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cz-pulsar: Fix problems with Java tmp dir #930

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cz-pulsar: Fix problems with Java tmp dir #930

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Update destinations.yml.j2
martindemko Oct 6, 2023
b7d04b5
Merge branch 'usegalaxy-eu:master' into master
martindemko Oct 9, 2023
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2 changes: 1 addition & 1 deletion files/galaxy/tpv/destinations.yml.j2
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Expand Up @@ -253,7 +253,7 @@ destinations:
params:
jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-eu/files/staging"
persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-eu/files/persistent"
singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,/cvmfs/data.galaxyproject.org/managed/:/data/db/data_managers/:ro"
singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR:rw,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu:rw,/cvmfs/data.galaxyproject.org/managed/:/data/db/data_managers/:ro,$SCRATCHDIR:/tmp:rw"
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You are mounting SCRATCHDIR twice as it seems. And Singularity was picky about /tmp afaik. Maybe you can check the documentation if mounting to /tmp is safe for Singularity.

Thanks!

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Hi, that's precisely why I am trying this solution cause, from what I have read, singularity is always binding some system locations (e.g., /tmp), but we don't want that. That's why I have set all the TMP, TMPDIR, TEMP to point to SCRATCHDIR, but JVM is ignoring this and tries to use bound /tmp inside the container pointing to /tmp outside. That was fine a few weeks ago, but now I noticed that something has changed, and singularity calls now contain --no-mount tmp parameter, and for example, FastQC is not working because of that. So I hope this direct bind of SCRATCHDIR to be used as /tmp inside the container is just another way of forcing tools to use SCRATCHDIR, if I'm not wrong. I tested such a singularity call and it finished without error. Do you think it may cause some security issues?

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@bgruening bgruening Oct 9, 2023 •
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Sorry, maybe this is a super stupid proposal, but have you tried setting:

_JAVA_OPTIONS: -Djava.io.tmpdir=/foo/bar/something

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Yes, it crossed my mind, and it works. I just wanted to solve this on a bigger scale than just for JAVA apps, originally. However, if you think it's not a good idea, let's try this solution and time will tell what other tools need a patch.

scheduling:
require:
- cz-pulsar
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