SGE-Slurm
https://docs.rc.uab.edu/
Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.
As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.
Thank you,
The Research Computing Team
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
|
squeue
|
qsub
|
sbatch
|
| qlogin for interctive via vnc | |
| qlogin -l h_rt=8:00:00, vf=1G | sinteractive --time=8:00:00 --mem=1024 |