container automatically mount path of input file?

[BoPeng]

Currently we only mount pwd by default but it seems to make sense to mount directories for _input

[gaow]

Sounds reasonable but why not directories of _output if applicable? How about all paths objects in the global/local environment, too?

[BoPeng]

You had a good argument on not sharing $HOME, but singularity

By default singularity bind mounts /home/$USER, /tmp, and $PWD into your container at runtime. You can specify additional directories to bind mount into your container with the - -bind option.

I suppose the idea is that singularity container tries to blur the boundary between container and host system so it tries to respect configurations in $HOME (e.g. even if a singularity R is used instead of host R).

[gaow]

I suppose the idea is that singularity container tries to blur the boundary between container and host system

it sounds bad idea right? suppose i have a messed up host and I rely on singularity to save me from my mess. It would be so disappointing it gets itself into that mess. Wondering if we should / could "undo" it.

[BoPeng]

I am not sure there is an option for it but you can always open a ticket if you have a good argument/example to demonstrate the problem. The cool thing about singularity is that it (tries to) behaves like a regular command in many cases so a singularity wrapped R would work like your local R but with all dependencies inside.

[gaow]

I have not used singularity myself. But since you are on it, maybe we can try get it work in SoS and I'll try to come up with an R related example to show how it messes up the self-contained environment.