Fmriprep nu_correct crashed on singularity: disk full?

1

Hi there,

I’m running fmriprep on my hospital HPC by slurm. First it worked fine under my home dir, but after I ran it uner the lab dir, it crahsed at the freesurfer autorecon:

The error was like this:
Number of iterations: 38
CV of field change: 0.000989279
ncendef: ncid 5: No space left on device
Error outputting volume: possibly disk full?
nu_evaluate: crashed while running evaluate_field (termination status=11)
nu_correct: crashed while running nu_evaluate (termination status=65280)
ERROR: nu_correct
Linux cn-0013 3.10.0-1160.31.1.el7.x86_64 #1 SMP Wed May 26 20:18:08 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-00022 exited with ERRORS at Mon Oct 2 14:47:40 EDT 2023

However I am sure that there is plenty of space under the lab directory

I tried to define SINGULARITY_TMPDIR=$workdir as suggested by @Steven but it didn’t work.

Any idea how to fix it?

Thank you very much!

2

Hi!

I had a similar problem. Adding --bind /tmp:/tmp to my singularity command (e.g. singularity exec--bind /tmp:/tmp <container-image.sif> <command>) worked for me.

Best,

Thomas