From SGE to SLURM conversion

Commands in SoGE and their respective equivalents in SLURM

Common user commands:

User Commands	SGE	SLURM
Interactive login	qlogin	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 username]	squeue -u [username]
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
GUI	qmon	sview

Common environment commands:

Environmental	SGE	SLURM
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

Job directives

Job Specification	SGE	SLURM
queue/partition	#$ -q [queue]	#SBATCH -p [partition]
count of nodes	N/A	#SBATCH -N [min[-max]]
CPU count	#$ -pe [PE] [count]	#SBATCH -n [count]
Wall clock limit	#$ -l h_rt=[seconds]	#SBATCH -t [min] OR -t [days-hh:mm:ss]
Standard out file	#$ -o [file_name]	#SBATCH -o [file_name]
Standard error file	#$ -e [file_name]	#SBATCH -e [file_name]
Combine STDOUT & STDERR files	#$ -j yes	(use -o without -e)
Copy environment	-V	--export=[ALL / NONE / variables]
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]
Tasks per node	(Fixed allocation_rule in PE)	--tasks-per-node=[count]/--cpus-per-task=[count]