Transparent Singularity

For more advanced users who wish to use Transparent Singularity directly

Transparent singularity is here https://github.com/NeuroDesk/transparent-singularity/

This project allows to use singularity containers transparently on HPCs, so that an application inside the container can be used without adjusting any scripts or pipelines (e.g. nipype).

Important: add bind points to .bashrc before executing this script

This script expects that you have adjusted the Singularity Bindpoints in your .bashrc, e.g.:

export SINGULARITY_BINDPATH="/gpfs1/,/QRISdata,/data"

This gives you a list of all tested images available in neurodesk:

https://github.com/NeuroDesk/neurocommand/blob/main/cvmfs/log.txt

curl -s https://raw.githubusercontent.com/NeuroDesk/neurocommand/main/cvmfs/log.txt

Clone repo into a folder with the intended image name

git clone https://github.com/NeuroDesk/transparent-singularity convert3d_1.0.0_20210104

Install

This will create scripts for every binary in the container located in the $DEPLOY_PATH inside the container. It will also create activate and deactivate scripts and module files for lmod (https://lmod.readthedocs.io/en/latest)

cd convert3d_1.0.0_20210104
./run_transparent_singularity.sh convert3d_1.0.0_20210104

Options for Transparent singularity:

  • --storage - this option can be used to force a download from docker, e.g.: --storage docker
  • --container - this option can be used to explicitly define the container name to be downloaded
  • --unpack - this will unpack the singularity container so it can be used on systems that do not allow to open simg / sif files for security reasons, e.g.: --unpack true
  • --singularity-opts - this will be passed on to the singularity call, e.g.: --singularity-opts '--bind /cvmfs'

Use in module system LMOD

Add the module folder path to $MODULEPATH

Manual activation and deactivation (in case module system is not available). This will add the paths to the .bashrc

Activate

source activate_convert3d_1.0.0_20210104.sh

Deactivate

source deactivate_convert3d_1.0.0_20210104.sif.sh

Uninstall container and cleanup

./ts_uninstall.sh