Dear HPC community,
Positron is a data science IDE based on VScode (https://positron.posit.co).
One of the interesting feature of the tool is its ability to have a kernel running remotely over a ssh connection. It would be nice for many of us if we could have it works on our HPC cluster, in a containerised environment…
This .ssh/config setup is kind of working for me, as it allows me to run a python kernel remotely on a worker node:
Host yggdrasil
HostName login1.yggdrasil.hpc.unige.ch
User prados
Host yggdrasil-worker
User prados
ForwardAgent yes
StrictHostKeyChecking no
UserKnownHostsFile=/dev/null
ProxyCommand ssh -T yggdrasil salloc bash -c 'nc $SLURM_NODELIST 22'
However, the R kernels are not working in my setup. I suspect there are issues when loading R modules dependencies (got a “ldd” library error). Furthermore, I would like to be able to run latest R version that are not available on the HPC for the moment.
The ideal would be to have the kernel running in this official R container on the worker node:
apptainer exec docker://docker.io/rocker/r-ver:4.5.1 bash
But cannot figure out how to change .ssh/config to have everything work together…
Can someone help me on this ?
Thanks a lot
Julien