Containers¶

The login, interactive and compute nodes have Singularity CE 4.4, with no module to load. You pull a container image on a login node and run it in a job.

Pull or copy the image on a login node, into a directory under /scratch or /data. Pulling downloads and converts the image, which takes minutes and up to several gigabytes:
```
$ cd /scratch/genomics/USERNAME/images
$ singularity pull docker://quay.io/biocontainers/samtools:1.19.2--h50ea8bc_0
```

Run it in a job. The container sees your home directory and the current directory. Bind other directories with --bind:

samtools.job

#$ -S /bin/sh
#$ -N samtools -cwd -j y -o samtools.log
#
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
singularity exec --bind /scratch /scratch/genomics/USERNAME/images/samtools_1.19.2--h50ea8bc_0.sif samtools view -c reads.bam
echo = `date` job $JOB_NAME done

A container that uses a GPU needs --nv on the singularity command and a GPU request on the job. ~hpc/examples/containers has working examples (lolcow.job, test1.job, test2.job) with their logs. The Singularity CE user guide at https://docs.sylabs.io/guides/latest/user-guide/ covers the command itself.

Containers¶

Further reading¶