Migrating from Torque to Slurm

Later this year GACRC will be implementing the Simple Linux Utility for Resource Management (Slurm) software for job scheduling and resource management on Sapelo2, to replace the Torque (PBS) resource manager and Moab scheduling system that it currently uses.

How is Slurm different from Torque?

Slurm is different from Torque in a number of ways, including the commands used to submit and monitor jobs, the syntax used to request resources, and the way environment variables behave.

Some specific ways in which Slurm is different from Torque include:

• Slurm will not allow a job to be submitted whose requested resources exceed the set of resources the job owner has access to--whether or not those resources have been already allocated to other jobs at the moment. Torque will queue the job, but the job would never run.
• What Torque calls queues, Slurm calls partitions.
• Resources in Slurm are assigned per “task”/process.
• In Slurm, environmental variables of the submitting process are passed to the job, except that by default Slurm does not source the files ~/.bashrc when requesting resources via sbatch.

How to Submit Jobs

To submit jobs in Slurm, replace qsub with one of the commands from the table below.

Info	Torque Command	Slurm Command
Submit a batch job to the queue	qsub <job script>	sbatch <job script>
Start an interactive job	qsub -I <options>	salloc <options>

where <job script> needs to be replaced by the name of your job submission script (e.g. sub.sh). Note that the syntax in the job submission script for Slurm is different from the Torque syntax.

Job Submission Options

As with Torque, job options and resource requests in Slurm can be set in the job submission script or as options to the job submission command. However, the syntax used to request resources is different and the table below summarizes some of the options that are frequently used.

Option	Torque (qsub)	Slurm (sbatch)
Script directive	#PBS	#SBATCH
Job name	-N <name>	--job-name=<name> -J <name>
Queue	-q <queue>	--partition=<queue>
Wall time limit	-l walltime=<hh:mm:ss>	--time=<hh:mm:ss>
Node count	-l nodes=<count>	--nodes=<count> -N <count>
Process count per node	-l ppn=<count>	--ntasks-per-node=<count>
core count (per process)		--cpus-per-task=<cores>
Memory limit	-l mem=<limit>	--mem=<limit> (Memory per node in mega bytes – MB)
Minimum memory per processor	-l pmem=<limit>	--mem-per-cpu=<memory>
Request GPUs	-l gpus=<count>	--gres=gpu:<count>
Request specific nodes	-l nodes=<node>[,node2[,...]]>	-w, --nodelist=<node>[,node2[,...]]> -F, --nodefile=<node file>
Request node feature	-l nodes=<count>:ppn=<count>:<feature>	--constraint=<feature>
Job array	-t <array indices>	--array <indexes> -a <indexes> Where <indexes> is replaced by a range (0-15), a list (0, 6, 16-32), or a step function (0-15:4)
Standard output file	-o <file path>	--output=<file path> (path must exist)
Standard error file	-e <file path>	--error=<file path> (path must exist)
Combine stdout/stderr to stdout	-j oe	--output=<combined out and err file path>
Copy environment	-V	--export=ALL (default) --export=NONE to not export environment
Copy environment variable	-v <variable[=value][,variable2=value2[,...]]>	--export=<variable[=value][,variable2=value2[,...]]>
Job dependency	-W depend=after:jobID[:jobID...] -W depend=afterok:jobID[:jobID...] -W depend=afternotok:jobID[:jobID...] -W depend=afterany:jobID[:jobID...]	--dependency=after:jobID[:jobID...] --dependency=afterok:jobID[:jobID...] --dependency=afternotok:jobID[:jobID...] --dependency=afterany:jobID[:jobID...]
Request event notification	-m <events>	--mail-type=<events> Note: multiple mail-type requests may be specified in a comma separated list: --mail-type=BEGIN,END,NONE,FAIL,REQUEUE
Email address	-M <email address>	--mail-user=<email address>
Defer job until the specified time	-a <date/time>	--begin=<date/time>
Node exclusive job	qsub -n	--exclusive

Common Job Commands

How to Submit and Manage Jobs

Info	Torque Command	Slurm Command
Submit a job	qsub <job script>	sbatch <job script>
Delete a job	qdel <job ID>	scancel <job ID>
Hold a job	qhold <job ID>	scontrol hold <job ID>
Release a job	qrls <job ID>	scontrol release <job ID>
Start an interactive job	qsub -I <options>	salloc <options> srun --pty <options>
Start an interactive job with X forwarding	qsub -I -X <options>	srun --x11 <options>

How to View Resources on the Cluster

Info	Torque Command	Slurm Command
Queue list / info	qstat -q [queue]	scontrol show partition [queue]
Node list	pbsnodes -a mdiag -n -v	scontrol show nodes
Node details	pbsnodes <node>	scontrol show node <node>
Cluster status	qstat -B	sinfo

How to Monitor Jobs

Info	Torque Command	Slurm Command
Job status (all)	qstat showq	squeue
Job status (by job)	qstat <job ID>	squeue -j <job ID>
Job status (by user)	qstat -u <user>	squeue -u <user>
Job status (only own jobs)	qstat_me	squeue --me squeue --me -l
Job status (detailed)	qstat -f <job ID> checkjob <job ID>	scontrol show job -dd <job ID>
Show expected start time	showstart <job ID>	squeue -j <job ID> --start
Monitor or review a job’s resource usage	qstat -f <job ID>	sacct -j <job ID> --format JobID,jobname,NTasks,nodelist,CPUTime,ReqMem,Elapsed
View job batch script		scontrol write batch_script <job ID> [filename]

Valid Job States

Below are the job states you may encounter when monitoring your job(s) in Slurm.

Code	State	Meaning
CA	Canceled	Job was canceled
CD	Completed	Job completed
CF	Configuring	Job resources being configured
CG	Completing	Job is completing
F	Failed	Job terminated with non-zero exit code
NF	Node Fail	Job terminated due to failure of node(s)
PD	Pending	Job is waiting for compute node(s)
R	Running	Job is running on compute node(s)

Job Environment and Environment Variables

In Slurm, environment variables will get passed to your job by default.

If you have certain environment variables set that you think might interfere with your job you can either:

• Log out then log back in and submit your job
• Run sbatch with one of these options to override the default behavior:

     sbatch --export=None 
     sbatch --export MYPARAM=3 
     sbatch --export=ALL,MYPARAM=3

NOTE: We recommend that you submit sbatch Slurm jobs with the #SBATCH --export=NONE option to establish a clean environment, otherwise Slurm will propagate current environmental variables to the job. This could impact the behavior of the job, particularly for MPI jobs.

Like Torque, Slurm sets its own environment variables within your job. The table below summarizes some environment variables that are frequently used.

Info	Torque	Slurm	Notes
Version	$PBS_VERSION	–	Can extract from sbatch --version
Job name	$PBS_JOBNAME	$SLURM_JOB_NAME
Job ID	$PBS_JOBID	$SLURM_JOB_ID
Batch or interactive	$PBS_ENVIRONMENT	–
Submit directory	$PBS_O_WORKDIR	$SLURM_SUBMIT_DIR	Slurm jobs start from the submit directory by default.
Submit host	$PBS_O_HOST	$SLURM_SUBMIT_HOST
Node file	$PBS_NODEFILE		A filename and path that lists the nodes a job has been allocated.
Node list	cat $PBS_NODEFILE	$SLURM_JOB_NODELIST	The Slurm variable has a different format to the Torque/PBS one. To get a list of nodes use: scontrol show hostnames $SLURM_JOB_NODELIST
Job array index	$PBS_ARRAYID $PBS_ARRAY_INDEX	$SLURM_ARRAY_TASK_ID	Only set when submitting a job array (with -a or –array)
Walltime	$PBS_WALLTIME	–
Queue name	$PBS_QUEUE	$SLURM_JOB_PARTITION
Number of nodes allocated	$PBS_NUM_NODES	$SLURM_JOB_NUM_NODES $SLURM_NNODES
Number of processes	$PBS_NP	$SLURM_NTASKS
Number of processes per node	$PBS_NUM_PPN	$SLURM_TASKS_PER_NODE
List of allocated GPUs	$PBS_GPUFILE	–
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

Slurm Documentation

Extensive documentation on Slurm is available at https://slurm.schedmd.com/documentation.html

This page was adapted from https://arc-ts.umich.edu/migrating-from-torque-to-slurm/ and https://hpcc.usc.edu/support/documentation/pbs-to-slurm/