[QUESTION]How to translate the code in geoschem.run from SLURM to PBS

[jiaying002]

My server uses PBS schedular, while the code provided (geoschem.run) was for SLURM. I tried translating the code from SLURM to PBS, but I failed. I cannot find all the code I need from google, and the one I found is still doubtful. It would be best if someone could guide me on where to find the translated version.

[yantosca]

Thanks for writing @jiaying002. Have you looked at this page? It is a pretty good description: https://www.marquette.edu/high-performance-computing/pbs-to-slurm.php

For SLURM we use e.g. #SBATCH -c 8 to request 8 cores. You can replace that with #PBS -l nodes=1:ppn=8, which will request 8 cores on 1 node.

Finally, in the PBS batch script, you'll have to change

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

to

export OMP_NUM_THREADS=8  # or however many cores you are using.

[yantosca]

Also tagging @Jourdan-He

[lizziel]

Hi @jiaying002, you could also take a look at the template run script for GCHP and adapt it for GEOS-Chem Classic. It includes PBS as one of the schedulers. See file here.

[jiaying002]

Thank u!

[jiaying002]

Hi, sorry for reopening this case. I tried to change the SLURM to PBS and here is the geoschem.run file I modified. geoschem.run.txt Then, I got an error like this: I am wondering is there anything wrong with my code?

[jiaying002]

Sorry for bothering you again. I have been struggling for days. Would you please give me some clues? @yantosca @lizziel

[yantosca]

@jiaying002: We are not as familiar with PBS as our cluster uses SLURM. Is there anyone at your institution who handles IT support?

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[yantosca]

Closing out this issue