- About
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- Containers contain applications in a way that keeps them isolated from the host system on which they run. Containers allow a developer to package up an application with all of the parts it needs, such as libraries and other dependencies, and ship it all out as one package.
- Singularity is a program that can launch containers securely in an HPC environment. Other similar programs are Docker, LXD, and Kubernetes.
- Module
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- Load Singularity Module to run any singularity commands
module load singularity/3.8.1 - Creating Containers
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- You CANNOT create containers on the Biocluster. It has to be done on your local machine. Creating a container requires root access which we do not allow.
- Download Containers
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- You need to use the biologin nodes (biologin-2 and biologin-3) to download containers
- This will not work from the compute nodes as they do not have access to the internet
- Download a pre-existing container from Singularity Hub - https://singularity-hub.org/. singularity-r is an example R container
singularity pull --name r-base_latest.sif shub://nickjer/singularity-r- Download a pre-existing container from Docker - https://hub.docker.com/. r-base is an example R container
singularity pull docker://r-base - Running Containers
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- Do not use the biologin nodes (biologin-2 and biologin-3) to run containers. The login nodes are only allowed to be used to download containers
- From a compute node or a SLURM job script, run the following. r-base_latest.sif is name of the container. R is the program to run in the container. This can be bash to get a command line.
singularity exec r-base_latest.sif R - Stroage
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- Your home folder is automatically mounted
- You should have access to any group folders in /home/groups, /home/labs, and /private_stores
- The local /scratch space is accessible.
- Issues
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- If the container does run properly or can't find the command it is trying to run, it's possible that the program exists in the /home folder within the singularity container. Since we automatically mount the Biocluster's /home folder in the container, it then can't find the command. To get around this, you can remount the Biocluster's /home folder in a new directory.
singularity exec --no-mount hostfs --bind /home:/newhome container.sif
References