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Temporary directories

Most programs which create temporary files will put those files in the directory specified by the environment variable TMPDIR if that is set, or /tmp otherwise.

It is best to avoid the /tmp directory since that is shared with other jobs and not automatically cleared. When a Slurm job starts, TMPDIR is set to a directory created just for that job, which gets automatically deleted when the job finishes. 

By default, this job-specific temporary directory is placed in /dev/shm, which is a “tmpfs” filesystem and so actually sits in ordinary RAM.  As a consequence, your job’s memory request should include enough to cover the size of any temporary files.

On the milan and hgx partitions you have the option of specifying #SBATCH --gres=ssd in your job script which will place TMPDIR on a 1.5 TB NVMe SSD attached to the node rather than in RAM. When --gres=ssd is set your job’s memory request does not need to include enough to cover the size of any temporary files (as this is a separate resource). These SSDs give the job a slower but very much larger temporary directory. They are allocated exclusively to jobs, so there can only be one such job per node at a time. This gives the job all the available bandwidth of the SSD device but does limit the number of such jobs.

Alternatively you can ignore the provided directory and set TMPDIR yourself, typically to a location in /nesi/nobackup.  This will be the slowest option with the largest capacity. Also if set to nobackup the files will remain after the job finishes, so be weary of how much space your jobs temporary files use. An example of how TMPDIR may be set yourself is shown below,

export TMPDIR=/nesi/nobackup/$SLURM_ACCOUNT/tmp/$SLURM_JOB_ID

Example of copying data into $TMPDIR for use mid-job

The per job temporary directory can also be used to store data that needs to be accessed as the job runs. For example you may wish to read the standard database of Kraken2 (located in /opt/nesi/db/Kraken2/standard-2018-09) from the milan SSDs instead of /opt. To do this, request the NVMe SSD on milan as described above. Then, after loading the Kraken2 module in your Slurm script, copy the database onto the SSD,

cp -r /opt/nesi/db/Kraken2/standard-2018-09/* $TMPDIR

To get Kraken2 to read the DB from the SSDs (and not from /opt), change the KRAKEN2_DEFAULT_DB variable,

export KRAKEN2_DEFAULT_DB=$TMPDIR

The variable KRAKEN2_DEFAULT_DB simply points to the database and is found by module show Kraken2.