Singularity Slurm error - mktemp failed to create file via template : Center for Computational Research

Singularity Slurm error - mktemp failed to create file via template Print

Modified on: Tue, Jun 25, 2019 at 10:03 AM

Users submitting job scripts with sbatch that run Singularity containers may notice this error:

mktemp: failed to create file via template ‘/scratch/[jobid]/tmp.XXXXXXXXXX’: No such file or directory

With sbatch, the environment variable TMPDIR gets set to be /scratch/[jobid], so when mktemp tries to execute, it looks for /scratch/[jobid], but the singularity container may not have a /scratch directory.

Recommended solution:

At the beginning of the job script, unset TMPDIR to clear that variable, which allows the Singularity container to use whatever directory is the default for it.

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