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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
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Relion / Slurm Issue #923

Closed JuergenUniVie closed 2 years ago

JuergenUniVie commented 2 years ago

Dear all,

I'm not sure if it's a RELION or a SLURM problem, but maybe someone has some advice for me. I have the following SLURM submit script created from RELION:

!/bin/tcsh

SBATCH --job-name=Relion4Job

SBATCH --nodes=1

SBATCH --ntasks=XXXmpinodesXXX

SBATCH --gres=gpu:XXXextra1XXX

SBATCH --cpus-per-task=XXXthreadsXXX

SBATCH --mem-per-cpu=XXXextra2XXX

SBATCH --partition=XXXqueueXXX

SBATCH --output=XXXoutfileXXX

SBATCH --error=XXXerrfileXXX

module purge module load RELION

srun --mpi=pmi2 XXXcommandXXX

The script works the same way, but the --output and --error data are not written as run.out and err.out but in the "root directory" as submission.script-oJOBID and submission.script-eJOBID.

I have no more ideas. Without RELION it works with every submitjob.

Thanks in advance, all the best. Juergen

biochem-fan commented 2 years ago

@JuergenUniVie

If you managed to solve the issue yourself, please post the solution so that others can learn.