Slurm

Job Submission

Slurm jobs can be submitted through a Job Composer app inside Slurm tab. This provides a graphical alternative to submitting jobs from the command line or from environments such as JupyterLab.

Job script examples can be taken from Templates.

Requeueing is disabled in the Job Composer app. If a node is rebooted, the job has to be restarted manually. You may explicitly enable requeueing by adding --requeue if your job supports safe restarts (e.g. uses checkpoints and does not restart from scratch).

Preemption

To allow other users to interrupt your long job (e.g., MD simulation) when they need resources, submit it with --qos=preemptible. If you are the one annoyed by constantly busy resources, use --qos=preempting for short tasks (e.g., neural network training). The preemptible job will be requeued and rescheduled by Slurm on any available node or wait for the preempting job to finish.

Ensure the job supports safe restarts (e.g. uses checkpoints) before submitting with --qos=preemptible — otherwise it will restart from scratch after being requeued!

There is no way to enforce that the preempting job is short, so use this feature responsibly.

Job Time Limit Extension

If your job is likely to hit the time limit before completing, contact an administrator to have it extended.

GRES

Available GPU models for “--gres=gpu:<GPU_MODEL>:<NUM_GPUS>”:

GPU model VRAM
nvidia_geforce_rtx_2080_ti 11 GB
nvidia_geforce_rtx_3070_ti 8 GB
nvidia_geforce_rtx_3080 10 GB
nvidia_rtx_a4500 20 GB
nvidia_rtx_a5000 24 GB
nvidia_rtx_a6000 48 GB

Partitions

Each user is assigned to exactly one partition based on their Unix group (users/intbio/struct_biotech).

Below are default parameters and limits for corresponding Slurm partitions:

users (a.k.a. guests)
  • Nodes: 9–12
  • Allowed groups: users, students
  • Max CPUs per node: 8
  • Max memory per node: 16G
  • Max nodes: 1
  • Default time: 08:00:00
  • Max time: 08:00:00
intbio
  • Nodes: 1–6, 9–14
  • Allowed groups: intbio
  • Default time: 08:00:00
  • Max time: 30-00:00:00
struct_biotech
  • Nodes: 7–8
  • Allowed groups: struct_biotech
  • Default time: 08:00:00

Resource Visibility

Unlike Newton, Darwin enforces strict resource isolation via Slurm cgroups. Limits are not advisory. Users cannot access resources that were not requested (CPU, memory, GPU). GPU devices outside the allocation are not visible (e.g., via nvidia-smi).