--contain, --containall, and --cleanenv

[Ben Fulton]

One of our systems has a default PYTHONPATH set, which causes problems with containers being able to run Python scripts correctly. I assume the correct solution is to use one of these flags, but could I get some details on exactly what each one does? The documentation states

• –contain: Contain suggests that we want to better isolate the container runtime from the host. Adding the --contain flag will use minimal /dev and empty other directories (e.g., /tmp).
• –containall: In addition to what is provided with --contain (filesystems) also contain PID, IPC, and environment.
• –cleanenv: Clean the environment before running the container.

What does it mean to "clean the environment"? What are "empty other directories"? Does containall actually clear all environment variables?

Thanks,

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Ben Fulton

Research Technologies

Scientific Applications and Performance Tuning

Indiana University

[Tyler Trafford]

This doesn't answer your question, but you can run python with "python -Es" if you want it to ignore all PYTHON* variables and the user's site packages (~/.local/lib/python*, usually).

-Tyler

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Tyler Trafford

[Dave Godlove]

Hi Ben,

Empty other directories means that Singularity will create new empty directories and bind them overtop of the directories that would normally be automatically bind mounted into the container.  For instance /tmp is normally bind mounted into the container by default.  If you use ls /tmp inside of a container you will normally see everything that is in there from the host.  If you use the --contain flag it will be empty.

The --cleanenv will set up a minimal environment for your container to run in.  Check the output of env inside the container with and without that flag.   

Dave

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Tyler Trafford

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Dave Godlove

Engineering Coordinator, Sylabs Inc.

sylabs.io