Mriqc in combination with singularity 3


Dear (mriqc) experts,

I have been running mriqc on HPC. This worked quite well in the past.
However, the HPC colleages upgraded the singularity version (3.0.1-1.e17)
My mriqc container crashes and after rebuilding (following Preferred way to create MRIQC singularity container?) it is broken and cannot find the run driver after calling:
FATAL: no run driver found inside container

Did anyone solve this matter or know howto? Otherwise we’ll have to rollback the singularity version.

Many thanks! Jan-Bernard


Maybe @vsoch would have some ideas of why this could be happening?


Yes I’d be happy to look into this. Could you point me to your recipe?

1 Like

Dear Oscar and Vanessa,

Thanks for your concern.
I have no particular recipe, and issue the command:
$> singularity pull docker://poldracklab/mriqc:latest

WARNING: Authentication token file not found : Only pulls of public images will succeed

INFO: Starting build…

Getting image source signatures

Skipping fetch of repeat blob sha256:c832082614738021cf51d68e84457a45a3f85dbe0ddbb93000c5dc5aae77fe93

INFO: Build complete: mriqc_latest.sif

$> singularity run mriqc_latest.sif

WARNING: passwd file doesn’t exist in container, not updating
WARNING: group file doesn’t exist in container, not updating
FATAL: no run driver found inside container


To followup:

I resolved this problem: In the end it was a problem with the Singularity cache. After clearing the cache (so before, half of the mriqc image was built with old cache files, I’m assuming the checksum procedure isn’t foolproof). No problems with mriqc whatsoever!

Thanks for your help and interest!