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Job control and useful commands

Below are some nice to know commands for controlling and checking up on jobs, current and past.

Get job status info

Use squeue, for example: 

$ squeue
JOBID         NAME       USER       TIME    TIME_LEFT CPU MIN_ME ST PARTITION NODELIST(REASON)
 2380         dRep ab12cd@bio 1-01:36:22  12-22:23:38  80   300G  R   general bio-oscloud02

To show only your own jobs use squeue --me. This is used quite often so sq has been made an alias of squeue --me.

Job state codes (ST)
Status Code Explaination
COMPLETED CD
COMPLETING CG
FAILED F
PENDING PD
PREEMPTED PR
RUNNING R
SUSPENDED S
STOPPED ST

A complete list can be found in SLURM's documentation

Job reason codes (REASON )
Reason Code Explaination
Priority One or more higher priority jobs is in queue for running. Your job will eventually run.
Dependency This job is waiting for a dependent job to complete and will run afterwards.
Resources The job is waiting for resources to become available and will eventually run.
InvalidAccount The job’s account is invalid. Cancel the job and rerun with correct account.
InvaldQoS The job’s QoS is invalid. Cancel the job and rerun with correct account.
QOSGrpCpuLimit All CPUs assigned to your job’s specified QoS are in use; job will run eventually.
QOSGrpMaxJobsLimit Maximum number of jobs for your job’s QoS have been met; job will run eventually.
QOSGrpNodeLimit All nodes assigned to your job’s specified QoS are in use; job will run eventually.
PartitionCpuLimit All CPUs assigned to your job’s specified partition are in use; job will run eventually.
PartitionMaxJobsLimit Maximum number of jobs for your job’s partition have been met; job will run eventually.
PartitionNodeLimit All nodes assigned to your job’s specified partition are in use; job will run eventually.
AssociationCpuLimit All CPUs assigned to your job’s specified association are in use; job will run eventually.
AssociationMaxJobsLimit Maximum number of jobs for your job’s association have been met; job will run eventually.
AssociationNodeLimit All nodes assigned to your job’s specified association are in use; job will run eventually.

A complete list can be found in SLURM's documentation

The columns to show can be customized using the --format option, but can also be set with the environment variable SQUEUE_FORMAT to avoid typing it every time. You can always override this to suit your needs in your .bashrc file. The default format is currently:

SQUEUE_FORMAT="%.12i %.16j %.10u %.10M %.12L %.3C %.6m %.2t %.9P %R"

See a full list here.

Prevent pending job from starting

Pending jobs can be marked in a "hold" state to prevent them from starting 

scontrol hold <job_id>

To release a queued job from the ‘hold’ or 'requeued held' states: 

scontrol release <job_id>

To cancel and rerun (requeue) a particular job: 

scontrol requeue <job_id>

Cancel a job

With sbatch you won't be able to just hit CTRL+c to stop what's running like you're used to in a terminal. Instead you must use scancel. Get the job ID from squeue --me, then use scancel to cancel a running job, for example: 

$ scancel <job_id>

# cancel ALL your jobs
$ scancel --me

If the particular job doesn't stop and doesn't respond, consider using skill instead.

Pause or resume a job

Use scontrol to control your own jobs, for example suspend a running job: 

$ scontrol suspend <job_id>

Resume again with 

$ scontrol resume <job_id>

Show details about a running or queued job

scontrol show jobid=<jobid>

Modifying job attributes

Only a few job attributes can be changed after a job is submitted and NOT running yet. These attributes include:

  • wall clock limit
  • job name
  • job dependency
  • partition or QOS

For example: 

$ scontrol update JobId=<jobid> timelimit=<new timelimit>
$ scontrol update JobId=<jobid> partition=high-mem

If the job is already running adjusting the time limit must be done by an administrator.