Help apptainer

[CPernet]

right now I have issues with apptainer beyond fast surfer, however I believe that the right way to call it now should be, for instance,

apptainer exec --nv ./fastsurfer-gpu.sif \ -B /home/user/my_mri_data:/data \ -B /home/user/my_fastsurfer_analysis:/output \ -B /home/user/my_fs_license_dir:/fs_license \ /fastsurfer/run_fastsurfer.sh fastsurfer-flags

for me it always wants at least 2 arguments for the build pointing directly to the image -- but I may be totally wrong! would be nice to have an example in the readme with that update for apptainer, thx a lot

[dkuegler]

apptainer should be called the same way singularity is called see https://github.com/Deep-MI/FastSurfer#example-2-fastsurfer-singularity

With respect to your example, make sure your linebreaks and the escaping of linebreaks is correct.

Also all apptainer arguments (like -B) go before the image name, fastsurfer arguments after.

[m-reuter]

I assume this is resolved, if not feel free to re-open.

[CPernet]

FYI apptainer messed up 'users' permissions on our server this can be resolved export

SINGULARITY_HOME=/users/yourusername
singularity run --cleanenv \
                 other arguments

[dkuegler]

Aptainer should often be run with --no-home as well (otherwise it will mount your user dir and your user options into the container). See our docs as well.

[CPernet]

Yes totally but somehow with no home it only runs always then cannot figure the user ID ... using both does the trick