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Clinical-Genomics / trailblazer

Keep track of and manage analyses
MIT License
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Update deployment instructions #447

Closed seallard closed 4 months ago

seallard commented 4 months ago

Update deployment instructions to reflect how to use the CLI images on Hasta.

sonarcloud[bot] commented 4 months ago

Quality Gate Passed Quality Gate passed

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0 Accepted issues

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seallard commented 4 months ago

Had to give up on this. Basically, when running the image you need to mount slurm from the host (to be able to use squeue). However, to authenticate you need access to the munge config on the host as well, specifically the socket and key. You need sudo for that, they cannot be mounted. Which means we cannot retrieve info about the slurm jobs from inside the container.

If we had somewhat more recent version of SLURM, we could retrieve the info via the slurm rest API instead.

This is the error 

[sebastian.allard@hasta:~] [S_base] $ singularity run --bind /usr/bin/squeue \
    --bind /etc/slurm \
    --bind /usr/lib64/slurm \
    --bind /usr/bin/munge \
    --bind /var/run/munge \
    --bind /usr/lib64/libmunge.so.2 \
    /home/proj/stage/singularity_containers/trailblazer_latest.sif squeue --all
squeue: error: If munged is up, restart with --num-threads=10
squeue: error: Munge encode failed: Failed to access "/var/run/munge/munge.socket.2": No such file or directory
squeue: error: authentication: Socket communication error
slurm_load_jobs error: Protocol authentication error