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CarineRey / pcoc

Convergent substitution detection tool based on the PCOC model
GNU General Public License v3.0
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WIP: Some small changes for Singularity #8

Closed aaronk closed 6 years ago

aaronk commented 6 years ago

We use Singularity for a container runtime on our cluster at Harvard. There are a few small changes in entrypoint.sh that I'm proposing, though I haven't gotten everything to work; perhaps you have some insight.

Since Singularity runs as the current user, the LOCAL_USER_ID setting can be bypassed; I just changed the echo from a hard-coded 'root' to whoami so they aren't confused.

Running an xvfb server is also a bit of a problem because /tmp is mapped in by default and we end up with contention on shared resources for files under /tmp/.X11-unix. xvfb-run seems to solve the latter problem for almost all cases, except when running under docker as root (without setting LOCAL_USER_ID). It just seems to hang and I can't get a handle on what it's waiting for.

Any thoughts?

CarineRey commented 6 years ago

Hello, It is a good improvement Thanks a lot for the changes.

aaronk commented 6 years ago

Is it OK for the docker-root use case to fail?

CarineRey commented 6 years ago

I misread your message. I fixed the "root" issue.