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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.

Important

Do not use /tmp/ for temporary file storage.

Do use local scratch or network scratch. When using scratch storage, remember that both network scratch and local scratch are temporary. Network scratch files are deleted when their creation time and last access time are both 90 or more days ago. Local scratch files are subject to deletion at any time and should be removed when your job is complete.

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.

  • FastQC: fastqc * -d /local/$USER/$SLURM_JOB_ID
  • GATK Tool: gatk --java-options * --tmp-dir /local/$USER/$SLURM_JOB_ID
  • Java: java * -Djava.io.tmpdir=/local/$USER/$SLURM_JOB_ID
  • MACS2: macs2 callpeak * --tempdir /local/$USER/$SLURM_JOB_ID
  • NVIDIA Clara Parabricks: pbrun * --tmp-dir=/local/$USER/$SLURM_JOB_ID.
  • Samtools Sort: samtools sort * -T /local/$USER/$SLURM_JOB_ID
  • Samtools Collate: samtools collate * -T /local/$USER/$SLURM_JOB_ID
  • Samtools Markdup: samtools markdup * -T /local/$USER/$SLURM_JOB_ID
  • UMI Tools: umi_tools * --temp-dir=/local/$USER/SLURM_JOB_ID

Software known to use /tmp/ by default with no known workaround: