Inspired from https://github.com/abretaud/docker-sf-blast
The following environment variables are available:
SLURMGID: '992' # the gid of the slurm group (should be the same as on your slurm cluster)
SLURMUID: '992' # the uid of the slurm user (should be the same as on your slurm cluster)
MUNGEGID: '991' # the gid of the munge group (should be the same as on your slurm cluster)
MUNGEUID: '991' # the uid of the munge user (should be the same as on your slurm cluster)
DRMAA_LIBRARY_PATH: '/etc/slurm/drmaa/lib/libdrmaa.so.1'
To use DRMAA, you need to pay attention to several things:
Slurm libraries are installed in version 21.08 (from Debian Buster). It should match the version installed on your cluster to work properly.
If you're using Slurm, you should set the DRMAA_METHOD environment variable to slurm
Make sure that the folder from where the jobs are launched is available on all cluster nodes!
You need to mount the slurm configuration files from your cluster to the /etc/slurm/ directory. You also need to mount the libdrmaa.so.1 library to $DRMAA_LIBRARY_PATH path (/etc/slurm/drmaa/lib/libdrmaa.so.1 by default). And you need to mount the munge conf directory which stores the munge key specific to your cluster. All this should look something like that:
volumes:
- /etc/slurm/slurm.conf:/etc/slurm/slurm.conf:ro
- /etc/slurm/gres.conf:/etc/slurm/gres.conf:ro
- /etc/slurm/cgroup.conf:/etc/slurm/cgroup.conf:ro
- /etc/slurm/slurmdbd.conf:/etc/slurm/slurmdbd.conf:ro
- /etc/slurm/drmaa/:/etc/slurm/drmaa/:ro
- /etc/munge/:/etc/munge/:ro
Jobs will probably need to be launched by a user known by the scheduler. You will need to use the following options to configure this:
UID: the uid of the user
GID: the gid of the user
RUN_USER: the username of the user
RUN_GROUP: the group of the user
OTHER_GID: list of supplementary gid (comma separated) which the user is also a member of
OTHER_RUN_GROUP: list of supplementary group (comma separated) which the user is also a member of. The order must match the order used for OTHER_GID.