Converting from PBS to Slurm
In March 2018, HPC will be implementing the Simple Linux Utility for Resource Management (Slurm) for job scheduling and resource management, replacing our current resource management/job scheduling utility, Adaptive Computing’s PBS Torque/Moab. Slurm is an open-source utility that is widely used at national research centers, higher education research centers, government institutions, and other research institutions across the globe.
How is Slurm different from PBS?
Slurm is different from PBS in a number of important ways, including the commands used to submit and monitor jobs, the syntax used to request resources, and the way environment variables behave.
Some specific ways in which Slurm is different from PBS include:
- ATTENTION: We recommend that you exit the head node, then log back in to establish a clean environment before submitting Slurm job(s). Slurm will pass environmental variables set from the process that is submitting the job. This could impact the behavior of the job, particularly for MPI jobs. We are working to update our setup scripts to address this issue.
- Slurm will not allow a job to be submitted if there are insufficient account cycles or no resources matching your request. PBS would queue the job, but it would never run.
- Slurm leverages the kernel’s control groups (cgroups) to limit memory and CPU usage for each job and shares those limits across all ssh sessions for the owner of the job. This impacts anyone accessing a compute node running their job. Instead of getting new system resources, you share the same limits as your running job.
- What PBS called queues, Slurm calls partitions.
- Resources are assigned per “task”/process.
- Environmental variables of the submitting process are passed to the job.
For full details on how to work with Slurm, see our documentation on running a job with Slurm
PBS-to-Slurm Command Cheat Sheets
The several charts below lists the PBS commands you currently use to process jobs, their Slurm equivalents, and the meaning of the new commands. These cheat sheets are intended to help you get up and running with Slurm quickly.
Cheat Sheet: General Commands
|PBS Command||Slurm Command||Meaning|
|qsub <job-file>||sbatch <job-file>||Submit <job script> to the queue|
|qsub -I||salloc <options>||Request interactive job|
|showstart||squeue --start||Show estimated start time|
|qstat <-u username>||squeue <-u username>||Check jobs for a particular user in the scheduling queue|
|qstat <queue>||squeue -p <partition>||Display queue/partition entries|
|qstat -f <job_id>||scontrol show job <job_id>||Show job details|
|qdel <job_id>||scancel <job_id>||Delete <job_id>|
Cheat Sheet: How to Submit Jobs
Submitting jobs in Slurm is straightforward. You just replace ‘qsub’ with one of the commands from the table below.
|PBS Command||Slurm Command||Meaning|
|qsub job.pbs||sbatch job.slurm||Submit batch job to queue|
|qsub -I||salloc <options>||Submit interactive job to queue. See resources below for options|
Cheat Sheet: How to Request Resources
The way that you work with resources in Slurm is similar to PBS but there are some significant differences, including the syntax used to submit requests. See the table below for some of the options most frequently used to request resources.
|qsub||sbatch/salloc||Submit batch/interactive job script to queue*|
|-l procs=<number>||--ntasks=<number>||# of processes to run|
|-l nodes=X:ppn=Y||--ntasks=<multiply X*Y>||# of processes to run|
|-l walltime=<HH:MM:SS>||--time=<HH:MM:SS>||How long the job will run|
|-l mem=<number>||--mem=<number>||Total memory (single node)|
|-l pmem=<number>||--mem_per_cpu=<number>||Memory per cpu|
|-l …:<attribute>||--constraint=<attribute>||Node property to request (avx, IB)|
|-q <queue_name>||--partition=<partition_name>||Which set of nodes to run job on|
NOTE: When using salloc to submit interactive jobs, you need to use the following string
Aside from the new syntax, Slurm places emphasis on the programs you want to run. You specify the needs of your program and Slurm will find the appropriate resources for it to run on. For example, most programs have memory, walltime, and CPU requirements.
If you want to run a single program (which Slurm calls a “task”) that needs 16 gigabytes of memory, 8 CPUs, and takes 12 hours to complete, you might use the following example job script:
#SBATCH --ntasks=8 #SBATCH --mem_per_cpu=2GB #SBATCH --time=12:00:00
Cheat Sheet: Useful SBATCH Options
You may find it useful to have email alerts, or have slurm help organize your log files by implementing one of these sbatch options.
|-l M <email>||--mail-user=<email>||Where to send email alerts|
|-l m <a|b|e>||--mail-type=<BEGIN|END|FAIL|REQUEUE|ALL>||When to send email alerts|
|-o <out_file>||--output=<out_file>||Name of output file|
|-e <error_file>||--error=<error_file>||File name is segregated errors are desired|
|-A <account>||--account=<account>||Which account to charge cpu time|
|-N <job_name>||--job-name=<job_name>||Job name|
*For more details on submitting a batch script to Slurm, see slurm.schedmd.com/sbatch.html.
Cheat Sheet: How to Read/Set Slurm Environment Variables
Like PBS, Slurm sets its own environment variables within your job
|$PBS_O_WORKDIR||$SLURM_SUBMIT_DIR||Directory job was submitted from|
|$PBS_NODEFILE||$SLURM_JOB_NODELIST||File containing allocated hostnames|
|$PBS_O_HOST||$SLURM_SUBMIT_HOST||Hostname job was submitted from|
In Slurm, environment variables will get passed to your job by default. If you have certain environment variables set that you think might interfere with your job you can either:
- Log out then log back in and submit your job
- Run sbatch with these options to override the default behavior:
sbatch --export=None sbatch --export TEST=3 sbatch --export=ALL,TEST=3
Cheat Sheet: How to Monitor Your Job(s)
After submitting your job you can check its status with these new commands:
|myqueue (in-house)||myqueue (in-house)||Check your queued jobs|
|qstat <-u username>||squeue <-u username>||Check jobs for a specific user|
|qstat -f <jobid>||sstat <jobid>||Displays resource usage|
|pbsnodes <:attribute>||sinfo||Display all nodes (with attribute)|
|checkjob <job_id>||scontrol show job <jobid>||Status of particular job|
|showstart <job_id>||squeue -j <job_id> --start||Get estimated start time of job|
|mybalance [-h]||(in development)||Check remaining core-hour allocation|
|qdel <job_id>||scancel <job_id>||Delete job|
Valid Job States
Below are the job states you may encounter when monitoring your job(s) in Slurm.
|CA||Canceled||Job was canceled|
|CG||Completing||Job is completing|
|F||Failed||Job terminated with non-zero exit code|
|NF||Node Fail||Job terminated due to failure of node(s)|
|PD||Pending||Job is waiting for compute node(s)|
|R||Running||Job is running on compute node(s)|
|TO||Timeout||Job terminated upon reaching its time limit|
If you need assistance converting your PBS scripts to Slurm, please email us at firstname.lastname@example.org.