Extended SLURM Job and Submission Options

Quest and Kellogg Linux Cluster Downtime, June 8th-14th, 2024.

Quest, including the Quest Analytics Nodes, the Genomics Compute Cluster (GCC), the Kellogg Linux Cluster (KLC), and Quest OnDemand, will be unavailable for scheduled maintenance starting at 7 A.M. on Saturday, June 8, and ending approximately at 5 P.M. on Friday, June 14. During the maintenance window, you will not be able to login to Quest, Quest Analytics Nodes, the GCC, KLC, or Quest OnDemand submit new jobs, run jobs, or access files stored on Quest in any way including Globus. For details on this maintenance, please see the Status of University IT Services page.

For more detailed information, see Slurm sbatch documentation.

Job Submission Options

Option Slurm (sbatch)
Script directive #SBATCH
Job name --job-name=<name>
-J <name>
Account --account=<account>
-A <account>
Queue --partition=<queue>
Wall time limit --time=<hh:mm:ss>
Node count --nodes=<count>
-N <count>
Core count -n <count>
Process count per node --ntasks-per-node=<count>
Core count (per process) --cpus-per-task=<cores>
Memory limit --mem=<limit> (Memory per node in MB)
Minimum memory per processor --mem-per-cpu=<memory>
Request GPUs --gres=gpu:<count>
Request specific nodes -w, --nodelist=<node>[,node2[,...]]>
-F, --nodefile=<node file>
Job array -a <array indices>
Standard output file --output=<file path> (path must exist)
Standard error file --error=<file path> (path must exist)
Combine stdout/stderr to stdout --output=<combined out and err file path>
Architecture constraint --constraint=<architecture>
-C <architecture>
Copy environment --export=ALL (default)
--export=NONE to not export environment
Copy environment variable --export=<variable[=value][,variable2=value2[,...]]>
Job dependency --dependency=after:jobID[:jobID...]
Request event notification --mail-type=<events>
Note: multiple mail-type requests may be specified in a comma separated list:
Email address --mail-user=<email address>
Defer job until the specified time --begin=<date/time>
Node exclusive job --exclusive

Common Job Commands

Option Slurm (sbatch)
Submit a job sbatch <job script>
Delete a job scancel <job ID>
Job status (all) squeue
Job status (by job) squeue -j <job ID>
Job status (by user) squeue -u <netID>
Job status (detailed) scontrol show job -dd <job ID>
checkjob <job ID>
Show expected start time squeue -j <job ID> --start
Queue list / info scontrol show partition [queue]
Hold a job scontrol hold <job ID>
Release a job scontrol release <job ID>
Start an interactive job salloc <args>
srun --pty <args>
X forwarding srun --pty <args> --x11
Monitor or review a job's resource usage sacct -j <job_num> --format JobID,jobname,NTasks,nodelist,CPUTime,ReqMem,Elapsed
(see sacct for all format options)
View job batch script scontrol write batch_script <jobID> [filename]

Script Variables

Info Slurm Notes
Version Can extract from sbatch --version
Job name $SLURM_JOB_NAME  
Submit directory $SLURM_SUBMIT_DIR Slurm jobs starts from the submit directory by default
Node list $SLURM_JOB_NODELIST The Slurm variable has a different format to the PBS one.
To get a list of nodes use:
scontrol show hostnames $SLURM_JOB_NODELIST
Job array index $SLURM_ARRAY_TASK_ID  
Number of nodes allocated $SLURM_JOB_NUM_NODES
Number of processes $SLURM_NTASKS  
Number of processes per node $SLURM_TASKS_PER_NODE  
Requested tasks per node $SLURM_NTASKS_PER_NODE  
Requested CPUs per task $SLURM_CPUS_PER_TASK  
Scheduling priority $SLURM_PRIO_PROCESS  
Job user $SLURM_JOB_USER  
Hostname $HOSTNAME == $SLURM_SUBMIT_HOST Unless a shell is invoked on an allocated resource, the $HOSTNAME variable is propagated (copied) from the submit machine environment to all allocated nodes.


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Article ID: 1795
Thu 5/12/22 12:39 PM
Wed 5/1/24 9:14 AM