Singularity on the SCC

The standard singularity software is installed in /opt/singularity.

The main command for using singularity is /opt/singularity/bin/singularity and can be called directly with singularity. Please refer to Singularity documentation at http://singularity.lbl.gov/ for general use information.

Wrapper for Singularity

In order to facilitate integration with the SCC, we provide a command wrapper scc-singularity:

[rcs@scc1 ~] scc-singularity run my_container.sif

The wrapper is available on the PATH for general use and provides the following features:

  1. Automatically binds:
    • user’s home directory
    • user’s project spaces
    • the node(s) /scratch
    • /usr/local
    • /share
  2. Preserves and passes into the container SCC environment variables:
    • DISPLAY
    • NSLOTS
    • TMPDIR
    • USER
  3. Will detect if using GPU(s) and pass CUDA_VISIBLE_DEVICES into the container.

If the container has code installed into its own /usr/local directory, then pass the --nolocal flag to scc-singularity:

[rcs@scc1 ~] scc-singularity --nolocal run my_container.sif

The --scc-preview and --scc-debug commands can be used to print out the command executed by the scc-singularity wrapper:

[rcs@scc1 ~] scc-singularity --scc-preview run my_container.sif
/usr/bin/singularity run -e  -B /share -B /usr1 -B /usr2 -B /usr3 -B /usr4 -B /var/spool/sge -B /project -B /projectnb -B /projectnb2 -B /scratch -B /net -B /ad -B /usr/local -B /var/lib/dbus/machine-id my_container.sif
preview mode - command not executed

Interactive Usage

Singularity can be used to run a shell interactively inside a container. This is accomplished using the shell subcommand. To try these commands, first get a copy of a container running the Debian 11 operating system from the Sylabs container library. This will create a container file called debian_11.sif:

[rcs@scc1 ~] singularity pull library://debian:11

Now try to run the container:

[rcs@scc1 ~] singularity shell debian_11.sif
Singularity> grep PRETTY_NAME /etc/os-release
PRETTY_NAME="Debian GNU/Linux 11 (bullseye)"

It is important to note that standard “shell” mode will not provide full environment settings required to interact with modules and other SCC provided features.

The scc-singularity command has an additional subcommand myshell which invokes your default login shell with your complete login environment.

[rcs@scc1 ~] scc-singularity myshell debian_11.sif

 

Batch Usage

There are two main subcommands for running Singularity in batch: exec and run.

  • Use the exec subcommand to execute the specified command within the container. 
    #!/bin/bash -l
#$ -P proj_name
#$ -N singularity_exec
#$ -j y
# Run the container and execute a command within it.
scc-singularity exec debian_11.sif grep PRETTY_NAME /etc/os-release

 

  • Use the run subcommand to run the command that the container is pre-configured to run. 
    #!/bin/bash -l
#$ -P proj_name
#$ -N singularity_run
#$ -j y
# Run the container and run its preconfigured command.
scc-singularity run debian_11.sif