Singularity crashes when running heudiconv fmri data conversion

[John-Chin]

Version of Singularity:

What version of Singularity are you using?

singularity version 3.1.0

Expected behavior

I ran this command:

singularity run --bind /home:/home --bind /mnt:/mnt --cleanenv /mnt/tools/singularity/heudiconv-0.13.0.simg -d /mnt/fmri/rawdata/LD001/*/*dcm -b -o /mnt/fmri/subjects -f convertall -s 001 -c none --overwrite --minmeta

For background, I am trying to run a fMRI data conversion command (dicom to BIDS) via heudiconv on the singularity container. (Loosely following this tutorial)

What did you expect to see when you do...?
When I ran the singularity run command, I expected to see a new folder LD001 created in my output directory (-o /mnt/fmri/subjects) that contains a file structure of converted fmri nifti data files and sidecar json files.

Actual behavior

What actually happened? Why was it incorrect?
Unfortunately nothing happened because when I ran the command, I immediately saw this error:
FATAL: failed to initialize runtime: engine "" is not found

Full debug output:

VERBOSE [U=0,P=10140]      print()                       Set messagelevel to: 5
DEBUG   [U=0,P=10140]      init()                        PIPE_EXEC_FD value: 7
VERBOSE [U=0,P=10140]      init()                        Container runtime
VERBOSE [U=0,P=10140]      is_suid()                     Check if we are running as setuid
DEBUG   [U=0,P=10140]      init()                        Overlay seems supported by kernel
DEBUG   [U=0,P=10140]      init()                        Drop privileges
DEBUG   [U=1000,P=10140]   init()                        Read json configuration from pipe
DEBUG   [U=1000,P=10140]   init()                        Set child signal mask
DEBUG   [U=1000,P=10140]   init()                        Wait completion of stage1
VERBOSE [U=1000,P=10151]   priv_escalate()               Get root privileges
DEBUG   [U=0,P=10151]      set_parent_death_signal()     Set parent death signal to 9
DEBUG   [U=0,P=10151]      prepare_stage()               Entering in stage 1
DEBUG   [U=1000,P=10151]   set_parent_death_signal()     Set parent death signal to 9
VERBOSE [U=1000,P=10151]   init()                        Spawn stage 1
VERBOSE [U=1000,P=10151]   startup()                     Execute stage 1
FATAL   [U=1000,P=10151]   getEngine()                   failed to initialize runtime: engine "" is not found
VERBOSE [U=1000,P=10140]   init()                        stage 1 exited with status 255

What's weird is that I've ran this command before with no error at all. Just yesterday when I was running this command on new fMRI data, did I suddenly see this error. Perhaps it's because the new subject data I was trying to convert yesterday had a lot of dicom files, but it was nothing unreasonable.

How did you install Singularity

By source.

[github-actions]

New issues are no longer accepted in this repository. If singularity --version says singularity-ce, submit instead to https://github.com/sylabs/singularity, otherwise submit to https://github.com/apptainer/apptainer.