Using Containers¶

Researchers can use Docker or Singularity containers within the cluster. This is a great way to run difficult-to-compile applications or to share workflows among colleagues.

See also: Singularity

Running an interactive container¶

User can run within a container interactively, this is great for testing code before running a job. Here is an example of running within a docker container that has the blockchain software called BlockSci:

module load singularity
srun --pty -c 4 --mem=16G bash
singularity pull docker://tislaamo/blocksci
singularity shell blocksci.simg

Once you have typed the singularity shell command you will be within the container and can type the commands available from within the container such as the BlockSci utility blocksci_parser

Running a container in batch¶

Running a batch job with containers is similar to running a regular job, but will ultimately depend on how the container was created, so your mileage may vary. Here is an example batch submit script that will run the autometa software that was created in a docker image, lets name the submit file runContainer.sh:

#SBATCH -J autometa-job
#SBATCH -c 4
#SBATCH --mem=16G
#SBATCH --mailtype=BEGIN,END,FAIL
#SBATCH --mail-user=myemail@email.net
#SBATCH --time=12:00:00

module load singularity
singularity pull docker://jasonkwan/autometa:latest
singularity exec autometa_latest.sif calculate_read_coverage.py somedata.dat

Now to run the file you can:

sbatch runContainer.sh

Note that singularity shell is primarily for interactive use and singularity exec (or possibly singularity run) are for executing the applications that were built within the container directly. It is important to know how the container was created to make effective use of the software.