SPM permission denied on HPC in a Singularity container

Hi all,

I’m currently trying to run Nipype inside a Singularity container (which was created on my local machine by converting the Nipype Docker image to Singularity). The workflow includes FSL and SPM and runs well inside the Docker container on my local machine. However, when attempting to run the workflow in the Singularity container on our lab’s HPC, I run into the following error:

Standard error:
/bin/sh: 1: /opt/spm12/run_spm12.sh: Permission denied

Return code: 126
Interface MatlabCommand failed to run.

I didn’t expect permission issues after having everything in Singularity. Any ideas on what the fix could be here?


@danjgale - the best would be to create a docker container using neurodocker, which has the appropriate mechanics to make the environment variables and matlab MCR paths proper to support singularity execution.

as a test you could pull this really large container (10G): satra/nhw17:0.6

but the intent of neurodocker is to allow you to build containers for your needs very quickly.