Apptainer config

Summary of what happened:

Hi container gurus.

We recently updated stuff on our linux server and now Apptainer fails. The issues related to mounting/finding user/session, with errors like

WARNING: user: lookup userid 4651: no such file or directory

Command used

  1. Any of the usual commands to execute an image fails (building works fine).
  2. One of our student (Ruben) figured that adding the arguments:
--bind /users/whatever_user_name:/users \

solves most of it, i.e. containers now run until they can’t find where some user things are (error above) ;

Anyone has experienced this? we can’t seem to find how to configure Apptainer to fix this :frowning:

Any suggestion is welcome

Ruben has found a solution - so I’m posting it for reference, --no-home somehow does not do a good job (half-way run) so instead set the home env for apptainer or singularity – for instance

export SINGULARITY_HOME=/users/rubendorfel
singularity run --cleanenv \
                --bind $data_dir:/data \
                --bind $output_dir:/out \
                $singularity_dir/mriqc29022024.sif \
                /data /out participant --nprocs 20 --mem_gb 100 -f --no-sub