Added Support for --reservation Flag for srun_fastsurfer.sh

[xuansean]

Feature Description

I am proposing adding support for a --reservation flag to the srun_fastsurfer.sh script. This would allow users to specify a reservation when submitting jobs to SLURM clusters using reserved GPU nodes.

Motivation

The FastSurfer script does not currently have an option to handle SLURM jobs that need to run on reserved GPU nodes. Without a --reservation flag, users have to manually modify the script, as I did, to submit jobs using a reservation. Adding this feature would streamline the process for users who need to specify a reservation on clusters with dedicated resources.

Although not everyone may need reserved nodes, I believe this would streamline the workflow for those who do.

Additional Context

I have already implemented this change in my local version of the srun_fastsurfer.sh script. Users would define the reservation as:
--reservation <reservation_name>

The changes I made locally:
Define the reservation variable at the beginning of the script:
reservation=""
Add a new case for the --reservation flag in the argument parser:

--reservation)
  reservation="$1"
  shift
  ;;

Update the SLURM job submission section to include the reservation flag if it is defined:

if [[ -n "$reservation" ]]; then
  seg_slurm_sched=(--reservation="$reservation" "${seg_slurm_sched[@]}")
fi

The changes I made are very simple and short, but I hope they help to make FastSurfer even better for users with similar needs.
I’ll leave it up to you to decide whether this would be useful to add to the official script.

[dkuegler]

We would be happy to support such a feature. I am wondering if it would be better (because more general) if this was in the style of --extra_singularity_options this would then enable any additional parameters for slurm scheduling (not just --reservation).

Also, if you are prepating a PR, you will be credited for this change.

Also, it seems your change only enables these reservations for the segmentation. So I believe this should probably be extended to surface pipeline as well (even if the surface pipeline does not use GPUs).

[xuansean]

Thank you for your suggestions! I’m happy to hear that you’re open to supporting this feature. As this is my first time contributing to a GitHub project, I’ll make sure to follow the contribution guidelines on your website.

I appreciate the feedback about generalizing the reservation flag and extending it to the surface pipeline as well. I’ll work on incorporating these improvements. However, I have a deadline coming up next week, so I’ll aim to prepare the PR sometime in the following month. Would it be alright if we continue the conversation here on GitHub, or should I reach out to you via email for further coordination?

[dkuegler]

Github is great, also for documentation purposes.
This specific PR will probably be on hold from our side until mid-November, because I will have to review the contribution and I will be unavailable for a bit. So no hassle :).

Thank you for considering to contribute to FastSurfer!

[dkuegler]

Hi @xuansean ,

is there an update on your effort to add this flag?

Cheers
David