Useful Slurm commands

Slurm provides a variety of tools that allow a user to manage and understand their jobs. This tutorial will introduce these tools, as well as provide details on how to use them.

Finding queuing information with squeue

The squeue command is a tool we use to pull up information about the jobs in queue. By default, the squeue command will print out the job ID, partition, username, job status, number of nodes, and name of nodes for all jobs queued or running within Slurm. Usually you wouldn’t need information for all jobs that were queued in the system, so we can specify jobs that only you are running with the --user flag:

$ squeue --user=your_rc-username

We can output non-abbreviated information with the --long flag. This flag will print out the non-abbreviated default information with the addition of a timelimit field:

$ squeue --user=your_rc-username --long

The squeue command also provides users with a means to calculate a job’s estimated start time by adding the --start flag to our command. This will append Slurm’s estimated start time for each job in our output information. (Note: The start time provided by this command can be inaccurate. This is because the time calculated is based on jobs queued or running in the system. If a job with a higher priority is queued after the command is run, your job may be delayed.)

$ squeue --user=your_rc-username --start

When checking the status of a job, you may want to repeatedly call the squeue command to check for updates. We can accomplish this by adding the --iterate flag to our squeue command. This will run squeue every n seconds, allowing for a frequent, continuous update of queue information without needing to repeatedly call squeue:

$ squeue --user=your_rc-username --start --iterate=n_seconds

Press ctrl-z to stop the command from looping and bring you back to the terminal.

For more information on squeue, visit the Slurm page on squeue

Stopping jobs with scancel

Sometimes you may need to stop a job entirely while it’s running. The best way to accomplish this is with the scancel command. The scancel command allows you to cancel jobs you are running on Research Computing resources using the job’s ID. The command looks like this:

$ scancel your_job-id

To cancel multiple jobs, you can use a comma-separated list of job IDs:

$ scancel your_job-id1, your_job-id2, your_jobiid3

For more information, visit the Slurm manual on scancel

Learning status information with sstat

The sstat command allows users to easily pull up status information about their jobs. This includes information about CPU usage, task information, node information, resident set size (RSS), and virtual memory (VM). We can invoke the sstat command as such:

$ sstat --jobs=your_job-id

By default, sstat will pull up significantly more information than what would be needed in the commands default output. To remedy this, we can use the --format flag to choose what we want in our output. The format flag takes a list of comma separated variables which specify output data:

$ sstat --jobs=your_job-id --format=var_1,var_2, ... , var_N

A chart of some these variables are listed in the table below:

Variable Description
avecpu Average CPU time of all tasks in job.
averss Average resident set size of all tasks.
avevmsize Average virtual memory of all tasks in a job.
jobid The id of the Job.
maxrss Maximum number of bytes read by all tasks in the job.
maxvsize Maximum number of bytes written by all tasks in the job.
ntasks Number of tasks in a job.

For an example, let’s print out a job’s average job id, cpu time, max rss, and number of tasks. We can do this by typing out the command:

sstat --jobs=your_job-id --format=jobid,cputime,maxrss,ntasks

A full list of variables that specify data handled by sstat can be found with the --helpformat flag or by visiting the slurm page on sstat.

Analyzing past jobs with sacct

The sacct command allows users to pull up status information about past jobs. This command is very similar to sstat, but is used on jobs that have been previously run on the system instead of currently running jobs. We can use a job’s id…

$ sacct --jobs=your_job-id

…or your rc username…

$ sacct --user=your_rc-username

…to pull up accounting information on jobs run at an earlier time.

By default, sacct will only pull up jobs that were run on the current day. We can use the --starttime flag to tell the command to look beyond its short-term cache of jobs.

$ sacct –-jobs=your_job-id –-starttime=YYYY-MM-DD

To see a non-abbreviated version of sacct output, use the --long flag:

$ sacct –-jobs=your_job-id –-starttime=YYYY-MM-DD --long

Formatting sacct output

Like sstat, the standard output of sacct may not provide the information we want. To remedy this, we can use the --format flag to choose what we want in our output. Similarly, the format flag is handled by a list of comma separated variables which specify output data:

$ sacct --user=your_rc-username --format=var_1,var_2, ... ,var_N

A chart of some variables is provided below:

Variable Description
account Account the job ran under.
avecpu Average CPU time of all tasks in job.
averss Average resident set size of all tasks in the job.
cputime Formatted (Elapsed time * CPU) count used by a job or step.
elapsed Jobs elapsed time formated as DD-HH:MM:SS.
exitcode The exit code returned by the job script or salloc.
jobid The id of the Job.
jobname The name of the Job.
maxdiskread Maximum number of bytes read by all tasks in the job.
maxdiskwrite Maximum number of bytes written by all tasks in the job.
maxrss Maximum resident set size of all tasks in the job.
ncpus Amount of allocated CPUs.
nnodes The number of nodes used in a job.
ntasks Number of tasks in a job.
priority Slurm priority.
qos Quality of service.
reqcpu Required number of CPUs
reqmem Required amount of memory for a job.
user Username of the person who ran the job.

As an example, suppose you want to find information about jobs that were run on March 12, 2018. You want to show information regarding the job name, the number of nodes used in the job, the number of cpus, the maxrss, and the elapsed time. Your command would look like this:

$ sacct --jobs=your_job-id --starttime=2018-03-12 --format=jobname,nnodes,ncpus,maxrss,elapsed

As another example, suppose you would like to pull up information on jobs that were run on February 21, 2018. You would like information on job ID, job name, QoS, Number of Nodes used, Number of CPUs used, Maximum RSS, CPU time, Average CPU time, and elapsed time. Your command would look like this:

$ sacct –-jobs=your_job-id –-starttime=2018-02-21 --format=jobid,jobname,qos,nnodes,ncpu,maxrss,cputime,avecpu,elapsed

A full list of variables that specify data handled by sacct can be found with the --helpformat flag or by visiting the slurm page on sacct.

Controlling queued and running jobs using scontrol

The scontrol command provides users extended control of their jobs run through Slurm. This includes actions like suspending a job, holding a job from running, or pulling extensive status information on jobs.

To suspend a job that is currently running on the system, we can use scontrol with the suspend command. This will stop a running job on its current step that can be resumed at a later time. We can suspend a job by typing the command:

$ scontrol suspend job_id

To resume a paused job, we use scontrol with the resume command:

$ scontrol resume job_id

Slurm also provides a utility to hold jobs that are queued in the system. Holding a job will place the job in the lowest priority, effectively “holding” the job from being run. A job can only be held if it’s waiting on the system to be run. We use the hold command to place a job into a held state:

$ scontrol hold job_id

We can then release a held job using the release command:

$ scontrol release job_id

Scontrol can also provide information on jobs using the show job command. The information provided from this command is quite extensive and detailed, so be sure to either clear your terminal window, grep certain information from the command, or pipe the output to a separate text file:

# Output to console
$ scontrol show job job_id

# Streaming output to a textfile
$ scontrol show job job_id > outputfile.txt

# Piping output to Grep and find lines containing the word "Time"
$ scontrol show job job_id | grep Time

For a full primer on grep and regular expressions, visit GNU’s page on Grep

For more information on scontrol, visit the Slurm page on scontrol