Singularity 2016

Introduction

Singularity is a portable application stack packaging and runtime utility. With Singularity, you can provide whole working environments and install the OS and Software you neet to use within a container. In the best case, "this means that you don’t have to ask your cluster admin to install anything for you - you can put it in a Singularity container and run."[¹ http://singularity.lbl.gov/]

Installed version

The currently installed version is available on environment hpc-env/6.4

Singularity/2.4.2-GCCcore-6.4.0

Using Singularity

Singularity can be a very powerful tool to create containers with your favoured OS environment and all the tools that you need - completely without the help or permission of the HPC administrators. But in order to use Singularity, you need to create your own containers on your own local device since you need root permissions to do so which is not possible on our cluster. in the following steps we will show you exemplarily how to create your own containers, fill them with the software you need and how you use them to do your work.

Installation

In our example, we use CentOS 7. With other distributions, the procedure should be similar but some steps might slightly differ, especially the needed dependencies for the installation.

To install Singularity on your system, you need to install one dependency, clone the GitHub repository and perform confingure/make/make install. To make this as simple as possible, open a terminal, and copy-paste this lines:

cd ~ && mkdir singularity_install && cd singularity_install
sudo yum install libarchive-devel -y
git clone https://github.com/singularityware/singularity.git
cd singularity
git fetch --all
git checkout 2.6.1
./autogen.sh
./configure --prefix=/usr/local
make
sudo make install

Now, singularity should be installed on your system. Just to be sure, check the version of the newly installed software:

singularity --version

Singularity should display the installed version.

#######WORK IN PROGRESS#######

If you want to find out more about Singularity on the HPC Cluster, you can use the command

module spider Singularity

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load hpc-env/6.4
module load Singularity

Always remember: this command is case sensitive!

To get familiar with the commands and options available for Singularity, you can use the help function:

singularity --help

Documentation

The developers offer a detailed website with further information and a Quick Stard Guide.