Update deployment instructions

[seallard]

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

[ChrOertlin]

Looks good, instructions on how to perform alembic migrations from a local machine would be great

[diitaz93]

👍

[Vince-janv]

Nice 👍

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
No data about Duplication

See analysis details on SonarCloud

[seallard]

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