SLURM some basic commands

Slurm offers many commands you can use to interact with the system.

The sinfo command gives an overview of the resources offered by the cluster

sinfo -N -l

The squeue command shows to jobs those resources are currently allocated (qstat). This command lists currently running jobs (they are in the RUNNING state, noted as ‘R’) or waiting for resources (noted as ‘PD’, short for PENDING).

squeue

You can show more complex information with -o option, -i parameter allow lauch squeue every n seconds

squeue -o "%.18i %.9P %.8j %.8c %.8u %.8T %.10M %.9l %.6D %R %D" -i 5

Allocate resources by using srun command

If you need simply to have an interactive Bash session on a compute node, with the same environment set as the batch jobs, use srun. srun allows allocate a interactive session with ressources determinated in parameters (similar to qrsh or qhost SGE mode).

srun --pty bash 
or
srun -p "partition name"--time=4:0:0 --pty bash

How do you create a job?

A job consists in two parts: resource requests and job steps.

Resource requests consist in a number of CPUs, computing expected duration, amounts of RAM or disk space, etc. Job steps describe tasks that must be done, software which must be run.

The typical way of creating a job is to write a submission script. A submission script is a shell script. If they are prefixed with SBATCH, are understood by Slurm as parameters describing resource requests and other submissions options. You can get the complete list of parameters from the sbatch manpage man sbatch.

in this exemple job.sh contains ressources request (lines starting with #SBATCH) and a sleep unix command.

#!/bin/bash

#SBATCH --job-name=test
#SBATCH --output=res.txt
#SBATCH --ntasks=1
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100

sleep 00:03:00 #slepping 3 minuts

job.sh request one CPU for 10 minutes, along with 100 MB of RAM, in the default queue. When started, the job would run a sleep unix command.

The sbatch command allows submit a script.

sbatch job.sh

Interestingly, you can get near-realtime information about your running program (memory consumption, etc.) with the sstat command

sstat -j job_id

If you want to cancel a job, use scancel command (qdel)

scancel job_id 

If you want to kwon ressources used by a finished job, use seff command

seff job_id

License

The resource material is licensed under the Creative Commons Attribution 4.0 International License (here).