ERROR : No valid /bin/sh in container

[Brunnocampos1]

Dear all,

I am new using Synb0 and singularity (actually, using Linux (mine, is Ubuntu 18)) and I am trying to execute the singularity container to run the Synb0. The image was created into the home/user dir, with the following command:

singularity pull docker://hansencb/synb0

(whitout sudo)

This, created an image file with ~11Gb at /home/user/ .

when I try o run the line:

export synb0PATH=/home/user/
singularity run -e -B "$imgPath/SynBo/INPUTS"/:/INPUTS \ 
-B "$imgPath/SynBo/OUTPUTS"/:/OUTPUTS \ 
-B "$imgPath/SynBo/license.txt":/extra/freesurfer/license.txt $synb0PATH

I instantaneously get the error:

ERROR  : No valid /bin/sh in container
ABORT  : Retval = 255

I found no other folder or files of SynB0.

Thank you all in advance

[Brunnocampos1]

Now, I added the image filename to the PATH:

singularity run -e -B "$imgPath/SynBo/INPUTS"/:/INPUTS -B "$imgPath/SynBo/OUTPUTS"/:/OUTPUTS -B "$imgPath/SynBo/license.txt":/extra/freesurfer/license.txt $synb0PATH"synb0.simg"

and the error changed to:

ERROR  : Failed to mount squashfs image in (read only): Invalid argument
ABORT  : Retval = 255

Any tip?

[schillkg]

Hello! A couple of quick questions - what version of singularity are you using? Older versions are the most likely cause here. Second, are you using a network mounted file system?

Thank you.

[Brunnocampos1]

Dear Dr Schilling, thank you! Indeed my issue was due to an OLD Singularity version, I followed the first tutorial I found and that lead me to an almost uninstallable Singularity 2.0 installation. After basically removing file by file manually, I could proceed with the newest version (3.8.2) installation and it is running fine now. Congrats for your idea and tool, by the way.

Just to register here: The old Singularity version was 2.0. I am creating the container locally, in a local workstation.

Thank you very much!