Convenient Slurm Commands

This page will give you a list of the commonly used commands for SLURM. Although there are a few advanced ones in here, as you start making significant use of the cluster, you’ll find that these advanced ones are essential!

A good comparison of SLURM, LSF, PBS/Torque, and SGE commands can be found here.

Also useful:

• What is FairShare and What’s My Lab’s Score?
• Managing FairShare in Multiple Groups
• Common Cluster Pitfalls
• My Job is Pending

General commands

Get documentation on a command:

Try the following commands:

Account & Partition Information

To see the Slurm account you are associated with on the cluster:

sacctmgr show associations where user=<username>

To see all the associations of your Slurm account:

sacctmgr -p show assoc format=cluster,account,user,qos,priority | grep <labname>

To see the status of nodes on a partition:

sinfo -p <partition-name>

To see a list of jobs running and pending on a partition:

showq -p <partition-name> -o

Submitting jobs

The following example script specifies a partition, time limit, memory allocation and number of cores. All your scripts should specify values for these four parameters. You can also set additional parameters as shown, such as jobname and output file. For This script performs a simple task — it generates of file of random numbers and then sorts it. A detailed explanation the script is available here.

#!/bin/bash
#
#SBATCH -p shared # partition (queue)
#SBATCH -c 1 # number of cores
#SBATCH --mem 100 # memory pool for all cores
#SBATCH -t 0-2:00 # time (D-HH:MM)
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
for i in {1..100000}; do
echo $RANDOM >> SomeRandomNumbers.txt
donesort SomeRandomNumbers.txt

Now you can submit your job with the command:

sbatch myscript.sh

Information on jobs

List all current jobs for a user:
squeue -u <username>

List all running jobs for a user:
squeue -u <username> -t RUNNING

List all pending jobs for a user:
squeue -u <username> -t PENDING

List priority order of jobs for the current user (you) in a given partition:
showq-slurm -o -u -q <partition>

List all current jobs in the shared partition for a user:
squeue -u <username> -p shared

List jobs run by the current user since a certain date:
sacct --starttime <YYYY-MM-DD> 

List jobs run by a user during an interval marked by a start, -S, and an end, -E, date along with the information on the job id, the allocated node, partition, number of allocated CPUs, state of the job, and the start time of the job:

sacct -S <YYYY-MM-DD> -E <YYYY-MM-DD> -u <username> --format=JobID,nodelist,Partition,AllocCPUs,State,start

If the end date is left out, then the sacct command will list the jobs starting from the start date until now.

List detailed information for a currently running job (useful for troubleshooting):
scontrol show jobid -dd <jobid>

List status info for a currently running job:
sstat --format=AveCPU,AvePages,AveRSS,AveVMSize,JobID -j <jobid> --allsteps

To view the command line argument at the time of submission of a job:
sacct -j <jobid> -o submitline -P

To see the batch script of a submitted job:
sacct -j <jobid> --batch

Once your job has completed, you can get additional information that was not available during the run. This includes run time, memory used, etc.
To get statistics on both completed jobs and currently running jobs by jobID:
sacct -j <jobid> --format=JobID,JobName,MaxRSS,Elapsed,nodelist -X

To view the same information for all jobs for a user:
sacct -u <username> --format=JobID,JobName,MaxRSS,Elapsed

To view how efficiently a job ran on the cluster, after it is completed, execute either the seff or seff-account command to get summary statistics on it:

seff <JOBID>

seff-account -A <LABNAME> -S <STARTTIME> -E <ENDTIME>

where <STARTTIME> & <ENDTIME> are in the format: YYYY-MM-DD

Controlling jobs

To cancel one job:
scancel <jobid>

To cancel all the jobs for a user:
scancel -u <username>

To cancel all the pending jobs for a user:
scancel -t PENDING -u <username>

To cancel one or more jobs by name:
scancel --name myJobName

To hold a particular job from being scheduled:
scontrol hold <jobid>

To release a particular job to be scheduled:
scontrol release <jobid>

To requeue (cancel and rerun) a particular job:
scontrol requeue <jobid>

Job arrays and useful commands

As shown in the commands above, its easy to refer to one job by its Job ID, or to all your jobs via your username. What if you want to refer to a subset of your jobs? The answer is to submit your job set as a job array. Then you can use the job array ID to refer to the set when running SLURM commands. See the following excellent resources for further information:
Running Jobs: Job Arrays
SLURM job arrays

To cancel an indexed job in a job array:
scancel <jobid>_<index>
e.g.
scancel 1234_4

Advanced (but useful!) commands

The following commands work for individual jobs and for job arrays, and allow easy manipulation of large numbers of jobs. You can combine these commands with the parameters shown above to provide great flexibility and precision in job control. (Note that all of these commands are entered on one line)

Suspend all running jobs for a user (takes into account job arrays):
squeue -ho %A -t R | xargs -n 1 scontrol suspend

Resume all suspended jobs for a user:
squeue -o "%.18A %.18t" -u <username> | awk '{if ($2 =="S"){print $1}}' | xargs -n 1 scontrol resume

After resuming, check if any are still suspended:
squeue -ho %A -u $USER -t S | wc -l

The following is useful if your group has its own queue and you want to quickly see utilization.
lsload |grep 'Hostname\|<partition>'

Example for the smith partition:
lsload |grep 'Hostname|smith'
Hostname Cores InUse Ratio Load Mem Alloc State
smith01 64 60 100.0 12.01 262 261 ALLOCATED
smith02 64 64 100.0 12.00 262 240 ALLOCATED
smith03 64 40 100.0 12.00 262 261 ALLOCATED

• Note that while node 03 has free cores, all its memory in use. So those cores are necessarily idle.
• Node 02 has a little free memory but all the cores are in use.
• The scheduler will shoot for 100% utilization, but jobs are generally stochastic; beginning and ending at different times with unpredictable amounts of CPU and RAM released/requested.

Custom Commands

We and users on the FASRC cluster have developed custom commands that also are deployed on the cluster for use.  If you have a command you want to contribute please contact us.  Below are the custom commands we have added.

spart shows you the partitions you have access to: https://github.com/fasrc/spart

showq which shows cluster state: https://github.com/fasrc/slurm_showq  

scalc which does various Slurm calculations such as projected fairshare usage: https://github.com/fasrc/scalc

find-best-partition shows which partition will schedule your job the quickest: https://github.com/fasrc/best_slurm_partition