Writing out restart files in stretched-grid simulations

[mcdonh1718]

Your name

Helena McDonald

Your affiliation

MIT

What happened? What did you expect to happen?

I'm running a stretched-grid simulation with base resolution C180 and a stretch factor of 30 (so approx 0.02 deg resolution) centered on Florida. Generating the initial restart file goes fine, though I did have to make sure I gave the longitude coordinates in [0,360] rather than [-180,180] space. When running a simulation, the input file works fine, but I can't string together simulations because the output restart file stores the longitude coordinate just slightly incorrectly, and so throws a 'factories not equal' error. From the initial restart file:

From the simulation write out:

This isn't challenging to fix myself by opening and editing the netcdf (and I can use the restart files after this edit), but it is irritating.

Similarly, I'm having issues where some simulations don't write out restart files at all; the model will be done generating collection files and the log file writes out the component time use breakdown, but it gets stuck converting the placeholder gcchem-internal-checkpoint file to a restart file. See logfile:

It results in this array of errors in my slurm log, but never kills the run; my cluster kills it by timing out.

<img width="609" alt="Image" src="https://github.com/user-attachments/assets/a1d97073-836f-436c-a5c5-e9e2a72aea7b"

What are the steps to reproduce the bug?

Generated a restart file with --stretched-grid --stretch-factor 30 --target-latitude 28.56 --target-longitude 279.56. Enabled NEI2016_MONMEAN in HEMCO_Config. Ran a 3hr simulation starting 07 01 1200z using the restart file I generated using gridspec, ESMF.

Please attach any relevant configuration and log files.

config:
ExtData.txt
gchp-20190701_1200z-log.txt
HEMCO_Config.txt
HISTORY.txt
setCommonRunSettings.txt

slurm files:
gchp_run.txt
slurm-488693-out.txt

What GCHP version were you using?

14.3.1

What environment were you running GCHP on?

Local cluster

What compiler and version were you using?

gcc 9.4.0

What MPI library and version were you using?

OpenMPI 4.0.3

Will you be addressing this bug yourself?

No

Additional information

No response

[lizziel]

Hi @mcdonh1718, this is a bug that was fixed in 14.4.0. You can either update versions or manually update your MAPL version by merge in main (let me know if you need help figuring out how to do this). You can see the fix in the linked PR on the issue report at #409.

[lizziel]

Regarding the output restart file write issue, is there a pattern to when it takes a long time and hangs?

[mcdonh1718]

Hi @mcdonh1718, this is a bug that was fixed in 14.4.0. You can either update versions or manually update your MAPL version by merge in main (let me know if you need help figuring out how to do this). You can see the fix in the linked PR on the issue report at #409.

yes, I'd like to try merging in the updated MAPL rather than installing a new gchp build. How do I do this?

[mcdonh1718]

Regarding the output restart file write issue, is there a pattern to when it takes a long time and hangs?

I figured this out, actually; it was a storage issue. At that stretch factor/resolution, restart files and the related checkpoint files can be 30GB+ and the Restarts directory was running out of space, so it would refuse to write. By softlinking to another directory with more storage space and changing the write-out directions in setrestartlink.sh and my run script, I avoided the issue entirely. Or at least, it's been fine so far!

[lizziel]

Great, I am glad you figured that out. Yes, high resolution restart files are very large since there are so many species in GEOS-Chem. We save out all species, not just advected species.

Regarding MAPL, you can go to your source code directory, then change directories to src/MAPL. Run git fetch -p which gives access to the latest updates on GitHub. Then do git checkout gchp/main. This will give you the latest MAPL used in GCHP, which is backwards compatible to version 14.3.1.

[github-actions]

This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the issue from closing this issue.

[github-actions]

Closing due to inactivity

[lizziel]

Hi @mcdonh1718, heads up there is a bug in stretched grid simulations, at least in 14.6.3. I am looking to figure out which version it came in with. #509