit status for it is not 0 (a run with no status yet is still going)
failed = [r for r in runs if r.get("payu_run_status") not in (0, None)]
print(len(runs), "runs recorded by payu,", len(failed), "failed")
# the model date reached is the finish date of the last run that has one
finished = [r for r in runs if r.get("model_finish_time")]
print("model date reached:", finished[-1]["model_finish_time"][:10] if finished else "unknown")
EOF
Model throughput
Simulated years per day, made by plot_sypd.py from the outputNNN/log/med.log files of the completed submissions in /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe.
Check this on Gadi: the rate in each output's med.log
# WHAT THIS DOES: for each output folder, finds the model's speed in its med.log (the mediator's
# log) and averages it. The speed, called the 'rate', is in simulated years per day (ypd). The
# figure plots these rates. You get one line per output folder: how many rate lines it had, and
# their average.
A=/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe
for o in "$A"/output[0-9]*; do
[ -f "$o/log/med.log" ] || continue # skip folders that have no med.log
# A line looks like: Model Date: 1958-09-04T00:00:00 ... rate = 7.09 ypd. awk reads the number just before
# 'ypd' (the second-last word), adds them up and counts them, then prints the average at the end.
awk -v name="$(basename "$o")" '/Model Date:/ && /ypd/ {count++; total += $(NF-1)} END {if (count) printf "%s: %d rate lines, mean %.2f ypd\n", name, count, total/count}' "$o/log/med.log"
done
Recent runs
From payu's job records in /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/payu_jobs; times are Canberra time.
| Run | PBS job | Result | Model period | Wall time (h) | SYPD | Record last modified |
|---|---|---|---|---|---|---|
| 24 | 180339684.gadi-pbs | ❌ | 1902-06-01 → ? | 1.7 | 2026-10-02 19:27 AEST | |
| 24 | 179710484.gadi-pbs | ❌ | 1902-06-01 → ? | 1.7 | 2026-09-24 12:13 AEST | |
| 24 | 179690609.gadi-pbs | ❌ | 1902-06-01 → ? | 1.4 | 2026-09-24 04:48 AEST | |
| 23 | 179683217.gadi-pbs | ✅ | 1902-04-01 → 1902-06-01 | 4.6 | 0.86 | 2026-09-24 03:21 AEST |
| 22 | 179665181.gadi-pbs | ✅ | 1902-02-01 → 1902-04-01 | 4.8 | 0.81 | 2026-09-23 22:32 AEST |
| 21 | 179625180.gadi-pbs | ✅ | 1901-12-01 → 1902-02-01 | 4.8 | 2026-09-23 14:23 AEST | |
| 21 | 179615973.gadi-pbs | queued | 1901-12-01 → ? | 2026-09-23 01:36 AEST | ||
| 20 | 179599200.gadi-pbs | ✅ | 1901-11-01 → 1901-12-01 | 2.9 | 0.69 | 2026-09-23 01:36 AEST |
| 19 | 179586220.gadi-pbs | ✅ | 1901-10-01 → 1901-11-01 | 2.9 | 0.70 | 2026-09-22 19:26 AEST |
| 18 | 179571160.gadi-pbs | ✅ | 1901-09-01 → 1901-10-01 | 2.9 | 0.68 | 2026-09-22 16:29 AEST |
Check this on Gadi: this table
# WHAT THIS DOES: prints the 'Recent runs' table: the 10 newest runs, newest first. 'ok' means
# payu's exit status was 0. SYPD is simulated years per day: the model time the run covered, divided
# by the wall-clock time it took. (If payu did not record a run's start date this shows ?; the page
# may fill it in from the previous run.)
A=/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe
python3 - "$A" <<'EOF'
import glob, json, os, sys
# payu keeps one small file for every run: payu_jobs/<number>/run/<job>.json. Read them all.
archive = sys.argv[1] # the archive folder, handed over by the shell line above
runs = []
for path in glob.glob(archive + "/payu_jobs/*/run/*.json"):
try:
with open(path) as f:
record = json.load(f)
record["file"] = path # remember which file it came from
runs.append(record)
except (OSError, ValueError):
pass # skip a file we may not read, or that is not valid JSON
# Put the runs in order: by run number, and by start time if a run was tried more than once.
runs.sort(key=lambda r: (int(r.get("payu_current_run") or 0), r.get("timings", {}).get("payu_start_time") or ""))
import time
from datetime import datetime
print("Run PBS job Result Model period Hours SYPD Record last modified")
for r in reversed(runs[-10:]): # the last 10 runs, newest first
status = r.get("payu_run_status")
result = "ok" if status == 0 else ("failed" if status is not None else str(r.get("stage")))
start, finish = r.get("model_start_time"), r.get("model_finish_time")
seconds = r.get("timings", {}).get("payu_total_duration_seconds") # wall-clock seconds the run took
hours = "%.1f" % (seconds / 3600) if seconds else ""
sypd = ""
if start and finish and seconds:
# the model time the run covered, in whole days (dates look like 1958-01-01T00:00:00)
days = (datetime.strptime(finish[:19], "%Y-%m-%dT%H:%M:%S") - datetime.strptime(start[:19], "%Y-%m-%dT%H:%M:%S")).days
sypd = "%.2f" % (days / 365.25 / (seconds / 86400)) # model years divided by wall-clock days
changed = time.strftime("%Y-%m-%d %H:%M %Z", time.localtime(os.path.getmtime(r["file"])))
print("%-4s %-18s %-10s %-10s -> %-10s %6s %6s %s" % (r.get("payu_current_run"), r.get("scheduler_job_id"), result,
(start or "?")[:10], (finish or "?")[:10], hours, sypd, changed))
EOF
Latest logs in the archive folder
/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/error_logs/access-om3.180339684.gadi-pbs.err (last lines; modified 2026-10-02 19:27 AEST)
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
Unknown
access-om3-MOM6-C 0000000001CB1F7E Unknown Unknown Unknown
--------------------------------------------------------------------------
prterun has exited due to process rank 92 with PID 0 on node gadi-cpu-spr-0003 calling
"abort". This may have caused other processes in the application to be
terminated by signals sent by prterun (as reported here).
--------------------------------------------------------------------------
/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/error_logs/access-om3.180339684.gadi-pbs.out (last lines; modified 2026-10-02 19:27 AEST)
swidr = 15.5648832728749
swidf = 8.53558114964105
flw = 288.161421183901
frain = 3.606367500160833E-008
fsnow = 0.000000000000000E+000
ocn states and fluxes
frzmlt = -9866.40687356572
sst = 0.234311174636105
sss = 3.20968264612705
Tf = -0.174606735949312
uocn = 9.424180033772288E-003
vocn = 1.842359842873333E-004
strtltxU= -7.410837525841108E-003
strtltyU= -9.000136240056859E-003
srf states and fluxes
Tref = 0.000000000000000E+000
Qref = 0.000000000000000E+000
Uref = 0.000000000000000E+000
fsens = 0.000000000000000E+000
flat = 0.000000000000000E+000
evap = 0.000000000000000E+000
flwout = 0.000000000000000E+000
(abort_ice)ABORTED:
(abort_ice) error =
(diagnostic_abort)ERROR: (step_therm1) icepack_step_therm1 aborted
(abort_ice)(diagnostic_abort)ERROR: (step_therm1) icepack_step_therm1 aborted
/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/output024/log/med.log (last lines; modified 2026-10-02 19:23 AEST)
Model Date: 1902-06-04T00:00:00 wall clock = 2026-10-02T18:13:18 avg dt = 315.81 s/day, dt = 300.27 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-04T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-05T00:00:00 wall clock = 2026-10-02T18:18:18 avg dt = 311.78 s/day, dt = 299.67 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-05T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-06T00:00:00 wall clock = 2026-10-02T18:23:19 avg dt = 309.60 s/day, dt = 300.88 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-06T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-07T00:00:00 wall clock = 2026-10-02T18:28:19 avg dt = 308.02 s/day, dt = 300.15 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-07T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-08T00:00:00 wall clock = 2026-10-02T18:33:17 avg dt = 306.68 s/day, dt = 298.61 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-08T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-09T00:00:00 wall clock = 2026-10-02T18:38:17 avg dt = 305.75 s/day, dt = 299.27 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-09T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-10T00:00:00 wall clock = 2026-10-02T18:43:15 avg dt = 304.97 s/day, dt = 298.70 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-10T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-11T00:00:00 wall clock = 2026-10-02T18:48:16 avg dt = 304.56 s/day, dt = 300.89 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-11T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-12T00:00:00 wall clock = 2026-10-02T18:53:17 avg dt = 304.16 s/day, dt = 300.20 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-12T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-13T00:00:00 wall clock = 2026-10-02T18:58:17 avg dt = 303.89 s/day, dt = 300.82 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-13T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-14T00:00:00 wall clock = 2026-10-02T19:03:19 avg dt = 303.73 s/day, dt = 301.81 s/day, rate = 0.78 ypd
memory_write: model date = 1902-06-14T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-15T00:00:00 wall clock = 2026-10-02T19:08:20 avg dt = 303.50 s/day, dt = 300.61 s/day, rate = 0.79 ypd
memory_write: model date = 1902-06-15T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-16T00:00:00 wall clock = 2026-10-02T19:13:22 avg dt = 303.44 s/day, dt = 302.58 s/day, rate = 0.78 ypd
memory_write: model date = 1902-06-16T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-17T00:00:00 wall clock = 2026-10-02T19:18:27 avg dt = 303.50 s/day, dt = 304.37 s/day, rate = 0.78 ypd
memory_write: model date = 1902-06-17T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
Model Date: 1902-06-18T00:00:00 wall clock = 2026-10-02T19:23:30 avg dt = 303.50 s/day, dt = 303.44 s/day, rate = 0.78 ypd
memory_write: model date = 1902-06-18T00:00:00 memory = -0.00 MB (highwater) 1972.01 MB (usage)
/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/pbs_logs/8km_jra_ryf.o179710484 (last lines; modified 2026-09-24 12:18 AEST)
Loading exe manifest: manifests/exe.yaml
Setting up access-om3
Checking exe, input and restart manifests
mod access-om3/dependencies/pr264-11/access3-share/2026.03.002-pko5hg7
mod access-om3/dependencies/pr264-11/access-cice/CICE6.6.3-2-lgdd6vc
mod access-om3/dependencies/pr264-11/access-mocsy/2025.07.002-pz75hi5
mod access-om3/dependencies/pr264-11/access-generic-tracers/2026.05.000-i7fz4v6
mod access-om3/dependencies/pr264-11/access-mom6/ee2ec415bc46e8b8de4d663f58dc65f72678a7ce-43xexcn
mod access-om3/dependencies/pr264-11/access-ww3/2026.03.001-tein63v
mod access-om3/dependencies/pr264-11/access3/2026.03.002-qvhjizz
mod access-om3/pr264-11
mod model-tools/mppnccombine-fast/2025.07.000
2026-09-24 10:31:32: Run 24
mpirun --mca mpi_yield_when_idle true -wdir /scratch/tm70/cyb561/access-om3/work/MC_8km_jra_ryf-test1-expt-4f2841fe -np 8216 /scratch/tm70/cyb561/access-om3/work/MC_8km_jra_ryf-test1-expt-4f2841fe/access-om3-MOM6-CICE6
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/access-om3.err /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/error_logs/access-om3.179710484.gadi-pbs.err
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/access-om3.out /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/error_logs/access-om3.179710484.gadi-pbs.out
/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1/env.yaml /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/error_logs/env.179710484.gadi-pbs.yaml
payu: Found modules in /opt/Modules/v4.3.0
======================================================================================
Resource Usage on 2026-09-24 12:18:08:
Job Id: 179710484.gadi-pbs
Project: e14
Exit Status: 1
Service Units: 28112.41
NCPUs Requested: 8216 CPU Time Used: 13674:17:14
Memory Requested: 38.57TB Memory Used: 9.82TB
Walltime Requested: 05:00:00 Walltime Used: 01:42:39
JobFS Requested: 10.0GB JobFS Used: 53.98MB
======================================================================================
/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/pbs_logs/8km_jra_ryf.e179710484 (last lines; modified 2026-09-24 12:13 AEST)
Loading access-om3/pr264-11
Loading requirement:
access-om3/dependencies/pr264-11/access3-share/2026.03.002-pko5hg7
access-om3/dependencies/pr264-11/access-cice/CICE6.6.3-2-lgdd6vc
access-om3/dependencies/pr264-11/access-mocsy/2025.07.002-pz75hi5
access-om3/dependencies/pr264-11/access-generic-tracers/2026.05.000-i7fz4v6
access-om3/dependencies/pr264-11/access-mom6/ee2ec415bc46e8b8de4d663f58dc65f72678a7ce-43xexcn access-om3/dependencies/pr264-11/access-ww3/2026.03.001-tein63v access-om3/dependencies/pr264-11/access3/2026.03.002-qvhjizz
Currently Loaded Modulefiles:
1) access-om3/dependencies/pr264-11/access3-share/2026.03.002-pko5hg7
2) access-om3/dependencies/pr264-11/access-cice/CICE6.6.3-2-lgdd6vc
3) access-om3/dependencies/pr264-11/access-mocsy/2025.07.002-pz75hi5
4) access-om3/dependencies/pr264-11/access-generic-tracers/2026.05.000-i7fz4v6
5) access-om3/dependencies/pr264-11/access-mom6/ee2ec415bc46e8b8de4d663f58dc65f72678a7ce-43xexcn
6) access-om3/dependencies/pr264-11/access-ww3/2026.03.001-tein63v
7) access-om3/dependencies/pr264-11/access3/2026.03.002-qvhjizz
8) access-om3/pr264-11
9) model-tools/mppnccombine-fast/2025.07.000
10) pbs
11) openmpi/5.0.8
[ERROR] Model exited with error code 1
Check this on Gadi: when these logs were written, and their last lines
# WHAT THIS DOES: for each log file listed above, prints when it was last changed and its last 30
# lines, which are the lines the page shows.
# 'for' repeats the three lines below once for each file; $f is the file it is on.
# 'ls -l' lists a file with details; --time-style=long-iso writes its time as 2026-07-01 00:02.
for f in /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/error_logs/access-om3.180339684.gadi-pbs.err /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/error_logs/access-om3.180339684.gadi-pbs.out /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/output024/log/med.log /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/pbs_logs/8km_jra_ryf.o179710484 /scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/pbs_logs/8km_jra_ryf.e179710484; do
echo "== $f" # which file this is
ls -l --time-style=long-iso "$f" # when it was last changed (the date and time are in the middle)
tail -n 30 "$f" # its last 30 lines
done
/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe/metadata.yaml
# ---- Automatically generated by Payu. Do not edit. ----
experiment_uuid: 4f2841fe-27a6-407f-ac9f-ebab255825ed
# ---- Automatically generated by Payu. User may edit if necessary. ----
name: MC_8km_jra_ryf-test1-expt-4f2841fe
contact: Christopher Bull
email: 5499680+chrisb13@users.noreply.github.com
created: '2026-09-18'
url: https://github.com/ACCESS-NRI/access-om3-configs
model: ACCESS-OM3
schema_version: 1-0-4
# ---- User feel free to update. ----
description: |-
8km ACCESS-OM3 global configuration under the RYF9091 Repeat
Year Forcing strategy outlined by Stewart et al (2020),
https://doi.org/10.1016/j.ocemod.2019.101557.
Initial conditions of temperature and salinity are from WOA23.
Run with JRA55-do v1.6.0 RYF9091 (1 May 1990 - 30 April 1991) repeated forcing.
Spin up starts from a nominal year of 1 Jan 1900.
notes: |-
ACCESS-NRI and COSIMA request that users of this model acknowledge those organisations
following the examples at https://www.access-nri.org.au/resources/acknowledging-us/
and https://cosima.org.au/index.php/get-involved/
keywords:
- JRA55
- access-om3
- repeat-year
- global
realm:
- ocean
- seaIce
nominal_resolution: 8 km
license: CC-BY-4.0
version: 0.0
long_description: __REPLACE_ME__ # Long description of the experiment (string)
# frequency: The frequency(/ies) included in the experiment (array of strings)
# variable: The variable(s) included in the experiment (array of strings)
# reference: Citation or reference information (string)
# parent_experiment: experiment_uuid for parent experiment if appropriate (string)
# related_experiments: experiment_uuids for any related experiment(s) (array of strings)
# parent_experiment_branch_time: The model time corresponding to the restart path used to create this branch, e.g., 1951-02-01T00:00:00 (string)
# parent_experiment_branch_commit: Git commit hash of the source branch when this new branch was created (string)
Truncation locations for all completed run segments
⚠️ MOM6 truncated velocities 485,692 times in 14 of 25 output folders (the Truncs column of each outputNNN/ocean.stats). MOM6 truncates a velocity when its CFL number exceeds CFL_TRUNCATE (0.5 by default), and stops the run if more than MAXTRUNC truncations happen between energy saves (MOM6's default is 0, so any truncation stops it; the ACCESS-OM3 configurations set 10,000). See MOM6 velocity truncations for how to read the records, and Examine_truncation_data.ipynb for mapping them.
Location records are the detailed records MOM6 also writes, one per truncation, to U_velocity_truncations (zonal velocity) and V_velocity_truncations (meridional velocity); the location table below is built from them. MOM6 writes at most 50 per PE per run, so there are usually fewer of them than truncations; – means no file of that kind.
| Output folder | Model period | Truncations | Max CFL | Location records (U / V) | PEs at the record cap |
|---|---|---|---|---|---|
| output000 | ? → 1900-03 | 770 | 0.17 | 16 / 1 | – |
| output001 | 1900-03 → 1900-05 | 10,248 | 0.12 | – / 50 | 6073 |
| output002 | 1900-05 → 1900-06 | 40,937 | 0.13 | – / 50 | 6073 |
| output003 | 1900-06 → 1900-07 | 58,793 | 0.13 | – / 50 | 6073 |
| output004 | 1900-07 → 1900-08 | 54,202 | 0.13 | – / 50 | 6073 |
| output005 | 1900-08 → 1900-09 | 44,036 | 0.60 | 412 / 269 | 6073 |
| output006 | 1900-09 → 1900-10 | 13,398 | 0.60 | 240 / 116 | – |
| output013 | 1901-04 → 1901-05 | 5,036 | 0.12 | – / 50 | 6073 |
| output014 | 1901-05 → 1901-06 | 39,880 | 0.15 | – / 50 | 6073 |
| output015 | 1901-06 → 1901-07 | 58,070 | 0.12 | – / 50 | 6073 |
| output016 | 1901-07 → 1901-08 | 53,658 | 0.12 | – / 50 | 6073 |
| output017 | 1901-08 → 1901-09 | 8,253 | 0.15 | – / 50 | 6073 |
| output023 | 1902-04 → 1902-06 | 66,166 | 0.14 | – / 50 | 6073 |
| output024 | 32,245 | 0.12 | – / 50 | 6073 |
The other 11 output folders had no truncations.
Where MOM6 truncates (1° boxes, most records first; from the U_velocity_truncations and V_velocity_truncations files):
| Location | Records | Grid cells | Seen in output | Velocity | Layers | Max speed (m/s) | Max CFL | Surface height (m) | Depth (m) |
|---|---|---|---|---|---|---|---|---|---|
| 73.3°E, 67.9°N | 600* | 5 | 001–005, 013–017, 023–024 | V | 1–6 | 4.0 | 0.74 | 4.45 | 10 |
| 144.9°W, 74.0°N | 48 | 21 | 006 | U, V | 1–15 | 16210000.0 | 1146000.00 | -1.41 | 2723 |
| 135.2°W, 74.9°N | 41 | 12 | 006 | U, V | 1–6 | 1063.0 | 77.26 | -0.99 | 3339 |
| 130.9°W, 73.0°N | 34 | 15 | 005 | U, V | 1–8 | 2099.0 | 142.80 | -1.35 | 819 |
| 123.7°W, 80.3°N | 29 | 12 | 006 | U, V | 1–12 | 2130.0 | 182.30 | -1.06 | 3201 |
| 145.7°W, 79.1°N | 28 | 13 | 005 | U, V | 1–12 | 46110.0 | 3820.00 | -2.96 | 3801 |
| 152.7°W, 75.7°N | 24 | 9 | 005 | U, V | 1–3 | 15620.0 | 1167.00 | -4.29 | 1288 |
| 131.9°W, 72.2°N | 24 | 8 | 005 | U, V | 1–3 | 13310.0 | 887.40 | -0.51 | 1329 |
| 138.2°W, 78.7°N | 21 | 6 | 005 | U, V | 1–11 | 4380.0 | 359.50 | -0.96 | 3648 |
| 131.9°W, 77.1°N | 21 | 7 | 006 | U, V | 1–7 | 1380.0 | 64.86 | -1.00 | 3237 |
| 157.0°W, 75.3°N | 19 | 5 | 005 | U, V | 1–13 | 5639.0 | 312.80 | -0.97 | 1314 |
| 156.1°W, 74.9°N | 19 | 6 | 005 | U, V | 1–7 | 1395.0 | 102.10 | -1.22 | 3843 |
| 156.1°W, 73.7°N | 19 | 6 | 005 | U, V | 1–8 | 1265.0 | 88.21 | -0.57 | 3609 |
| 151.8°W, 74.5°N | 18 | 8 | 005 | U, V | 1–18 | 165.7 | 11.91 | -0.39 | 3842 |
| 135.9°W, 74.8°N | 18 | 5 | 006 | U, V | 1–6 | 78.2 | 3.63 | -0.72 | 3367 |
| 2.9°E, 79.1°N | 17 | 3 | 000 | U, V | 1–68 | 8.7 | 0.56 | -2.21 | 5420 |
| 137.6°W, 71.9°N | 17 | 4 | 005 | V | 1–2 | 382700.0 | 26510.00 | -1.05 | 2323 |
| 155.0°W, 75.0°N | 16 | 5 | 005 | U, V | 1–7 | 246.0 | 18.17 | -0.51 | 2111 |
| 137.4°W, 71.8°N | 16 | 6 | 005–006 | U, V | 1–7 | 3486.0 | 243.50 | -1.18 | 2250 |
| 153.4°W, 74.4°N | 15 | 6 | 005 | U, V | 1–7 | 193.9 | 13.92 | -0.67 | 3801 |
* MOM6 writes at most 50 records per PE per run (MAX_TRUNC_FILE_SIZE_PER_PE), and this box's PE hit that cap in at least one run, so it truncated more often than the record count shows. Surface height is the top-interface height e, shown only for records that include layer 1; depth is the shallower of the two cells (D).
Check this on Gadi: the truncation counts, locations and settings
# WHAT THIS DOES: re-checks the 'Truncation locations' section from the files MOM6 wrote. A
# truncation is when MOM6 had to cut a velocity that was too fast (its CFL number was above 0.5): a
# sign of numerical trouble. The steps below are separate, so you can paste just the one you need.
# Each prints something you can compare with the page.
A=/scratch/tm70/cyb561/access-om3/archive/MC_8km_jra_ryf-test1-expt-4f2841fe
R=/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1
# Step 1: for each output folder: how many truncations MOM6 reported, the largest CFL number, and how many location records were written
for o in "$A"/output[0-9]*; do
# ocean.stats is a table with one line per time step. Its 3rd column ('Truncs') is the truncations at that
# step. awk adds that column up. (-F, means the columns are separated by commas. The header line is skipped
# because its first column is not a number.)
total=$(awk -F, '$1+0 == $1 {sum += $3} END {print sum+0}' "$o/ocean.stats" 2>/dev/null)
# The 5th column holds two numbers; the second one is the CFL number. awk keeps the largest.
cfl=$(awk -F, '$1+0 == $1 {split($5, a, " "); if (a[2] > max) max = a[2]} END {if (max != "") printf "%.2f", max}' "$o/ocean.stats" 2>/dev/null)
# Every truncation also gets a 'location record' in the U and V files. grep -c counts the matching lines.
u=$(grep -c 'velocity violation' "$o/U_velocity_truncations" 2>/dev/null)
v=$(grep -c 'velocity violation' "$o/V_velocity_truncations" 2>/dev/null)
# ${x:--} means: use x, or a dash if x is empty (no such file)
echo "$(basename "$o"): truncations ${total:--}, max CFL ${cfl:--}, location records U/V ${u:--}/${v:--}"
done
# Step 2: where it happens. Each record contains the place, like '( 73.27 E 67.89 N)'. This counts the records in
# boxes one degree wide (negative longitude means west), busiest first. The pipeline does this:
# grep: keep the lines that start a record sed: keep only the longitude and latitude
# awk: round them to whole degrees sort | uniq -c: count the records in each box
# sort -rn | head: busiest boxes first
grep -h 'velocity violation' "$A"/output[0-9]*/[UV]_velocity_truncations 2>/dev/null \
| sed -E 's/.*\( *(-?[0-9.]+) E +(-?[0-9.]+) N\).*/\1 \2/' \
| awk '{printf "%4.0fE %4.0fN\n", $1, $2}' \
| sort | uniq -c | sort -rn | head -n 15
# Step 3: MOM6 writes at most 50 records per PE (one of the parallel processes) in one run, then stops. A PE with
# 50 records may have truncated more often than the records show. This lists the PEs that reached 50.
for f in "$A"/output[0-9]*/[UV]_velocity_truncations; do
[ -f "$f" ] || continue # skip if there is no such file
# each record says which PE it came from ('violation at 6073:'); count the records per PE, keep PEs with 50
busy=$(grep -h 'velocity violation' "$f" | sed -E 's/.*violation at ([0-9]+):.*/PE\1/' | sort | uniq -c | awk '$1 >= 50 {printf "%s (%d records) ", $2, $1}')
echo "$(basename "$(dirname "$f")")/$(basename "$f"): $busy"
done
# Step 4: one record in full. The page reads the speed (u, v), the CFL number, the surface height (e) and the
# depth (D) from lines like these.
head -n 30 "$A"/output000/U_velocity_truncations
# Step 5: the model period of each output folder, from payu's run records (output NNN is run NNN)
python3 - "$A" <<'EOF'
import glob, json, os, sys
# payu keeps one small file for every run: payu_jobs/<number>/run/<job>.json. Read them all.
archive = sys.argv[1] # the archive folder, handed over by the shell line above
runs = []
for path in glob.glob(archive + "/payu_jobs/*/run/*.json"):
try:
with open(path) as f:
record = json.load(f)
record["file"] = path # remember which file it came from
runs.append(record)
except (OSError, ValueError):
pass # skip a file we may not read, or that is not valid JSON
# Put the runs in order: by run number, and by start time if a run was tried more than once.
runs.sort(key=lambda r: (int(r.get("payu_current_run") or 0), r.get("timings", {}).get("payu_start_time") or ""))
for r in runs:
run, finish = r.get("payu_current_run"), r.get("model_finish_time")
if str(run).isdigit() and finish: # only runs that finished have a model period
start = r.get("model_start_time") or "?" # payu did not record the start of the first run
print("output%03d %s -> %s" % (int(run), start[:7], finish[:7]))
EOF
# Step 6: the settings that decide when MOM6 truncates (CFL_TRUNCATE) and when it stops the run (MAXTRUNC).
# Each is shown as it is set in MOM_input and in MOM6's own record of every setting, which also gives its default.
grep -hE '^(CFL_TRUNCATE|MAXTRUNC) ' "$R"/MOM_input "$R"/docs/MOM_parameter_doc.all
Settings changed during this run
Every edit to the model's settings and build during this experiment, from the git history of the payu control directory (/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1), starting at its first run commit (18 Sep 2026; 25 completed runs, 8 redone so far). It covers the completed runs (the archive folder above) and the current or crashed run (the run directory above): the dashed vertical line marks where the completed runs end. It reads MOM_input, MOM_override, nuopc.runconfig, ice_in and, from config.yaml, the model build (model, exe, modules) and the input files (input), plus the run length (stop_n and restart_n in nuopc.runconfig: the model time each run covers and how often it writes restarts). Each numbered dot is one edit: hover it to see the change, or use the table below, which gives the old and new value and the commit message. The column on the right of the chart gives each setting's value at the first run and now, and a setting's name links to where it is documented or set in access-om3-configs.
Current build
Entry in config.yaml |
Now | Changes |
|---|---|---|
| Model | access-om3 |
unchanged since the first run |
| Executable | access-om3-MOM6-CICE6 |
unchanged since the first run |
| Modules loaded | access-om3/pr278-2model-tools/mppnccombine-fast/2025.07.000 |
changed 1×: last after run 23 (2 Oct 2026, model date 1902-06-01); see #11 below |
| # | When | After run (model date) | Setting | Change | Commit |
|---|---|---|---|---|---|
| 1 | 19 Sep 15:08 | 1 1900-05-01 | Run length · CLOCK_attributesrestart_n | 2 → 1 | 2026-09-19 15:08:52: Run 2 2fce08a1 |
| 2 | 19 Sep 15:08 | 1 1900-05-01 | Run length · CLOCK_attributesstop_n | 2 → 1 | 2026-09-19 15:08:52: Run 2 2fce08a1 |
| 3 | 21 Sep 14:00 | 16 1901-08-01 | Run length · CLOCK_attributesrestart_n | 1 → 2 | 2026-09-21 14:00:20: Run 17 85c46d73 |
| 4 | 21 Sep 14:00 | 16 1901-08-01 | Run length · CLOCK_attributesstop_n | 1 → 2 | 2026-09-21 14:00:20: Run 17 85c46d73 |
| 5 | 21 Sep 14:43 | 16 1901-08-01 | Run length · CLOCK_attributesrestart_n | 2 → 1 | 2026-09-21 14:43:30: Run 17 e3b0f8da |
| 6 | 21 Sep 14:43 | 16 1901-08-01 | Run length · CLOCK_attributesstop_n | 2 → 1 | 2026-09-21 14:43:30: Run 17 e3b0f8da |
| 7 | 23 Sep 09:37 | 20 1901-12-01 | Run length · CLOCK_attributesrestart_n | 1 → 2 | 2026-09-23 09:37:35: Run 21 bb3e6867 |
| 8 | 23 Sep 09:37 | 20 1901-12-01 | Run length · CLOCK_attributesstop_n | 1 → 2 | 2026-09-23 09:37:35: Run 21 bb3e6867 |
| 9 | 24 Sep 10:31 | 23 1902-06-01 | Run length · CLOCK_attributesrestart_n | 2 → 1 | 2026-09-24 10:31:32: Run 24 83079519 |
| 10 | 24 Sep 10:31 | 23 1902-06-01 | Run length · CLOCK_attributesstop_n | 2 → 1 | 2026-09-24 10:31:32: Run 24 83079519 |
| 11 | 2 Oct 17:49 | 23 1902-06-01 | Buildmodules.load | -access-om3/pr264-11+access-om3/pr278-2 | 2026-10-02 17:49:02: Run 24 97eb9e5f |
Housekeeping: 6 changes to 3 settings in 5 commits (job setup, paths, diagnostic output)
| When | After run | Component | Setting | Change | Commit |
|---|---|---|---|---|---|
| 21 Sep 13:46 | 16 | Job setup | sync.base_path |
/g/data/ol01/outputs/access-om3-8km/MC_8km_jra_ryf-test1-expt-4f2841fe/ → /g/data/ol01/outputs/access-om3-8km/ |
2026-09-21 13:46:11: Run 17 6eff4acf |
| 23 Sep 09:37 | 20 | Job setup | project |
ol01 → x77 |
2026-09-23 09:37:35: Run 21 bb3e6867 |
| 23 Sep 17:48 | 21 | Job setup | project |
x77 → y99 |
2026-09-23 17:48:12: Run 22 cafa649a |
| 24 Sep 10:31 | 23 | Job setup | project |
y99 → e14 |
2026-09-24 10:31:32: Run 24 83079519 |
| 2 Oct 17:49 | 23 | Job setup | manifest.reproduce.exe |
True → False |
2026-10-02 17:49:02: Run 24 97eb9e5f |
| 2 Oct 17:49 | 23 | Job setup | project |
e14 → tm70 |
2026-10-02 17:49:02: Run 24 97eb9e5f |
Check this on Gadi: the build and every edit listed here
# WHAT THIS DOES: checks the 'Settings changed during this run' section. It prints the current build
# from config.yaml, counts payu's run commits, and lists every edit made to the settings files since
# the first run, using git (the history of changes kept in the control directory). The page shows
# these as setting values, so edits to comments or formatting do not appear there, and paths,
# layout, output and job settings are under its Housekeeping note. In the list of edits, a line
# starting with '-' was removed and a line starting with '+' was added.
R=/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1
# Step 1: the current build: the 'model' and 'exe' lines of config.yaml, and its 'modules:' block
# (sed prints the lines from 'modules:' down to the next empty line)
grep -E '^(model|exe):' "$R/config.yaml"
sed -n '/^modules:/,/^$/p' "$R/config.yaml"
# Step 2: payu makes a git commit each time it starts a run, with a message ending in 'Run <number>'.
# This counts them. A run that crashed and was redone has two, and the page counts it once.
git -C "$R" log --first-parent --format=%s | grep -c ': Run [0-9]*$'
# These are the redone runs: how many run commits each has, then the run (prints nothing if none).
git -C "$R" log --first-parent --format=%s | grep -o 'Run [0-9]*$' | sort | uniq -c -d
# Step 3: find the first run commit (the history starts there)
FIRST=$(git -C "$R" log --first-parent --reverse --format='%H %s' | grep -m1 ': Run [0-9]*$' | cut -d' ' -f1)
# Step 4: every edit to the settings files after that, oldest first. Each edit starts with a line like
# '=== <commit> <date> <message>', followed by what changed.
git -C "$R" log -p --first-parent --reverse --format='=== %h %cI %s' "$FIRST"..HEAD -- config.yaml MOM_input MOM_override nuopc.runconfig ice_in
# If git says 'dubious ownership', the folder belongs to someone else: add -c safe.directory="$R" after the word git.
Where are my friends?
How this run's configuration relates to access-om3-configs: the newest commit that the control directory's history (latest commit 97eb9e5f) shares with the configurations repository.
- Closest shared commit: 050aadc on branch dev-MC_8km_jra_ryf · 2026-09-18 · “Updating Angus' 8km ryf configuration to use the latest
dev-MC_25km_jra_ryf(#1432)” - Changes in this run since then: 5 files changed, 41 insertions(+), 117 deletions(-)
- Closest tag: release-MC_25km_jra_ryf-1.0-beta-1, 147 commits before the shared commit
- Changes in this run since that tag: 26 files changed, 6745 insertions(+), 1785 deletions(-)
Diff: this run vs dev-MC_8km_jra_ryf @ 050aadc
diff --git a/config.yaml b/config.yaml
index d8e9154..af59e8a 100644
--- a/config.yaml
+++ b/config.yaml
@@ -2,15 +2,15 @@
# If submitting to a different project to your default, uncomment line below
# and change project code as appropriate; also set shortpath below
-# project: x77
+project: tm70
# Force payu to always find, and save, files in this scratch project directory
-# shortpath: /scratch/tm70
+shortpath: /scratch/tm70
# Using payu sync is recommend to copy data from ephemeral scratch space to
# longer term storage
sync:
- enable: False # set path below and change to true
- base_path: null # Set to location on /g/data (e.g. /g/data/PROJECT/USER/)
+ enable: True # set path below and change to true
+ base_path: /g/data/ol01/outputs/access-om3-8km/ # Set to location on /g/data (e.g. /g/data/PROJECT/USER/)
restarts: True
exclude_uncollated: False
@@ -20,7 +20,7 @@ modules:
- /g/data/vk83/modules
- /g/data/vk83/prerelease/modules
load:
- - access-om3/pr264-11
+ - access-om3/pr278-2
- model-tools/mppnccombine-fast/2025.07.000
queue: normalsr
@@ -55,7 +55,7 @@ metadata:
enable: true
manifest:
reproduce:
- exe: True
+ exe: False
input: True
mpi:
diff --git a/docs/MOM_parameter_doc.all b/docs/MOM_parameter_doc.all
index e521b9b..eb42bd2 100644
--- a/docs/MOM_parameter_doc.all
+++ b/docs/MOM_parameter_doc.all
@@ -634,85 +634,10 @@ FATAL_INCONSISTENT_RESTART_TIME = False ! [Boolean] default = False
! If true and a time_in value is provided to MOM_initialize_state, verify that
! the time read from a restart file is the same as time_in, and issue a fatal
! error if it is not. Otherwise, simply set the time to time_in if present.
-INIT_LAYERS_FROM_Z_FILE = True ! [Boolean] default = False
- ! If true, initialize the layer thicknesses, temperatures, and salinities from a
- ! Z-space file on a latitude-longitude grid.
-
-! === module MOM_initialize_layers_from_Z ===
-TEMP_SALT_Z_INIT_FILE = "./INPUT/woa23_ts_01_mom.nc" ! default = "temp_salt_z.nc"
- ! The name of the z-space input file used to initialize temperatures (T) and
- ! salinities (S). If T and S are not in the same file, TEMP_Z_INIT_FILE and
- ! SALT_Z_INIT_FILE must be set.
-TEMP_Z_INIT_FILE = "./INPUT/woa23_ts_01_mom.nc" ! default = "./INPUT/woa23_ts_01_mom.nc"
- ! The name of the z-space input file used to initialize temperatures, only.
-SALT_Z_INIT_FILE = "./INPUT/woa23_ts_01_mom.nc" ! default = "./INPUT/woa23_ts_01_mom.nc"
- ! The name of the z-space input file used to initialize temperatures, only.
-Z_INIT_FILE_PTEMP_VAR = "ptemp" ! default = "ptemp"
- ! The name of the potential temperature variable in TEMP_Z_INIT_FILE.
-Z_INIT_FILE_SALT_VAR = "salt" ! default = "salt"
- ! The name of the salinity variable in SALT_Z_INIT_FILE.
-Z_INIT_HOMOGENIZE = False ! [Boolean] default = False
- ! If True, then horizontally homogenize the interpolated initial conditions.
-Z_INIT_ALE_REMAPPING = True ! [Boolean] default = False
- ! If True, then remap straight to model coordinate from file.
-Z_INIT_REMAPPING_SCHEME = "PPM_IH4" ! default = "PPM_IH4"
- ! The remapping scheme to use if using Z_INIT_ALE_REMAPPING is True.
-Z_INIT_REMAP_GENERAL = True ! [Boolean] default = False
- ! If false, only initializes to z* coordinates. If true, allows initialization
- ! directly to general coordinates.
-Z_INIT_REMAP_FULL_COLUMN = True ! [Boolean] default = True
- ! If false, only reconstructs profiles for valid data points. If true, inserts
- ! vanished layers below the valid data.
-Z_INIT_REMAP_OLD_ALG = False ! [Boolean] default = False
- ! If false, uses the preferred remapping algorithm for initialization. If true,
- ! use an older, less robust algorithm for remapping.
-TEMP_SALT_INIT_VERTICAL_REMAP_ONLY = True ! [Boolean] default = False
- ! If true, initial conditions are on the model horizontal grid. Extrapolation
- ! over missing ocean values is done using an ICE-9 procedure with vertical ALE
- ! remapping .
Z_INIT_REMAPPING_USE_OM4_SUBCELLS = False ! [Boolean] default = False
! If true, use the OM4 remapping-via-subcells algorithm for initialization. See
! REMAPPING_USE_OM4_SUBCELLS for more details. We recommend setting this option
! to false.
-HOR_REGRID_ANSWER_DATE = 99991231 ! default = 99991231
- ! The vintage of the order of arithmetic for horizontal regridding. Dates
- ! before 20190101 give the same answers as the code did in late 2018, while
- ! later versions add parentheses for rotational symmetry. Dates after 20230101
- ! use reproducing sums for global averages.
-LAND_FILL_TEMP = 0.0 ! [degC] default = 0.0
- ! A value to use to fill in ocean temperatures on land points.
-LAND_FILL_SALIN = 35.0 ! [ppt] default = 35.0
- ! A value to use to fill in ocean salinities on land points.
-HORIZ_INTERP_TOL_TEMP = 0.001 ! [degC] default = 0.001
- ! The tolerance in temperature changes between iterations when interpolating
- ! from an input dataset using horiz_interp_and_extrap_tracer. This routine
- ! converges slowly, so an overly small tolerance can get expensive.
-HORIZ_INTERP_TOL_SALIN = 0.001 ! [ppt] default = 0.001
- ! The tolerance in salinity changes between iterations when interpolating from
- ! an input dataset using horiz_interp_and_extrap_tracer. This routine converges
- ! slowly, so an overly small tolerance can get expensive.
-DEPRESS_INITIAL_SURFACE = False ! [Boolean] default = False
- ! If true, depress the initial surface to avoid huge tsunamis when a large
- ! surface pressure is applied.
-TRIM_IC_FOR_P_SURF = False ! [Boolean] default = False
- ! If true, cuts way the top of the column for initial conditions at the depth
- ! where the hydrostatic pressure matches the imposed surface pressure which is
- ! read from file.
-REGRID_ACCELERATE_INIT = False ! [Boolean] default = False
- ! If true, runs REGRID_ACCELERATE_ITERATIONS iterations of the regridding
- ! algorithm to push the initial grid to be consistent with the initial
- ! condition. Useful only for state-based and iterative coordinates.
-VELOCITY_CONFIG = "zero" ! default = "zero"
- ! A string that determines how the initial velocities are specified for a new
- ! run:
- ! file - read velocities from the file specified
- ! by (VELOCITY_FILE).
- ! zero - the fluid is initially at rest.
- ! uniform - the flow is uniform (determined by
- ! parameters INITIAL_U_CONST and INITIAL_V_CONST).
- ! rossby_front - a mixed layer front in thermal wind balance.
- ! soliton - Equatorial Rossby soliton.
- ! USER - call a user modified routine.
ODA_INCUPD = False ! [Boolean] default = False
! If true, oda incremental updates will be applied everywhere in the domain.
SPONGE = False ! [Boolean] default = False
diff --git a/docs/MOM_parameter_doc.short b/docs/MOM_parameter_doc.short
index a7fb6da..82be398 100644
--- a/docs/MOM_parameter_doc.short
+++ b/docs/MOM_parameter_doc.short
@@ -233,24 +233,6 @@ REMAPPING_USE_OM4_SUBCELLS = False ! [Boolean] default = True
! recommend setting this option to false.
! === module MOM_state_initialization ===
-INIT_LAYERS_FROM_Z_FILE = True ! [Boolean] default = False
- ! If true, initialize the layer thicknesses, temperatures, and salinities from a
- ! Z-space file on a latitude-longitude grid.
-
-! === module MOM_initialize_layers_from_Z ===
-TEMP_SALT_Z_INIT_FILE = "./INPUT/woa23_ts_01_mom.nc" ! default = "temp_salt_z.nc"
- ! The name of the z-space input file used to initialize temperatures (T) and
- ! salinities (S). If T and S are not in the same file, TEMP_Z_INIT_FILE and
- ! SALT_Z_INIT_FILE must be set.
-Z_INIT_ALE_REMAPPING = True ! [Boolean] default = False
- ! If True, then remap straight to model coordinate from file.
-Z_INIT_REMAP_GENERAL = True ! [Boolean] default = False
- ! If false, only initializes to z* coordinates. If true, allows initialization
- ! directly to general coordinates.
-TEMP_SALT_INIT_VERTICAL_REMAP_ONLY = True ! [Boolean] default = False
- ! If true, initial conditions are on the model horizontal grid. Extrapolation
- ! over missing ocean values is done using an ICE-9 procedure with vertical ALE
- ! remapping .
! === module MOM_diag_mediator ===
NUM_DIAG_COORDS = 2 ! default = 1
diff --git a/metadata.yaml b/metadata.yaml
index da76e99..ee9b5bb 100644
--- a/metadata.yaml
+++ b/metadata.yaml
@@ -1,27 +1,44 @@
-contact: Add your name here
-email: Add your email address here
-created: Add the date you started the experiment here (YYYY-MM-DD)
+
+# ---- Automatically generated by Payu. Do not edit. ----
+experiment_uuid: 4f2841fe-27a6-407f-ac9f-ebab255825ed
+
+# ---- Automatically generated by Payu. User may edit if necessary. ----
+name: MC_8km_jra_ryf-test1-expt-4f2841fe
+contact: Christopher Bull
+email: 5499680+chrisb13@users.noreply.github.com
+created: '2026-09-18'
+url: https://github.com/ACCESS-NRI/access-om3-configs
+model: ACCESS-OM3
+schema_version: 1-0-4
+
+# ---- User feel free to update. ----
description: |-
- 8km ACCESS-OM3 global configuration under the RYF9091 Repeat
- Year Forcing strategy outlined by Stewart et al (2020),
- https://doi.org/10.1016/j.ocemod.2019.101557.
- Initial conditions of temperature and salinity are from WOA23.
- Run with JRA55-do v1.6.0 RYF9091 (1 May 1990 - 30 April 1991) repeated forcing.
- Spin up starts from a nominal year of 1 Jan 1900.
+ 8km ACCESS-OM3 global configuration under the RYF9091 Repeat
+ Year Forcing strategy outlined by Stewart et al (2020),
+ https://doi.org/10.1016/j.ocemod.2019.101557.
+ Initial conditions of temperature and salinity are from WOA23.
+ Run with JRA55-do v1.6.0 RYF9091 (1 May 1990 - 30 April 1991) repeated forcing.
+ Spin up starts from a nominal year of 1 Jan 1900.
notes: |-
ACCESS-NRI and COSIMA request that users of this model acknowledge those organisations
following the examples at https://www.access-nri.org.au/resources/acknowledging-us/
and https://cosima.org.au/index.php/get-involved/
keywords:
- - JRA55
- - access-om3
- - repeat-year
- - global
+- JRA55
+- access-om3
+- repeat-year
+- global
realm:
- - ocean
- - seaIce
+- ocean
+- seaIce
nominal_resolution: 8 km
license: CC-BY-4.0
-model: ACCESS-OM3
-url: https://github.com/ACCESS-NRI/access-om3-configs/tree/dev-MC_8km_jra_ryf
version: 0.0
+long_description: __REPLACE_ME__ # Long description of the experiment (string)
+# frequency: The frequency(/ies) included in the experiment (array of strings)
+# variable: The variable(s) included in the experiment (array of strings)
+# reference: Citation or reference information (string)
+# parent_experiment: experiment_uuid for parent experiment if appropriate (string)
+# related_experiments: experiment_uuids for any related experiment(s) (array of strings)
+# parent_experiment_branch_time: The model time corresponding to the restart path used to create this branch, e.g., 1951-02-01T00:00:00 (string)
+# parent_experiment_branch_commit: Git commit hash of the source branch when this new branch was created (string)
diff --git a/nuopc.runseq b/nuopc.runseq
index d7939c5..ff6766b 100644
--- a/nuopc.runseq
+++ b/nuopc.runseq
@@ -1,5 +1,5 @@
runSeq::
-@240
+@200
MED med_phases_aofluxes_run
MED med_phases_scalefreshwater_run
MED med_phases_prep_ocn_accum
Diff: this run vs tag release-MC_25km_jra_ryf-1.0-beta-1
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 0000000..14199f2
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,18 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+# Required
+version: 2
+# Set the OS, Python version, and other tools you might need
+build:
+ os: ubuntu-24.04
+ tools:
+ python: "3.13"
+
+ jobs:
+ post_checkout:
+ # Cancel building pull requests which dont have docs
+ - |
+ exit 183;
+
+mkdocs:
+ configuration: documentation/mkdocs.yml
\ No newline at end of file
diff --git a/CITATION.cff b/CITATION.cff
deleted file mode 100644
index 812137b..0000000
--- a/CITATION.cff
+++ /dev/null
@@ -1,144 +0,0 @@
-cff-version: 1.2.0
-title: 'ACCESS-OM3 Configurations'
-message: >-
- If you use this software, please cite it using the
- metadata from this file.
-type: software
-authors:
- - given-names: Jo
- family-names: Basevi
- email: Johanna.Basevi@anu.edu.au
- affiliation: ACCESS-NRI
- - given-names: Christopher Yit Sen
- family-names: Bull
- email: chris.bull@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0000-0001-8362-3446'
- - given-names: Martin
- family-names: Dix
- email: Martin.Dix@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0000-0002-7534-0654'
- - given-names: Tommy
- family-names: Gatti
- email: Tommy.Gatti@anu.edu.au
- affiliation: ACCESS-NRI
- - given-names: Angus
- family-names: Gibson
- email: Angus.Gibson@anu.edu.au
- affiliation: Research School of Earth Sciences, Australian National University
- - given-names: Aidan
- family-names: Heerdegen
- email: Aidan.Heerdegen@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0000-0002-4481-4896'
- - given-names: Andrew McC
- family-names: Hogg
- email: Andy.Hogg@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0000-0001-5898-7635'
- - given-names: Harshula
- family-names: Jayasuriya
- email: Harshula.Jayasuriya@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0009-0009-2679-050X'
- - given-names: Ezhilsabareesh
- family-names: Kannadasan
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0000-0003-1441-4311'
- - given-names: Andrew E.
- family-names: Kiss
- email: andrew.kiss@anu.edu.au
- affiliation: Research School of Earth Sciences, Australian National University
- orcid: 'https://orcid.org/0000-0001-8960-9557'
- - given-names: Minghang
- family-names: Li
- email: Minghang.Li1@anu.edu.au
- affiliation: ACCESS-NRI
- - given-names: Davide
- family-names: Marchegiani
- email: Davide.Marchegiani@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0000-0002-7619-7976'
- - given-names: Adele
- family-names: Morrison
- email: Adele.Morrison@anu.edu.au
- affiliation: Research School of Earth Sciences, Australian National University
- orcid: 'https://orcid.org/0000-0002-9904-4980'
- - given-names: Siobhan
- family-names: O'Farrell
- email: Siobhan.O'Farrell@csiro.au
- affiliation: Commonwealth Scientific and Industrial Research
- orcid: 'https://orcid.org/0000-0002-9019-6136'
- - given-names: Micael
- family-names: Oliveira
- email: Micael.Oliveira@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0000-0003-1364-0907'
- - given-names: Kieran
- family-names: Ricardo
- email: Kieran.Ricardo@anu.edu.au
- affiliation: ACCESS-NRI
- - given-names: Manodeep
- family-names: Sinha
- email: Manodeep.Sinha@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0000-0002-4845-1228'
- - given-names: Dougal
- family-names: Squire
- email: Dougie.Squire@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0000-0003-3271-6874'
- - given-names: Anton
- family-names: Steketee
- email: anton.steketee@anu.edu.au
- affiliation: ACCESS-NRI
- orcid: 'https://orcid.org/0009-0002-9081-4106'
- - given-names: Spencer
- family-names: Wong
- email: spencer.wong@anu.edu.au
- affiliation: ACCESS-NRI
- - given-names: Luwei
- family-names: Yang
- email: Luwei.Yang@anu.edu.au
- affiliation: Research School of Earth Sciences, Australian National University
-identifiers:
- - description: "The concept DOI of all ACCESS-OM3 configurations."
- type: doi
- value: 10.5281/zenodo.16294824
- - description: "The versioned DOI"
- type: doi
- value: 10.5281/zenodo.16294825
-repository-code: 'https://github.com/accESS-NRI/access-om3-configs'
-url: 'https://access-om3-configs.access-hive.org.au/'
-repository-artifact: >-
- https://github.com/ACCESS-NRI/access-om3-configs/archive/refs/tags/release-MC_25km_jra55_ryf_1.0-beta.tar.gz
-abstract: >-
- This is an initial beta prerelease of a model
- configuration of ACCESS-OM3. This uses a release of the
- ACCESS-OM3 software (version 2025.05.001), a global grid
- with 25km nominal resolution, bathymetry generated from
- GEBCO 2024 and initial conditions generated from WOA2023.
- A 1990-91 Repeat Year Forcing (RYF) extracted from the
- JRA55-do v1.6 reanalysis is used as input data.
-
-
- ACCESS-OM3 is the third generation of the ACCESS global
- ocean-seaice model. It uses up to date releases of the
- MOM6 ocean mode and CICE6 sea-ice model. It is the first
- ACCESS model release using CMEPS (Community Mediator for
- Earth Prediction Systems), built on top of NUOPC (
- National Unified Operational Prediction Capability),
- infrastructure to connect these model components.
-license: CC-BY-4.0
-version: release-MC_25km_jra_ryf-1.0-beta
-date-released: "2025-07-24"
-keywords:
- - access-om3
- - climate
- - model
- - "ocean - sea ice"
- - CICE
- - MOM6
- - NUOPC
- - ESMF
diff --git a/MOM_input b/MOM_input
index 67943ed..d2a2197 100644
--- a/MOM_input
+++ b/MOM_input
@@ -17,12 +17,26 @@ FATAL_UNUSED_PARAMS = True ! [Boolean] default = False
! This section contains non default layout parameters which are set.
! ------------------------
! === module MOM_domains ===
-AUTO_MASKTABLE = True ! [Boolean] default = False
- ! Turn on automatic mask table generation to eliminate land blocks.
-AUTO_IO_LAYOUT_FAC = 6 ! default = 0
- ! When AUTO_MASKTABLE is enabled, io layout is calculated by performing integer
- ! division of the runtime-determined domain layout with this factor. If the
- ! factor is set to 0 (default), the io layout is set to 1,1.
+NONBLOCKING_UPDATES = True ! [Boolean] default = False
+ ! If true, non-blocking halo updates may be used.
+MASKTABLE = "./auxiliary_input/mask_table.3671.108x96" ! default = "MOM_mask_table"
+ ! A text file to specify n_mask, layout and mask_list. This feature masks out
+ ! processors that contain only land points. The first line of mask_table is the
+ ! number of regions to be masked out. The second line is the layout of the model
+ ! and must be consistent with the actual model layout. The following (n_mask)
+ ! lines give the logical positions of the processors that are masked out. The
+ ! mask_table can be created by tools like check_mask. The following example of
+ ! mask_table masks out 2 processors, (1,2) and (3,6), out of the 24 in a 4x6
+ ! layout:
+ ! 2
+ ! 4,6
+ ! 1,2
+ ! 3,6
+LAYOUT = 108, 96 !
+ ! The processor layout that was actually used.
+IO_LAYOUT = 9, 8 ! default = 1, 1
+ ! The processor layout to be used, or 0,0 to automatically set the io_layout to
+ ! be the same as the layout.
! This section is formatted the same as the MOM_parameter_short.doc output file.
! ------------------------
@@ -37,31 +51,26 @@ USE_CONTEMP_ABSSAL = True ! [Boolean] default = False
USE_REGRIDDING = True ! [Boolean] default = False
! If True, use the ALE algorithm (regridding/remapping). If False, use the
! layered isopycnal algorithm.
-THICKNESSDIFFUSE = True ! [Boolean] default = False
- ! If true, isopycnal surfaces are diffused with a Laplacian coefficient of KHTH.
-THICKNESSDIFFUSE_FIRST = True ! [Boolean] default = False
- ! If true, do thickness diffusion or interface height smoothing before dynamics.
- ! This is only used if THICKNESSDIFFUSE or APPLY_INTERFACE_FILTER is true.
-DT = 900.0 ! [s]
+DT = 240.0 ! [s]
! The (baroclinic) dynamics time step. The time-step that is actually used will
! be an integer fraction of the forcing time-step (DT_FORCING in ocean-only mode
! or the coupling timestep in coupled mode.)
-DT_THERM = 7200.0 ! [s] default = 900.0
- ! The thermodynamic and tracer advection time step. Ideally DT_THERM should be
- ! an integer multiple of DT and less than the forcing or coupling time-step,
- ! unless THERMO_SPANS_COUPLING is true, in which case DT_THERM can be an integer
- ! multiple of the coupling timestep. By default DT_THERM is set to DT.
+DT_THERM = 3600.0 ! [s] default = 240.0
+ ! The thermodynamic time step. Ideally DT_THERM should be an integer multiple of
+ ! DT and of DT_TRACER_ADVECT and less than the forcing or coupling time-step.
+ ! However, if THERMO_SPANS_COUPLING is true, DT_THERM can be an integer multiple
+ ! of the coupling timestep. By default DT_THERM is set to DT.
THERMO_SPANS_COUPLING = True ! [Boolean] default = False
- ! If true, the MOM will take thermodynamic and tracer timesteps that can be
- ! longer than the coupling timestep. The actual thermodynamic timestep that is
- ! used in this case is the largest integer multiple of the coupling timestep
- ! that is less than or equal to DT_THERM.
+ ! If true, the MOM will take thermodynamic timesteps that can be longer than the
+ ! coupling timestep. The actual thermodynamic timestep that is used in this case
+ ! is the largest integer multiple of the coupling timestep that is less than or
+ ! equal to DT_THERM.
HFREEZE = 10.0 ! [m] default = -1.0
! If HFREEZE > 0, melt potential will be computed. The actual depth over which
! melt potential is computed will be min(HFREEZE, OBLD), where OBLD is the
! boundary layer depth. If HFREEZE <= 0 (default), melt potential will not be
! computed.
-DTBT_RESET_PERIOD = 0.0 ! [s] default = 7200.0
+DTBT_RESET_PERIOD = 0.0 ! [s] default = 3600.0
! The period between recalculations of DTBT (if DTBT <= 0). If DTBT_RESET_PERIOD
! is negative, DTBT is set based only on information available at
! initialization. If 0, DTBT will be set every dynamics time step. The default
@@ -91,23 +100,25 @@ BAD_VAL_SST_MAX = 55.0 ! [deg C] default = 45.0
BAD_VAL_SST_MIN = -3.0 ! [deg C] default = -2.1
! The value of SST below which a bad value message is triggered, if
! CHECK_BAD_SURFACE_VALS is true.
-SAVE_INITIAL_CONDS = True ! [Boolean] default = False
- ! If true, write the initial conditions to a file given by IC_OUTPUT_FILE.
+WRITE_GEOM = 2 ! default = 1
+ ! If =0, never write the geometry and vertical grid files. If =1, write the
+ ! geometry and vertical grid files only for a new simulation. If =2, always
+ ! write the geometry and vertical grid files. Other values are invalid.
+GEOM_FILE = "access-om3.mom6.geometry.nc" ! default = "ocean_geometry"
+ ! The file into which to write the ocean geometry.
! === module MOM_domains ===
TRIPOLAR_N = True ! [Boolean] default = False
! Use tripolar connectivity at the northern edge of the domain. With
! TRIPOLAR_N, NIGLOBAL must be even.
-NIGLOBAL = 1440 !
+NIGLOBAL = 4320 !
! The total number of thickness grid points in the x-direction in the physical
! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
-NJGLOBAL = 1142 !
+NJGLOBAL = 3672 !
! The total number of thickness grid points in the y-direction in the physical
! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
! === module MOM_fixed_initialization ===
-INPUTDIR = "./INPUT/" ! default = "."
- ! The directory in which input files are found.
! === module MOM_grid_init ===
GRID_CONFIG = "mosaic" !
@@ -118,7 +129,7 @@ GRID_CONFIG = "mosaic" !
! cartesian - use a (flat) Cartesian grid.
! spherical - use a simple spherical grid.
! mercator - use a Mercator spherical grid.
-GRID_FILE = "ocean_hgrid.nc" !
+GRID_FILE = "./INPUT/ocean_hgrid.nc" !
! Name of the file from which to read horizontal grid data.
RAD_EARTH = 6.371229E+06 ! [m] default = 6.378E+06
! The radius of the Earth.
@@ -149,8 +160,26 @@ TOPO_CONFIG = "file" !
! Phillips - ACC-like idealized topography used in the Phillips config.
! dense - Denmark Strait-like dense water formation and overflow.
! USER - call a user modified routine.
+TOPO_FILE = "./INPUT/topog.nc" ! default = "topog.nc"
+ ! The file from which the bathymetry is read.
MAXIMUM_DEPTH = 6000.0 ! [m]
! The maximum depth of the ocean.
+CHANNEL_CONFIG = "list" ! default = "none"
+ ! A parameter that determines which set of channels are
+ ! restricted to specific widths. Options are:
+ ! none - All channels have the grid width.
+ ! global_1deg - Sets 16 specific channels appropriate
+ ! for a 1-degree model, as used in CM2G.
+ ! list - Read the channel locations and widths from a
+ ! text file, like MOM_channel_list in the MOM_SIS
+ ! test case.
+ ! file - Read open face widths everywhere from a
+ ! NetCDF file on the model grid.
+CHANNEL_LIST_FILE = "./auxiliary_input/MOM_channel_list" ! default = "MOM_channel_list"
+ ! The file from which the list of narrowed channels is read.
+FATAL_UNUSED_CHANNEL_WIDTHS = True ! [Boolean] default = False
+ ! If true, trigger a fatal error if there are any channel widths in
+ ! CHANNEL_LIST_FILE that do not cause any open face widths to change.
! === module MOM_verticalGrid ===
! Parameters providing information about the vertical grid.
@@ -158,7 +187,7 @@ NK = 75 ! [nondim]
! The number of model layers.
! === module MOM_EOS ===
-EQN_OF_STATE = "ROQUET_RHO" ! default = "WRIGHT"
+EQN_OF_STATE = "ROQUET_RHO" ! default = "WRIGHT_FULL"
! EQN_OF_STATE determines which ocean equation of state should be used.
! Currently, the valid choices are "LINEAR", "UNESCO", "JACKETT_MCD", "WRIGHT",
! "WRIGHT_REDUCED", "WRIGHT_FULL", "NEMO", "ROQUET_RHO", "ROQUET_SPV" and
@@ -168,12 +197,22 @@ TFREEZE_FORM = "TEOS_POLY" ! default = "TEOS10"
! point. Currently, the valid choices are "LINEAR", "MILLERO_78", "TEOS_POLY",
! "TEOS10"
+! === module MOM_restart ===
+PARALLEL_RESTARTFILES = True ! [Boolean] default = False
+ ! If true, the IO layout is used to group processors that write to the same
+ ! restart file or each processor writes its own (numbered) restart file. If
+ ! false, a single restart file is generated combining output from all PEs.
+
! === module MOM_tracer_flow_control ===
USE_IDEAL_AGE_TRACER = True ! [Boolean] default = False
! If true, use the ideal_age_example tracer package.
! === module ideal_age_example ===
+! === module MOM_fixed_initialization ===
+
+! === module MOM_grid_init ===
+
! === module MOM_coord_initialization ===
REGRIDDING_COORDINATE_MODE = "ZSTAR" ! default = "LAYER"
! Coordinate mode for vertical regridding. Choose among the following
@@ -185,7 +224,7 @@ REGRIDDING_COORDINATE_MODE = "ZSTAR" ! default = "LAYER"
! HYCOM1 - HyCOM-like hybrid coordinate
! HYBGEN - Hybrid coordinate from the Hycom hybgen code
! ADAPTIVE - optimize for smooth neutral density surfaces
-ALE_COORDINATE_CONFIG = "FILE:ocean_vgrid.nc,interfaces=zeta" ! default = "UNIFORM"
+ALE_COORDINATE_CONFIG = "FILE:./INPUT/ocean_vgrid.nc,interfaces=zeta" ! default = "UNIFORM"
! Determines how to specify the coordinate resolution. Valid options are:
! PARAM - use the vector-parameter ALE_RESOLUTION
! UNIFORM[:N] - uniformly distributed
@@ -199,8 +238,23 @@ ALE_COORDINATE_CONFIG = "FILE:ocean_vgrid.nc,interfaces=zeta" ! default = "UNIFO
! FNC1:string - FNC1:dz_min,H_total,power,precision
! HYBRID:string - read from a file. The string specifies
! the filename and two variable names, separated
- ! by a comma or space, for sigma-2 and dz. e.g.
- ! HYBRID:vgrid.nc,sigma2,dz
+ ! by a comma or space, for sigma-2 and dz.
+ ! e.g. HYBRID:vgrid.nc,sigma2,dz
+ ! HYBRID_3D:string - read from a file. The string specifies
+ ! the filename and two 3D variable names, separated
+ ! by a comma or space, for sigma-2 and dz. The
+ ! latter can be FNC1:string which is used everywhere.
+ ! e.g. HYBRID_3D:vgrid.nc,sigma2,dz
+ ! HYBRID_MAP:string - read from a file. The string specifies
+ ! the filename and three variable names, separated
+ ! by a comma or space, for map, sigma-2 and dz.
+ ! Map is a spatial index array with, maxval(map)=N,
+ ! and the others are 2D arrays containing N profiles.
+ ! Map typically contains integer values, but it can
+ ! contain real values, I+w, which imply using
+ ! the weighted sum of profiles I and I+1.
+ ! Dz can be FNC1:string which is used everywhere.
+ ! e.g. HYBRID_MAP:vgrid.nc,map,sigma2,dz
!ALE_RESOLUTION = 1.0825614929199219, 1.1963462829589844, 1.322089672088623, 1.4610481262207031, 1.614609718322754, 1.784308910369873, 1.9718408584594727, 2.1790781021118164, 2.4080896377563477, 2.661160469055176, 2.940814971923828, 3.249845504760742, 3.591329574584961, 3.968667984008789, 4.385614395141602, 4.846321105957031, 5.355350494384766, 5.917766571044922, 6.539115905761719, 7.225547790527344, 7.983818054199219, 8.821372985839844, 9.746376037597656, 10.767845153808594, 11.895652770996094, 13.140586853027344, 14.514511108398438, 16.030319213867188, 17.7020263671875, 19.544876098632812, 21.575271606445312, 23.810821533203125, 26.270294189453125, 28.973419189453125, 31.94091796875, 35.194000244140625, 38.75390625, 42.641632080078125, 46.876739501953125, 51.476593017578125, 56.45489501953125, 61.82025146484375, 67.5743408203125, 73.70965576171875, 80.207763671875, 87.03759765625, 94.1534423828125, 101.4951171875, 108.9879150390625, 116.5452880859375, 124.0714111328125, 131.4671630859375, 138.6346435546875, 145.484130859375, 151.938232421875, 157.93701171875, 163.439697265625, 168.42431640625, 172.8876953125, 176.842041015625, 180.3125, 183.33154296875, 185.938720703125, 188.175048828125, 190.08251953125, 191.701171875
REMAPPING_SCHEME = "PPM_H4" ! default = "PLM"
! This sets the reconstruction scheme used for vertical remapping for all
@@ -226,12 +280,10 @@ INIT_LAYERS_FROM_Z_FILE = True ! [Boolean] default = False
! Z-space file on a latitude-longitude grid.
! === module MOM_initialize_layers_from_Z ===
-TEMP_SALT_Z_INIT_FILE = "ocean_temp_salt.res.nc" ! default = "temp_salt_z.nc"
+TEMP_SALT_Z_INIT_FILE = "./INPUT/woa23_ts_01_mom.nc" ! default = "temp_salt_z.nc"
! The name of the z-space input file used to initialize temperatures (T) and
! salinities (S). If T and S are not in the same file, TEMP_Z_INIT_FILE and
! SALT_Z_INIT_FILE must be set.
-Z_INIT_FILE_PTEMP_VAR = "temp" ! default = "ptemp"
- ! The name of the potential temperature variable in TEMP_Z_INIT_FILE.
Z_INIT_ALE_REMAPPING = True ! [Boolean] default = False
! If True, then remap straight to model coordinate from file.
Z_INIT_REMAP_GENERAL = True ! [Boolean] default = False
@@ -241,24 +293,16 @@ TEMP_SALT_INIT_VERTICAL_REMAP_ONLY = True ! [Boolean] default = False
! If true, initial conditions are on the model horizontal grid. Extrapolation
! over missing ocean values is done using an ICE-9 procedure with vertical ALE
! remapping .
-Z_INIT_REMAPPING_USE_OM4_SUBCELLS = False ! [Boolean] default = True
- ! If true, use the OM4 remapping-via-subcells algorithm for initialization. See
- ! REMAPPING_USE_OM4_SUBCELLS for more details. We recommend setting this option
- ! to false.
! === module MOM_diag_mediator ===
NUM_DIAG_COORDS = 2 ! default = 1
! The number of diagnostic vertical coordinates to use. For each coordinate, an
! entry in DIAG_COORDS must be provided.
-DIAG_REMAPPING_USE_OM4_SUBCELLS = False ! [Boolean] default = True
- ! If true, use the OM4 remapping-via-subcells algorithm for diagnostics. See
- ! REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting this option to
- ! false.
DIAG_COORDS = "z Z ZSTAR", "rho2 RHO2 RHO" !
! A list of string tuples associating diag_table modules to a coordinate
! definition used for diagnostics. Each string is of the form
! "MODULE_SUFFIX,PARAMETER_SUFFIX,COORDINATE_NAME".
-DIAG_COORD_DEF_Z = "FILE:ocean_vgrid.nc,interfaces=zeta" ! default = "WOA09"
+DIAG_COORD_DEF_Z = "FILE:./INPUT/ocean_vgrid.nc,interfaces=zeta" ! default = "WOA09"
! Determines how to specify the coordinate resolution. Valid options are:
! PARAM - use the vector-parameter DIAG_COORD_RES_Z
! UNIFORM[:N] - uniformly distributed
@@ -272,13 +316,23 @@ DIAG_COORD_DEF_Z = "FILE:ocean_vgrid.nc,interfaces=zeta" ! default = "WOA09"
! FNC1:string - FNC1:dz_min,H_total,power,precision
! HYBRID:string - read from a file. The string specifies
! the filename and two variable names, separated
- ! by a comma or space, for sigma-2 and dz. e.g.
- ! HYBRID:vgrid.nc,sigma2,dz
-REGRIDDING_ANSWER_DATE = 99991231 ! default = 20181231
- ! The vintage of the expressions and order of arithmetic to use for regridding.
- ! Values below 20190101 result in the use of older, less accurate expressions
- ! that were in use at the end of 2018. Higher values result in the use of more
- ! robust and accurate forms of mathematically equivalent expressions.
+ ! by a comma or space, for sigma-2 and dz.
+ ! e.g. HYBRID:vgrid.nc,sigma2,dz
+ ! HYBRID_3D:string - read from a file. The string specifies
+ ! the filename and two 3D variable names, separated
+ ! by a comma or space, for sigma-2 and dz. The
+ ! latter can be FNC1:string which is used everywhere.
+ ! e.g. HYBRID_3D:vgrid.nc,sigma2,dz
+ ! HYBRID_MAP:string - read from a file. The string specifies
+ ! the filename and three variable names, separated
+ ! by a comma or space, for map, sigma-2 and dz.
+ ! Map is a spatial index array with, maxval(map)=N,
+ ! and the others are 2D arrays containing N profiles.
+ ! Map typically contains integer values, but it can
+ ! contain real values, I+w, which imply using
+ ! the weighted sum of profiles I and I+1.
+ ! Dz can be FNC1:string which is used everywhere.
+ ! e.g. HYBRID_MAP:vgrid.nc,map,sigma2,dz
DIAG_COORD_DEF_RHO2 = "RFNC1:76,999.5,1020.,1034.1,3.1,1041.,0.002" ! default = "WOA09"
! Determines how to specify the coordinate resolution. Valid options are:
! PARAM - use the vector-parameter DIAG_COORD_RES_RHO2
@@ -293,35 +347,23 @@ DIAG_COORD_DEF_RHO2 = "RFNC1:76,999.5,1020.,1034.1,3.1,1041.,0.002" ! default =
! FNC1:string - FNC1:dz_min,H_total,power,precision
! HYBRID:string - read from a file. The string specifies
! the filename and two variable names, separated
- ! by a comma or space, for sigma-2 and dz. e.g.
- ! HYBRID:vgrid.nc,sigma2,dz
-
-! === module MOM_MEKE ===
-USE_MEKE = True ! [Boolean] default = False
- ! If true, turns on the MEKE scheme which calculates a sub-grid mesoscale eddy
- ! kinetic energy budget.
-MEKE_GMCOEFF = 1.0 ! [nondim] default = -1.0
- ! The efficiency of the conversion of potential energy into MEKE by the
- ! thickness mixing parameterization. If MEKE_GMCOEFF is negative, this
- ! conversion is not used or calculated.
-MEKE_BGSRC = 1.0E-13 ! [W kg-1] default = 0.0
- ! A background energy source for MEKE.
-MEKE_KHTH_FAC = 0.5 ! [nondim] default = 0.0
- ! A factor that maps MEKE%Kh to KhTh.
-MEKE_KHTR_FAC = 0.5 ! [nondim] default = 0.0
- ! A factor that maps MEKE%Kh to KhTr.
-MEKE_KHMEKE_FAC = 1.0 ! [nondim] default = 0.0
- ! A factor that maps MEKE%Kh to Kh for MEKE itself.
-MEKE_VISCOSITY_COEFF_KU = 1.0 ! [nondim] default = 0.0
- ! If non-zero, is the scaling coefficient in the expression forviscosity used to
- ! parameterize harmonic lateral momentum mixing byunresolved eddies represented
- ! by MEKE. Can be negative torepresent backscatter from the unresolved eddies.
-MEKE_ALPHA_RHINES = 0.15 ! [nondim] default = 0.0
- ! If positive, is a coefficient weighting the Rhines scale in the expression for
- ! mixing length used in MEKE-derived diffusivity.
-MEKE_ALPHA_EADY = 0.15 ! [nondim] default = 0.0
- ! If positive, is a coefficient weighting the Eady length scale in the
- ! expression for mixing length used in MEKE-derived diffusivity.
+ ! by a comma or space, for sigma-2 and dz.
+ ! e.g. HYBRID:vgrid.nc,sigma2,dz
+ ! HYBRID_3D:string - read from a file. The string specifies
+ ! the filename and two 3D variable names, separated
+ ! by a comma or space, for sigma-2 and dz. The
+ ! latter can be FNC1:string which is used everywhere.
+ ! e.g. HYBRID_3D:vgrid.nc,sigma2,dz
+ ! HYBRID_MAP:string - read from a file. The string specifies
+ ! the filename and three variable names, separated
+ ! by a comma or space, for map, sigma-2 and dz.
+ ! Map is a spatial index array with, maxval(map)=N,
+ ! and the others are 2D arrays containing N profiles.
+ ! Map typically contains integer values, but it can
+ ! contain real values, I+w, which imply using
+ ! the weighted sum of profiles I and I+1.
+ ! Dz can be FNC1:string which is used everywhere.
+ ! e.g. HYBRID_MAP:vgrid.nc,map,sigma2,dz
! === module MOM_lateral_mixing_coeffs ===
USE_VARIABLE_MIXING = True ! [Boolean] default = False
@@ -345,14 +387,10 @@ USE_STORED_SLOPES = True ! [Boolean] default = False
! If true, the isopycnal slopes are calculated once and stored for re-use. This
! uses more memory but avoids calling the equation of state more times than
! should be necessary.
-KH_RES_FN_POWER = 100 ! default = 2
+KH_RES_FN_POWER = 3 ! default = 2
! The power of dx/Ld in the Kh resolution function. Any positive integer may be
! used, although even integers are more efficient to calculate. Setting this
! greater than 100 results in a step-function being used.
-EBT_REMAPPING_USE_OM4_SUBCELLS = False ! [Boolean] default = True
- ! If true, use the OM4 remapping-via-subcells algorithm for calculating EBT
- ! structure. See REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting
- ! this option to false.
! === module MOM_set_visc ===
CHANNEL_DRAG = True ! [Boolean] default = False
@@ -390,11 +428,6 @@ FGNV_FILTER_SCALE = 0.1 ! [nondim] default = 1.0
! streamfunction formulation.
! === module MOM_dynamics_split_RK2 ===
-VISC_REM_BUG = False ! [Boolean] default = True
- ! If true, visc_rem_[uv] in split mode is incorrectly calculated or accounted
- ! for in two places. This parameter controls the defaults of two individual
- ! flags, VISC_REM_TIMESTEP_BUG in MOM_dynamics_split_RK2(b) and
- ! VISC_REM_BT_WEIGHT_BUG in MOM_barotropic.
! === module MOM_continuity_PPM ===
ETA_TOLERANCE = 1.0E-06 ! [m] default = 3.75E-09
@@ -403,8 +436,23 @@ ETA_TOLERANCE = 1.0E-06 ! [m] default = 3.75E-09
! total tolerance for SSH is 4 times this value. The default is
! 0.5*NK*ANGSTROM, and this should not be set less than about
! 10^-15*MAXIMUM_DEPTH.
+VELOCITY_TOLERANCE = 1.0E-04 ! [m s-1] default = 3.0E+08
+ ! The tolerance for barotropic velocity discrepancies between the barotropic
+ ! solution and the sum of the layer thicknesses.
! === module MOM_CoriolisAdv ===
+CORIOLIS_SCHEME = "SADOURNY75_ENSTRO" ! default = "SADOURNY75_ENERGY"
+ ! CORIOLIS_SCHEME selects the discretization for the Coriolis terms. Valid
+ ! values are:
+ ! SADOURNY75_ENERGY - Sadourny, 1975; energy cons.
+ ! ARAKAWA_HSU90 - Arakawa & Hsu, 1990
+ ! SADOURNY75_ENSTRO - Sadourny, 1975; enstrophy cons.
+ ! ARAKAWA_LAMB81 - Arakawa & Lamb, 1981; En. + Enst.
+ ! ARAKAWA_LAMB_BLEND - A blend of Arakawa & Lamb with
+ ! Arakawa & Hsu and Sadourny energy
+ ! WENOVI5TH_PV_ENSTRO - 5th-order WENO PV enstrophy
+ ! WENOVI3RD_PV_ENSTRO - 3rd-order WENO PV enstrophy
+ ! WENOVI7TH_PV_ENSTRO - 7th-order WENO PV enstrophy
BOUND_CORIOLIS = True ! [Boolean] default = False
! If true, the Coriolis terms at u-points are bounded by the four estimates of
! (f+rv)v from the four neighboring v-points, and similarly at v-points. This
@@ -436,26 +484,13 @@ AH_VEL_SCALE = 0.01 ! [m s-1] default = 0.0
! scaled viscosity, the Smagorinsky and Leith viscosities, and AH.
SMAGORINSKY_AH = True ! [Boolean] default = False
! If true, use a biharmonic Smagorinsky nonlinear eddy viscosity.
-BACKSCATTER_UNDERBOUND = False ! [Boolean] default = True
- ! If true, the bounds on the biharmonic viscosity are allowed to increase where
- ! the Laplacian viscosity is negative (due to backscatter parameterizations)
- ! beyond the largest timestep-dependent stable values of biharmonic viscosity
- ! when no Laplacian viscosity is applied. The default is true for historical
- ! reasons, but this option probably should not be used because it can contribute
- ! to numerical instabilities.
SMAG_BI_CONST = 0.06 ! [nondim] default = 0.0
! The nondimensional biharmonic Smagorinsky constant, typically 0.015 - 0.06.
-FRICTWORK_BUG = False ! [Boolean] default = True
- ! If true, retain an answer-changing bug in calculating the FrictWork, which
- ! cancels the h in thickness flux and the h at velocity point. This isnot
- ! recommended.
! === module MOM_vert_friction ===
HMIX_FIXED = 0.5 ! [m]
! The prescribed depth over which the near-surface viscosity and diffusivity are
! elevated when the bulk mixed layer is not used.
-MAXVEL = 6.0 ! [m s-1] default = 3.0E+08
- ! The maximum velocity allowed before the velocity components are truncated.
CFL_TRUNCATE_RAMP_TIME = 7200.0 ! [s] default = 0.0
! The time over which the CFL truncation value is ramped up at the beginning of
! the run.
@@ -514,13 +549,10 @@ MIN_WSTAR2 = 1.0E-09 ! [m2 s-2] default = 1.0E-24
MLE_USE_PBL_MLD = True ! [Boolean] default = False
! If true, the MLE parameterization will use the mixed-layer depth provided by
! the active PBL parameterization. If false, MLE will estimate a MLD based on a
- ! density difference with the surface using the parameter MLE_DENSITY_DIFF.
+ ! density difference with the surface using the parameter MLE_DENSITY_DIFF,
+ ! unless BODNER_DETECT_MLD is true.
! === module MOM_diagnostics ===
-INTWAVE_REMAPPING_USE_OM4_SUBCELLS = False ! [Boolean] default = True
- ! If true, use the OM4 remapping-via-subcells algorithm for calculating EBT
- ! structure. See REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting
- ! this option to false.
! === module MOM_diabatic_driver ===
! The following parameters are used for diabatic processes.
@@ -562,7 +594,10 @@ TKE_ITIDE_MAX = 0.1 ! [W m-2] default = 1000.0
READ_TIDEAMP = True ! [Boolean] default = False
! If true, read a file (given by TIDEAMP_FILE) containing the tidal amplitude
! with INT_TIDE_DISSIPATION.
-H2_FILE = "bottom_roughness.nc" !
+TIDEAMP_FILE = "./INPUT/tideamp.nc" ! default = "tideamp.nc"
+ ! The path to the file containing the spatially varying tidal amplitudes with
+ ! INT_TIDE_DISSIPATION.
+H2_FILE = "./INPUT/bottom_roughness.nc" !
! The path to the file containing the sub-grid-scale topographic roughness
! amplitude with INT_TIDE_DISSIPATION.
BBL_EFFIC = 0.01 ! [nondim] default = 0.2
@@ -624,6 +659,19 @@ PRESSURE_DEPENDENT_FRAZIL = True ! [Boolean] default = False
! If true, use a pressure dependent freezing temperature when making frazil. The
! default is false, which will be faster but is inappropriate with ice-shelf
! cavities.
+DO_RIVERMIX = True ! [Boolean] default = False
+ ! If true, apply additional mixing wherever there is runoff, so that it is mixed
+ ! down to RIVERMIX_DEPTH if the ocean is that deep.
+RIVERMIX_DEPTH = 40.0 ! [m] default = 0.0
+ ! The depth to which rivers are mixed if DO_RIVERMIX is defined.
+VAR_PEN_SW = True ! [Boolean] default = False
+ ! If true, use one of the CHL_A schemes specified by OPACITY_SCHEME to determine
+ ! the e-folding depth of incoming short wave radiation.
+CHL_FILE = "./INPUT/chl_globcolour_monthly_clim.nc" !
+ ! CHL_FILE is the file containing chl_a concentrations in the variable CHL_A. It
+ ! is used when VAR_PEN_SW and CHL_FROM_FILE are true.
+CHL_VARNAME = "CHL" ! default = "CHL_A"
+ ! Name of CHL_A variable in CHL_FILE.
! === module MOM_energetic_PBL ===
ML_OMEGA_FRAC = 0.001 ! [nondim] default = 0.0
@@ -640,10 +688,10 @@ EPBL_MSTAR_SCHEME = "OM4" ! default = "CONSTANT"
! REICHL_H18 - Use the scheme documented in Reichl & Hallberg, 2018.
MSTAR_CAP = 1.25 ! [nondim] default = -1.0
! If this value is positive, it sets the maximum value of mstar allowed in ePBL.
- ! (This is not used if EPBL_MSTAR_SCHEME = CONSTANT).
+ ! (This is not used if EPBL_mstar_scheme = CONSTANT).
MSTAR2_COEF1 = 0.29 ! [nondim] default = 0.3
! Coefficient in computing mstar when rotation and stabilizing effects are both
- ! important (used if EPBL_MSTAR_SCHEME = OM4).
+ ! important (used if EPBL_mstar_scheme = OM4).
MSTAR2_COEF2 = 0.152 ! [nondim] default = 0.085
! Coefficient in computing mstar when only rotation limits the total mixing
! (used if EPBL_MSTAR_SCHEME = OM4)
@@ -670,12 +718,12 @@ EPBL_LANGMUIR_SCHEME = "ADDITIVE" ! default = "NONE"
! NONE - Do not do any extra mixing due to Langmuir turbulence
! RESCALE - Use a multiplicative rescaling of mstar to account for Langmuir
! turbulence
- ! ADDITIVE - Add a Langmuir turblence contribution to mstar to other
+ ! ADDITIVE - Add a Langmuir turbulence contribution to mstar to other
! contributions
LT_ENHANCE_COEF = 0.044 ! [nondim] default = 0.447
! Coefficient for Langmuir enhancement of mstar
LT_ENHANCE_EXP = -1.5 ! [nondim] default = -1.33
- ! Exponent for Langmuir enhancementt of mstar
+ ! Exponent for Langmuir enhancement of mstar
LT_MOD_LAC1 = 0.0 ! [nondim] default = -0.87
! Coefficient for modification of Langmuir number due to MLD approaching Ekman
! depth.
@@ -687,11 +735,8 @@ LT_MOD_LAC5 = 0.22 ! [nondim] default = 0.95
! unstable Obukhov depth.
! === module MOM_opacity ===
-PEN_SW_SCALE = 15.0 ! [m] default = 0.0
- ! The vertical absorption e-folding depth of the penetrating shortwave
- ! radiation.
-PEN_SW_FRAC = 0.42 ! [nondim] default = 0.0
- ! The fraction of the shortwave radiation that penetrates below the surface.
+PEN_SW_NBANDS = 3 ! default = 1
+ ! The number of bands of penetrating shortwave radiation.
! === module MOM_tracer_advect ===
TRACER_ADVECTION_SCHEME = "PPM:H3" ! default = "PLM"
@@ -701,12 +746,14 @@ TRACER_ADVECTION_SCHEME = "PPM:H3" ! default = "PLM"
! PPM - Piecewise Parabolic Method (Colella-Woodward)
! === module MOM_tracer_hor_diff ===
-KHTR = 50.0 ! [m2 s-1] default = 0.0
- ! The background along-isopycnal tracer diffusivity.
CHECK_DIFFUSIVE_CFL = True ! [Boolean] default = False
! If true, use enough iterations the diffusion to ensure that the diffusive
! equivalent of the CFL limit is not violated. If false, always use the greater
! of 1 or MAX_TR_DIFFUSION_CFL iteration.
+MAX_TR_DIFFUSION_CFL = 2.0 ! [nondim] default = -1.0
+ ! If positive, locally limit the along-isopycnal tracer diffusivity to keep the
+ ! diffusive CFL locally at or below this value. The number of diffusive
+ ! iterations is often this value or the next greater integer.
! === module MOM_neutral_diffusion ===
! This module implements neutral diffusion of tracers
@@ -718,6 +765,8 @@ MAXTRUNC = 10000 ! [truncations save_interval-1] default = 0
! The run will be stopped, and the day set to a very large value if the velocity
! is truncated more than MAXTRUNC times between energy saves. Set MAXTRUNC to 0
! to stop if there is any truncation of velocities.
+MAXVEL = 6.0 ! [m s-1] default = 3.0E+08
+ ! The maximum velocity allowed before the velocity components are truncated.
! === module ocean_stochastics_init ===
@@ -738,23 +787,33 @@ LATENT_HEAT_FUSION = 3.337E+05 ! [J/kg] default = 3.34E+05
! The latent heat of fusion.
LATENT_HEAT_VAPORIZATION = 2.501E+06 ! [J/kg] default = 2.5E+06
! The latent heat of fusion.
-ADJUST_NET_FRESH_WATER_TO_ZERO = True ! [Boolean] default = False
- ! If true, adjusts the net fresh-water forcing seen by the ocean (including
- ! restoring) to zero.
+ADJUST_NET_SRESTORE_BY_SCALING = True ! [Boolean] default = False
+ ! If true, adjustments to salt restoring to achieve zero net are made by scaling
+ ! values without moving the zero contour.
WIND_STAGGER = "A" ! default = "C"
! A case-insensitive character string to indicate the staggering of the input
! wind stress field. Valid values are 'A', 'B', or 'C'.
+ENTHALPY_FROM_COUPLER = True ! [Boolean] default = False
+ ! If True, the heat (enthalpy) associated with mass entering/leaving the ocean
+ ! is provided via coupler.
FLUXCONST = 0.11 ! [m day-1] default = 0.0
! The constant that relates the restoring surface fluxes to the relative surface
! anomalies (akin to a piston velocity). Note the non-MKS units.
-SALT_RESTORE_FILE = "salt_sfc_restore.nc" ! default = "salt_restore.nc"
+SALT_RESTORE_FILE = "./INPUT/salt_sfc_restore.nc" ! default = "salt_restore.nc"
! A file in which to find the surface salinity to use for restoring.
+SALT_RESTORE_VARIABLE = "asalt" ! default = "salt"
+ ! The name of the surface salinity variable to read from SALT_RESTORE_FILE for
+ ! restoring salinity.
SRESTORE_AS_SFLUX = True ! [Boolean] default = False
! If true, the restoring of salinity is applied as a salt flux instead of as a
! freshwater flux.
+MAX_DELTA_SRESTORE = 0.5 ! [PSU or g kg-1] default = 999.0
+ ! The maximum salinity difference used in restoring terms.
USE_RIGID_SEA_ICE = True ! [Boolean] default = False
! If true, sea-ice is rigid enough to exert a nonhydrostatic pressure that
! resist vertical motion.
SEA_ICE_RIGID_MASS = 100.0 ! [kg m-2] default = 1000.0
! The mass of sea-ice per unit area at which the sea-ice starts to exhibit
! rigidity
+
+! === module MOM_restart ===
diff --git a/auxiliary_input/MOM_channel_list b/auxiliary_input/MOM_channel_list
new file mode 100644
index 0000000..1f7a015
--- /dev/null
+++ b/auxiliary_input/MOM_channel_list
@@ -0,0 +1,11 @@
+! This file specifies restricted channel widths in MOM. The order is:
+! [U|V]_width, min_longitude, max_longitude, min_latitude, max_latitude, width
+! This is a modified version of
+! https://raw.githubusercontent.com/NOAA-GFDL/MOM6-examples/4e9bf1c22f4d6f267389711715b68b3f3f53eea9/ocean_only/tides_025/INPUT/MOM_channels_global_025
+
+! U_width, -5.9, -5.4, 35.8, 36.2, 12000.0 ! Gibraltar
+U_width, 26.3, 26.8, 40.2, 40.3, 5000.0 ! Dardanelles
+
+V_width, 28.8, 29.2, 41.0, 41.18, 1000.0 ! Bosporus - should be 1km wide.
+! V_width, 43.25, 43.5, 12.6, 12.8, 10000.0 ! Red Sea, Bab-el-Mendeb
+! V_width, 141.5, 141.7, 52.0, 52.15, 2500.0 ! Between Sakhalin & Russia
diff --git a/auxiliary_input/mask_table.3671.108x96 b/auxiliary_input/mask_table.3671.108x96
new file mode 100644
index 0000000..73b145e
--- /dev/null
+++ b/auxiliary_input/mask_table.3671.108x96
@@ -0,0 +1,3681 @@
+3671
+108, 96
+# Created by ml0072 (minghangli-uni) on 2026-09-14, using /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/masktable_generation/gen_masktable.py (md5 hash: 6fec36fc83b2b4af2f20c72d855b1c72): /g/data/xp65/public/apps/med_conda_scripts/analysis3-26.08.d/bin/python3 gen_masktable.py -g /g/data/vk83/prerelease/configurations/inputs/access-om3/share/grids/global.8km/2026.09.08/ocean_hgrid.nc -t /g/data/vk83/prerelease/configurations/inputs/access-om3/share/grids/global.8km/2026.09.11/topog.nc -l 108 96 -m mom6 -a
+# /g/data/vk83/prerelease/configurations/inputs/access-om3/share/grids/global.8km/2026.09.08/ocean_hgrid.nc (md5 hash: e8ed1f1dd04ecba95b81f2dfcfaa9d7c), /g/data/vk83/prerelease/configurations/inputs/access-om3/share/grids/global.8km/2026.09.11/topog.nc (md5 hash: 85c26ec14c3047fd3323841f3a28cdd0)
+#
+# Grid size: 4320 x 3672
+# periodx: 360.0
+# periody: unset (aperiodic)
+# Target model: mom6
+# mom6 compatibility check: OK
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Check this on Gadi: the closest shared commit and tag
# WHAT THIS DOES: checks the 'Where are my friends?' section. It makes a temporary copy of access-
# om3-configs (the repository of released configurations), adds this run's history to it, and asks
# git which commits the two share. The newest shared commit is the run's closest 'friend'; git
# describe then names the nearest tag before it.
R=/g/data/tm70/cyb561/access-om3-runs/8k/MC_8km_jra_ryf-test1
# Step 1: a temporary copy of access-om3-configs (about 30 MB; deleted at the end)
T=$(mktemp -d)
git clone -q --bare https://github.com/ACCESS-NRI/access-om3-configs.git "$T/configs.git"
# Step 2: add this run's history to the copy (nothing is changed in the run's own folder)
git -c safe.directory='*' --git-dir="$T/configs.git" fetch -q "$R" +HEAD:refs/runs/this
# Step 3: the commits this run shares with any branch or tag (the lines starting with '-'), newest first
git --git-dir="$T/configs.git" rev-list --boundary refs/runs/this --not --branches --tags | grep '^-' \
| cut -c2- | xargs -r git --git-dir="$T/configs.git" log --no-walk --format='%h %cI %s'
# Step 4: which branches contain the newest shared commit, and the nearest tag before it
S=050aadc
git --git-dir="$T/configs.git" branch --contains "$S"
git --git-dir="$T/configs.git" describe --tags --abbrev=0 "$S"
rm -rf "$T" # remove the temporary copy