Running on a cluster (HPC)

Before the Connectome Mapper 3 BIDS App can be run on a cluster, it first needs to be saved to an Singularity-compatible image file (Please check the Singularity documentation website for more details).

Conversion to a Singularity image

It actually exists two options for Docker to Singularity container image conversion. Let’s say we want to store Singularity-compatible image file in ~/Softwares/singularity/.

Option 2 : Using singularity directly

$ singularity build ~/Softwares/singularity/cmp-v3.0.0-beta-RC2.simg docker://sebastientourbier/connectomemapper-bidsapp:v3.0.0-beta-RC2

This command will directly download the latest version release of the Docker image from the DockerHub and convert it to a Singularity image.

Advantage(s): Can be executed on the cluster directly

Disadvantage(s): Has shown to fail because of some docker/ singularity version uncompatibilities

Running the singularity image

The following example shows how to call from the terminal the Singularity image of the CMP3 BIDS App to perform both anatomical and diffusion pipelines for sub-01, sub-02 and sub-03 of a BIDS dataset whose root directory is located at ${localDir}:

$ singularity run --bind ${localDir}:/bids_dir --bind ${localDir}/derivatives:/output_dir \
~/Softwares/singularity/cmp-v3.0.0-beta-RC2.simg \
/bids_dir /output_dir participant --participant_label 01 02 03 \
--anat_pipeline_config /bids_dir/code/ref_anatomical_config.ini \
--dwi_pipeline_config /bids_dir/code/ref_diffusion_config.ini \
--fs_license /bids_dir/code/license.txt \
--number_of_participants_processed_in_parallel 3

Useful singularity commands

  • Display a container’s metadata:

    $ singularity inspect ~/Softwares/singularity/cmp-v3.0.0-beta-RC2.simg
  • Clean cache:

    $ singularity cache clean

Created by Sebastien Tourbier - 2020 Mar 04 - Latest update: 2020 Jun 03