Use clustermq with HPC that requires interactive session

[Aariq]

My current HPC requires an interactive session to load R (module load R doesn't work on login node). Is there a way to get clustermq working? They provide a nice shortcut interactive that does:

salloc --job-name=interactive --mem-per-cpu=4GB --nodes=1  --ntasks=1 --time=01:00:00 --account=windfall --partition=windfall

Could I add interactive somewhere to either my ~/.ssh/config or in ssh_clustermq.tmpl, and then add an appropriately long timeout to get this working? I haven't had success so far, and I just wanted to see if this was even a possibility before trying much more.

[mschubert]

I'm assuming you are referring to using clustermq via SSH because you mentioned the log/template files. You can do that in the SSH.tmpl file. The line that starts R:

clustermq/inst/SSH.tmpl

Line 5 in 7812577

"R --no-save --no-restore -e \

will perform these steps if you modify it to something like

    "srun ..parameters.. module load R && R --no-save --no-restore -e \

(I think you need srun instead of salloc here)

Alternatively, if you have an interactive node that you can connect to without a job allocation and would like to use that instead, you can specify this host in your ~/.ssh/config via ProxyJump.