Add TMPDIR environment variables to handle non-default temp directories

[marcelzwiers]

See Github issue #11

[stebo85]

thank you for sending that pull request. I am hoping to be able to test this next week. Did you test your changes on your system and did it work? I think it also needs mount points in addition for this to work?

[marcelzwiers]

Yes, you are right. I copied over what I had on our HPC, but indeed for us the non-default tmpdir is automatically mounted on all apptainers. So perhaps it is better to script this and check if any of the TMPDIR variables (as used in this PR) are non-empty and then bindmount them as /tmp?

[marcelzwiers]

So something like:

CUSTOMTMPDIR="/tmp"
for CUSTOMDIR in $TMP $TMPDIR $TEMP $TEMPDIR; do
   CUSTOMTMPDIR=$CUSTOMDIR
done

apptainer run --cleanenv --no-mount tmp --bind ${CUSTOMTMPDIR}:/tmp etc

[stebo85]

cool! Does this work on your system now? Then I test on the HPCs I have access to and we can make it available for all

[marcelzwiers]

If I manually edit our singularity run-scripts likewise then it works for us :-)

[stebo85]

thank you for confirming :)

[marcelzwiers]

I didn't look into setting this bind option centrally, perhaps that is also possible as an alternative

[marcelzwiers]

https://apptainer.org/docs/user/main/bind_paths_and_mounts.html#system-defined-bind-paths https://apptainer.org/docs/user/main/cli/apptainer_config_global.html#apptainer-config-global

[stebo85]

yes, that would also be possible

[marcelzwiers]

Indeed, I now see that there exists a variable for this, i.e. APPTAINER_WORKDIR (see here). But that also does something with the HOME directory?

[marcelzwiers]

I just tested the new run_fetch code and it works nicely :-)