Requirements

• Contact us in order to deploy your ssh key for this service.
• Do not forget to run and add your ssh agent when connecting to hpc-login.u-strasbg.fr.
• Load the singularity module :

module load singularity/singularity

Create a singularity image

• Create a directory and move to it.
• Create a image definition file <project_name>.def (e.g. exemple.def)
• Generate the singularity image with the following script:

hpc_login_gen.sh <project_name>

• When successful, the image is generated as <project_name>.sif

Test a singularity image (run on your PC or hpc-login)

singularity run <project_name>.sif

Submit a singularity image (run on cluster nodes)

This is a simple sbatch script example:

#!/bin/bash

#SBATCH -n 8 # Request 8 cores

module load singularity/singularity
singularity run <project_name>.sif

Submit the sbatch script:

sbatch my_script

Singularity with intel18

Create image

• Create a image definition with the following example: jacobi.def
• Generate the singularity image with the following script:

hpc_login_gen.sh <project_name>

• When successful, run the image with the specific bind:

singularity run --bind /opt/intel/compilers_and_libraries_2018.1.163:/opt/intel/compilers_and_libraries_2018.1.163 <project_name>.sif

Singularity with GPU

Create image

• Create a image definition with the following example: gpu.def
• Generate the singularity image with the following script:

hpc_login_gen.sh <project_name>

• When successful, run the image with the specific option:

singularity run --nv <project_name>.sif

Singularity with MPI

Create image

• Create a image definition with the following example: bandwidth.def
• Generate the singularity image with the following script:

hpc_login_gen.sh <project_name>

• When successful, run the image with the specific option:

singularity run --bind /usr/local/openmpi/openmpi-3.1.3-i18:/usr/local/openmpi/openmpi-3.1.3-i18 --bind /opt/intel/compilers_and_libraries_2018.1.163:/opt/intel/compilers_and_libraries_2018.1.163 <project_name>.sif

Transform a docker image to singularity (without MPI)

From the docker hub

From a docker image available on docker hub, create your <project_name>.def file with:

Bootstrap: docker
From: <my_image>:<my_tag>

From a docker local image

• Get an archive from your docker image

docker image save -o my_image.tar image_name:version

• Write the corresponding singularity .def file

  From a docker local image, create your <project_name>.def file with:

Bootstrap: docker
From: hpc-singularity.di.unistra.fr:5000/<my_image>

• Generate the singularity image with the following script:

hpc_login_docker.sh <project_name>

• When successful, the image is generated as <my_image>.sif

Singularity help pages

Singularity official documentation