Most common commands
| Command | Purpose |
|---|---|
sbatch job.sh | Submit a job script |
squeue -u $USER | Check your jobs |
scancel JOBID | Cancel a job |
sinfo | Check node/partition status |
module load SOFTWARE | Load a software module |
scontrol show job JOBID | View job details |
Three ways to run work
sbatch job_script.sh # batch: queued, background srun --partition=short-40core --time=01:00:00 --ntasks=1 my_program # direct: blocks until done salloc --partition=short-40core --time=02:00:00 --ntasks=4 # interactive allocation
Job script template
#!/bin/bash #SBATCH --job-name=my_job #SBATCH --output=results_%j.txt #SBATCH --error=errors_%j.txt #SBATCH --time=02:00:00 #SBATCH --partition=short-40core #SBATCH --ntasks=40 #SBATCH --cpus-per-task=1 #SBATCH --mail-type=END,FAIL #SBATCH --mail-user=your.email@stonybrook.edu module load intel-stack mpirun ./executable
Job management
squeue -u $USER --format="%.10i %.12j %.8T %.10M %.6D %R" # custom queue view scancel -u $USER --state=pending # cancel all pending sacct --starttime=2026-01-01 --format=JobID,JobName,State,ExitCode # history
System information
sinfo -p short-40core # partition status sinfo -N -l # all nodes, detailed sinfo --format="%.15N %.10c %.10m %.25f %.10G %.6t" # nodes/cores/memory/GPUs sshare -u $USER # fairshare info
File transfer
scp local_file.txt username@milan.seawulf.stonybrook.edu:~/ # upload scp -r local_directory/ username@milan.seawulf.stonybrook.edu:~/ # upload dir rsync -avz --progress username@milan.seawulf.stonybrook.edu:~/data/ ./local_data/ # download
Rsync flags: -a archive, -v verbose, -z compress, --progress, --dry-run to test first.
Modules
module avail python module load gcc/9.3.0 openmpi/4.1.0 module list && module purge
Storage
myquota # quota info df -h $HOME && df -h /gpfs/scratch/$USER # disk usage find $HOME -name "*.log" -mtime +30 -delete # clean old logs tar -czf archive.tar.gz directory/ # archive
Performance
sstat -j $SLURM_JOB_ID --format=AveCPU,AveRSS,MaxRSS # while running seff 123456 # efficiency after sacct -j 123456 --format=JobID,MaxRSS,AveCPU,Elapsed,State
Troubleshooting
tail -20 slurm-123456.out # last 20 lines of output grep -i error slurm-123456.out # find errors ssh -v username@milan.seawulf.stonybrook.edu # verbose SSH debug
Job pending? Check availability with sinfo -p your_partition and requirements with scontrol show job JOBID.
Applies to