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
$$./ts_uninstall.sh$$