Written for software version 2.5.2.
Singularity is a virtualization tool that allows users to containerize workflows, applications, and environments to allow for portability, customization, and reproducibility. Additionally, Singularity is integrated with the Message Passage Interface (MPI) to be used in High Performance Computing (HPC) systems as well as CADES OpenStack Virtual Machines (VMs). Lastly, you may also utilize Docker containers with Singularity!
Note: These instructions are adapted from the official Singularity documentation.
Getting Started with Singularity
CADES SHPC Condo
Singularity is already installed on CADES SHPC Condos.
To use it, login to condo and do:
module purge module load PE-gnu module load singularity
Singularity Containers over MPI-IB on Condo
By default, singularity does not use the InfiniBand libraries when doing message passing with MPI. In order to make sure Singularity uses the InfiniBand libraries while using MPI, perform the following step after loading the Singularity module:
Following the above step, the Singularity containers should use the InfiniBand libraries when running MPI applications.
CADES Cloud VMs
- A command line environment in Ubuntu or CentOS.
- Software dependencies (these may be numerous):
sudo apt-get update && \ sudo apt-get install \ python \ dh-autoreconf \ build-essential \ libarchive-dev
sudo yum update && \ sudo yum groupinstall 'Development Tools' && \ sudo yum install \ libarchive-devel \ squashfs-tools
The most up-to-date version is housed in a GitHub repository. The software is installed from the source. Use Git to clone the repository and run the following commands.
git clone https://github.com/singularityware/singularity.git cd singularity ./autogen.sh ./configure --prefix=/usr/local --sysconfdir=/etc make sudo make install
Building a Container using an Existing Container
The following command executes the
build command, specifies the path and name of the container (
lolcow.simg), and provides the location of the container on the Singularity Hub (
singularity build lolcow.simg shub://GodloveD/lolcow
Interacting with Containers
There are three primary ways to interact with a Singularity container.
Run: Creates an ephemeral container that runs a predefined script
singularity run lolcow.simgor
Shell: Supplies a command line prompt to interface with the container
singularity shell lolcow.simg
Execute: Sends a command into the container and provides output
singularity exec lolcow.simg
Congratulations! You have successfully deployed a Singularity container!