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What version of Apptainer (or 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 dcm2niix --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 ran the command?
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, which should not be so. 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 a couple days ago this command was running fine on older data. Today, however, when I ran this command on new fMRI data, I suddenly saw this error. Perhaps it's because the new data I am trying to convert has a lot of dicom files, but that shouldn't really make Synology crash, I don't think.
What OS/distro are you running
Ubuntu 18.04.6 LTS
How did you install Apptainer
From source.
The text was updated successfully, but these errors were encountered:
Version of Apptainer
What version of Apptainer (or 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 dcm2niix --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 ran the command?
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, which should not be so. When I ran the command, I immediately saw this error:
FATAL: failed to initialize runtime: engine "" is not found
Full debug output:
What's weird is that I've ran this command before with no error at all. Just a couple days ago this command was running fine on older data. Today, however, when I ran this command on new fMRI data, I suddenly saw this error. Perhaps it's because the new data I am trying to convert has a lot of dicom files, but that shouldn't really make Synology crash, I don't think.
What OS/distro are you running
Ubuntu 18.04.6 LTS
How did you install Apptainer
From source.
The text was updated successfully, but these errors were encountered: