CODEWITHSUNDEEP
dockervirtual-machinebinaryfilesapptainer
zhujh
zhujh

Reputation: 1

Script in apptainer work for one user but stuck for other users in computing clusters

We tried to pull a docker from docker hub and use the apptainer to shell into it and run the script inside the shell. However, only one user can run the script correctly but others will get stuck after setting the LD variables.

I've added the -X flags and see the script stuck at execution of the executable binary file. We've tried to set the ~/.bashrc and ~/.bash_profile for user who can run the script to the default setting, the apptainer can still work. Is there any other possible troubleshooting direction we can go?

Minimal reproducible example/ Procedure:

  1. apptainer pull --name quantisnp_docker docker://samesense/quantisnp-matlab:byHand
  2. apptainer shell -H <Directory that contain quantisnp_docker> quantisnp_docker
  3. sh /usr/local/bin/quantisnp/quantisnp/linux64/run_quantisnp2.sh /usr/local/bin/quantisnp/MATLAB/MATLAB_Compiler_Runtime/v79 --chr 1:23 --outdir <outdir> The script will stuck here.

Upvotes: 0

Views: 81

Answers (0)

Related Questions