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.

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>
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

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 these options to override the default behavior:

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

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

Common Job Commands

How to Monitor Jobs

Valid Job States