Between 2020 and 2021, all HPC clusters were transitioned from using the PBS job scheduler to SLURM. In general, SLURM can translate and execute scripts written for PBS. This means that if you submit a PBS script written for Ocelote or ElGato on Puma (with the necessary resource request modifications), your script will likely run. However, there are a few caveats that should be noted:
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Refer to the following list of common PBS commands, directives, and environment variables and their SLURM counterparts. For a PDF version, click here.
| PBS | SLURM | Purpose |
|---|---|---|
| Job Management | ||
| sbatch <options> | Batch submission of jobs to run without user input |
qsub -I <options> | salloc <options> | Request an interactive job |
N/A | srun <options> | Submit a job for realtime execution. Can also be used to submit an interactive session |
qstat | squeue | Show all jobs |
qstat <jobid> | squeue --job <jobid> | Check status of a specific job |
qstat -u <netid> | squeue -u <netid> | Check status of jobs specific to user |
tracejob <jobid> | sacct -j <jobid> | Check history of a completed job |
qdel <jobid> | scancel <jobid> | Delete a specific job |
qdel -u <netid> | scancel -u <netid> | Delete all user jobs |
qstat -Q | sinfo | View information about nodes and queues |
qhold <jobid> | scontrol hold <jobid> | Places a hold on a job to prevent it from being executed |
qrls <jobid> | scontrol release <jobid> | Releases a hold placed on a job allowing it to be executed |
| Job Directives | ||
#PBS -W group_list=group_name | #SBATCH --account=group_name | Specify group name where hours are charged |
#PBS -q standard | #SBATCH --partition=standard | Set job queue |
#PBS -l walltime=HH:MM:SS | #SBATCH --time HH:MM:SS | Set job walltime |
#PBS -l select=<N> |
| Select N nodes |
#PBS -l ncpus=<N> | #SBATCH --ntasks=<N>#SBATCH --cpus-per-task=<M> | PBS: Select N cpus SLURM: Each task is assume to require one cpu. Optionally, you may include cpus-per-task if more are required. Requests NxM cpus Note: Puma has 94 cpus available on each node |
#PBS -l mem=<N>gb | #SBATCH --mem=<N>gb | Select N gb of memory per node |
#PBS -l pcmem=<N>gb | #SBATCH --mem-per-cpu=<N>gb | Select N gb of memory per cpu Note: Puma defaults to 5GB per cpu |
#PBS J N-M | #SBATCH --array=N-M | Array job submissions where N and M are integers |
#PBS -l np100s=1 |
| Optional: Request a GPU |
#PBS -N JobName | #SBATCH --job-name=JobName | Optional: Set job name |
#PBS -j oe | (default) | Optional: Combine stdout and error |
(default) | #SBATCH-e <job_name>-%j.err | Optional: Separate stdout and stderr (SLURM: %j is a stand-in for $SLURM_JOB_ID) |
#PBS -o filename | #SBATCH -o filename | Optional: Standard output filename |
#PBS -e filename | #SBATCH -e filename | Optional: Error filename |
N/A | #SBATCH --open-mode=append | Optional: Combine all output into single file. Note: If this is selected, each job run will append to that filename, including preexisting files with that name |
#PBS -v var=<value> | #SBATCH --export=var | Optional: Export single environment variable var to job |
#PBS -V | #SBATCH --export=all (default) | Optional: Export all environment variables to job |
(default) | #SBATCH --export=none | Optional: Do not export working environment to job |
#PBS -m be | #SBATCH --mail-type=BEGIN|END|FAIL|ALL | Optional: Request email notifications Beware of mail bombing yourself |
#PBS -M | ||
<netid>@email.arizona.edu | #SBATCH --mail-user= |
<netid>@email.arizona.edu | Optional: email address used for notifications | |
#PBS -l place=excl | #SBATCH --exclusive | Optional: Request exclusive access to node |
| Environment Variables | ||
$PBS_O_WORKDIR | $SLURM_SUBMIT_DIR | Job submission directory |
$PBS_JOBID | $SLURM_JOB_ID | Job ID |
$PBS_JOBNAME | $SLURM_JOB_NAME | Job name |
$PBS_ARRAY_INDEX | $SLURM_ARRAY_TASK_ID | Index to differentiate tasks in an array |
$PBS_O_HOST | $SLURM_SUBMIT_HOST | Hostname where job was submitted |
$PBS_NODEFILE | $SLURM_JOB_NODELIST | List of nodes allocated to current job |
| Terminology | ||
| Queue | Partition | |
| Group List | Association | |
| PI | Account | |