Open calvinp0 opened 2 months ago
The error you are facing with --export
is because --export
in Slurm is confusing, see this:
https://github.com/NVIDIA/pyxis/wiki/Frequently-asked-questions#why-am-i-getting-errors-when-using-the---export-argument-of-slurm
The error you are facing with
--export
is because--export
in Slurm is confusing, see this: https://github.com/NVIDIA/pyxis/wiki/Frequently-asked-questions#why-am-i-getting-errors-when-using-the---export-argument-of-slurm
Ah, I see, thanks for that. So even if I attempt to add 'ALL' in front of the variables in the --export
section, it will not act like it does in Docker?
It should be close to what docker is doing.
But in your case, even if you fix the export
issue, it will probably still fail if the container entrypoint is attempting to do things that are not possible under pyxis/enroot.
Yeah, I did attempt
srun -p mig -G 0 \
--container-image=/home/calvin.p/deepchem-cuda.sqsh \
--container-mounts=/home/calvin.p/work/CMPNN_HydrogenAbstraction:/home/mambauser/deepchem \
--container-save=/home/calvin.p/deepchem-cuda-modified.sqsh \
--container-entrypoint \
--no-container-remap-root \
--export ALL,ENV=deepchem_cuda,USER=mambauser \
--pty bash
But that lead me to logging in as my current username on the server, calvin.p
and the conda environment hadn't been initialized.
In the end, the workaround I am using is:
srun -p mig -G 0 \
--container-image=/home/calvin.p/deepchem-cuda.sqsh \
--container-mounts=/home/calvin.p/work/CMPNN_HydrogenAbstraction:/home/mambauser/deepchem \
--container-save=/home/calvin.p/deepchem-cuda-modified.sqsh \
--container-entrypoint \
--container-remap-root \
--export ENV=deepchem_cuda \
--pty bash -c "su - mambauser"
This way, even though it shows me as root
in whoami
, I have the conda environment initialized and it starts in me in /home/mambauser/
directory.
Thanks for the help!
Hey, I am relatively new to
enroot
andpyxis
and utilisingsrun
, so apologies in advanceI am trying to use a container based upon
micromamba
container from here.I want to log in as the user
mambauser
that is already set in the Docker image as logging in as this user will automatically activate the micromamba environment. Usually in Docker I would pass-u mambauser
in the command line.I tried to understand the Pyxis documentation, but also realised that our servers are not using the latest Pyxis as
--container-env
is not available. So I tried to use the--export
function and receive this error:So is there anyway that I can log in as
mambauser
?