Temporary Files (/tmp/
Directory)¶
The /tmp/
directory is local to each node and reserved for Linux operating system use. A full /tmp/
directory on a compute node reduces compute performance for everyone using the node. Do not use the directory /tmp/
as storage for temporary files. Instead, please use local scratch for fastest access and network scratch for largest space.
Some software packages default to using /tmp/
without warning or documentation, especially software designed for personal computers. We may reach out to inform you if your software fills /tmp/
, as it can harm performance on that compute node. If that happens we will work with you to redirect temporary storage to one of the scratch spaces.
Software Known to Use /tmp/
¶
The following software are known to use /tmp/
by default, and can be worked around by using the listed flags. See our Local Scratch page for more information about creating a local temporary directory. Also see our Network Scratch page for larger scratch storage. Be sure to delete files when your jobs are finished.
- Java:
java * -Djava.io.tmpdir=/local/$USER/$SLURM_JOB_ID
- UMI Tools:
umi_tools * --temp-dir=/local/$USER/SLURM_JOB_ID
- Samtools Sort:
samtools sort * -T /local/$USER/$SLURM_JOB_ID
- GATK Tool:
gatk --java-options * --tmp-dir /local/$USER/$SLURM_JOB_ID
- NVIDIA Clara Parabricks:
pbrun * --tmp-dir=/local/$USER/$SLURM_JOB_ID
. - FastQC:
fastqc * -d /local/$USER/$SLURM_JOB_ID
- MACS2:
macs2 callpeak * --tempdir /local/$USER/$SLURM_JOB_ID
Software known to use /tmp/
by default with no known workaround:
- Keras has
/tmp/.keras
hardcoded as a fallback cache directory if~/.keras
is inaccessible. See TensorFlow GitHub Pages issues for a discussion of the issue.