[slurm-users] Slurm doesn't call mpiexec or mpirun when run through a GUI app
reuti at staff.uni-marburg.de
Thu Apr 4 10:15:22 UTC 2019
> The user added
> #SBATCH --export=none
> to his submission script to prevent any environment variables in the GUI's environment from being applied to his job. After making that change, his job worked as expected, so this confirmed it was an environment issue. We compared the differences in 'env' from GUI-submitted and manually submitted, jobs, and found a handfule of variables that were set in the GUI environment that were not present in the manual-submission environment. If memory serves me correctly, they were all Open MPI parameters.
> The user was happy using "--export=none" to fix this problem, so we didn't bother going through the tedious task of removing the environment variables one by one until we found the offending one. While still testing/debugging, I did do one run where I thought I removed all the offending variables by unsetting them all in the sbatch script, but the error still occurred, so i must have missed the one that was causing the issue.
> Since the user was happy with the --export=none fix, and I had other issues to fix in my queue, that's where we left it.
Thanks for the info. Good to know to try this in case a problem arises. Surprisingly enough this was one feature I liked in SGE and always recommend not to use -V there, as the acutal environment might corrupt the job script.
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