Singularity

Current installation of Singularity on Cypress works on Centos7 nodes only.

​Singularity allows you to create and run containers that package up pieces of software in a way that is portable and reproducible. You can build a container using Singularity on your laptop, and then run it on many of the largest HPC clusters like Cypress. Your container is a single file, and you don’t have to worry about how to install all the software you need on each different operating system and system.

Possible uses for Singularity on Cypress

• Run an application that was built for a different distribution of Linux than Cypress OS (Centos).
• Reproduce an environment to run a workflow created by someone else.
• Run a series of applications (a 'pipeline') that includes applications built on different platforms.
• Run an application from ​Singularity Hub or ​Docker Hub or ​BioContainers without actually installing anything.

Build Singularity Container on Cypress

• Build Singularity Containers from Dockerhub.
• Build Singularity Containers from Recipes

Run Singularity Container on Cypress

For example, the container built this page. In an interactive session by idev --partition=centos7,

[fuji@cypress01-013 SingularityTest]$ singularity exec ubuntu_14.04.sif cat /etc/os-release 
NAME="Ubuntu"
VERSION="14.04.6 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.6 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"

The user in the container is the same as in the host machine.

[fuji@cypress01-013 SingularityTest]$ singularity exec ubuntu_14.04.sif whoami
fuji

Singularity has a dedicated syntax to open an interactive shell prompt in a container:

[fuji@cypress01-013 SingularityTest]$ singularity shell ubuntu_14.04.sif
Singularity> pwd
/home/fuji
Singularity> whoami
fuji
Singularity> cat /etc/os-release
NAME="Ubuntu"
VERSION="14.04.6 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.6 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
Singularity> exit
exit

Use host directories

The container filesystem is read-only, so if you want to write output files you must do it in a bind-mounted host directory. '/home/userid' containing data and software are mounted by default.

Following environ variable sets '/lustre/project/hpcstaff/fuji' as '/home/fuji' in the container.

export SINGULARITY_BINDPATH=/lustre/project/hpcstaff/fuji:/home/fuji

Run containters in a batch job

For example,

#!/bin/bash
#SBATCH --job-name=Singularity # Job Name
#SBATCH --partition=centos7    # Partition
#SBATCH --qos=normal           # Quality of Service
#SBATCH --time=0-00:10:00      # Wall clock time limit in Days-HH:MM:SS
#SBATCH --nodes=1              # Node count required for the job
#SBATCH --ntasks-per-node=1    # Number of tasks to be launched per Node
#SBATCH --cpus-per-task=1     # Number of threads per task (OMP threads)

# Load Singularity module
module load singularity/3.9.0

# Set $TMPDIR in containar to /tmp, keeping $TMPDIR in host (/local/tmp/...)
export SINGULARITYENV_TMPDIR=/tmp

# Mount the lustre directory to home, $TMPDIR to /tmp
export SINGULARITY_BINDPATH=/lustre/project/hpcstaff/fuji:/home/fuji,$TMPDIR:/tmp

# Run container
singularity exec ubuntu_14.04.sif ls

By default, the cache is stored in ~/.singularity; this location can be customized using the environment variable SINGULARITY_CACHEDIR. A subcommand, singularity cache, can be used to manage the cache.