SGE-Slurm

SGE-Slurm user comamnds

Some common commands and flags in SGE and Slurm with their respective equivalents:

User Commands	SGE	Slurm
Interactive login	qrsh	srun --pty bash
Job submission	qsub [script_file]	sbatch [script_file]
Job deletion	qdel [job_id]	scancel [job_id]
Job status by job	qstat -u \* [-j job_id]	squeue [job_id]
Job status by user	qstat [-u user_name]	squeue -u [user_name]
Job hold	qhold [job_id]	scontrol hold [job_id]
Job release	qrls [job_id]	scontrol release [job_id]
Queue list	qconf -sql	squeue
List nodes	qhost	sinfo -N OR scontrol show nodes
Cluster status	qhost -q	sinfo
Graphical queue view	qmon	sview
Job ID	$JOB_ID	$SLURM_JOBID
Submit directory	$SGE_O_WORKDIR	$SLURM_SUBMIT_DIR
Submit host	$SGE_O_HOST	$SLURM_SUBMIT_HOST
Node list	$PE_HOSTFILE	$SLURM_JOB_NODELIST
Job Array Index	$SGE_TASK_ID	$SLURM_ARRAY_TASK_ID
Script directive	#$	#SBATCH
queue	-q [queue]	-p [queue]
count of nodes	N/A	-N [min[-max]]
CPU count	-pe [PE] [count]	-n [count]
Wall clock limit	-l h_rt=[seconds]	-t [min] OR -t [days-hh:mm:ss]
Standard out file	-o [file_name]	-o [file_name]
Standard error file	-e [file_name]	e [file_name]
Combine STDOUT & STDERR files	-j yes	(use -o without -e)
Copy environment	-V	--export=[ALL | NONE | variables]
Event notification	-m abe	--mail-type=[events]
send notification email	-M [address]	--mail-user=[address]
Job name	-N [name]	--job-name=[name]
Restart job	-r [yes|no]	--requeue OR --no-requeue (NOTE: configurable default)
Set working directory	-wd [directory]	--workdir=[dir_name]
Resource sharing	-l exclusive	--exclusive OR--shared
Memory size	-l mem_free=[memory][K|M|G]	--mem=[mem][M|G|T] OR --mem-per-cpu= [mem][M|G|T]
Charge to an account	-A [account]	--account=[account]
Tasks per node	(Fixed allocation_rule in PE)	--tasks-per-node=[count]
		--cpus-per-task=[count]
Job dependancy	-hold_jid [job_id | job_name]	--depend=[state:job_id]
Job project	-P [name]	--wckey=[name]
Job host preference	-q [queue]@[node] OR -q [queue]@@[hostgroup]	--nodelist=[nodes] AND/OR --exclude= [nodes]
Quality of service		--qos=[name]
Job arrays	-t [array_spec]	--array=[array_spec] (Slurm version 2.6+)
Generic Resources	-l [resource]=[value]	--gres=[resource_spec]
Licenses	-l [license]=[count]	--licenses=[license_spec]
Begin Time	-a [YYMMDDhhmm]	--begin=YYYY-MM-DD[THH:MM[:SS]]

SGE - Slurm conversion examples

SGE	Slurm
qstat qstat -u username qstat -f	squeue squeue -u username squeue -al
qsub qsub -N jobname qsub -m beas qsub -M $USER@uab.edu qsub -l h_rt=24:00:00 qsub -pe smp 16 qsub -l vf=4G qsub -P projectname qsub -o filename qsub -e filename	sbatch sbatch -J jobname sbatch --mail-type=ALL sbatch --mail-user=$USER@uab.edu sbatch -t 24:00:00 sbatch -p partition -n 16 sbatch --mem-per-cpu=4096 sbatch -A projectname sbatch -o filename sbatch -e filename
qlogin for interactive via vnc	sinteractive for interactive via vnc
qlogin -l h_rt=8:00:00, vf=1G	sinteractive --time=8:00:00 --mem=1024