How to Run Commands in a Singularity from Shell Script

Question

I wish to run a Python script in a singularity container.

In particular, I have attempted writing the following in the shell script

singularity shell <name.sif>
python3 <python-script.py>

I expected the python script to be run within the singularity container, but it outputs a segmentation fault (which occurs when I run the script on its own, outside the singularity container). However, when I try to do this manually by executing the commands individually, it works well. I would like to know how to shell script this properly. Thank you!

Barmar · Accepted Answer · 2024-04-05 16:28:32Z

1

You're starting an interactive Singularity shell. The command after that will be executed when you exit the shell.

Use singularity exec to execute a command inside the container.

singularity exec <name.sif> python3 <python-script.py>

answered Apr 5, 2024 at 16:28

Barmar

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