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High Performance & Scientific Computing


The ISAAC Legacy (formerly ACF) and ISAAC-NG computing clusters now both utilize SLURM for workload management to manage and schedule jobs submitted to the clusters.

A variety of example SLURM jobs are available on ISAAC Legacy at /lustre/haven/examples/jobs and on ISAAC NG at /lustre/isaac/examples/jobs.

Command Differences

Command DescriptionTorqueSLURM
Batch job submissionqsub <Job File Name>sbatch <Job File Name>
Interactive job submissionqsub -lsalloc | srun –pty /bin/bash
Job listqstatsqueue -l
Job list by usersqstat -u <User Name>squeue -l -u <User Name>
Job deletionqdel <Job ID>scancel <Job ID>
Job holdqhold <Job ID>scontrol hold <Job ID>
Job releaseqrls <Job ID>scontrol release <Job ID>
Job updateqalter <Job ID>scontrol update job <Job ID>
Job detailsqstat -f <Job ID>scontrol show job <Job ID>
Node listpbsnodes -lsinfo -N
Node detailspbsnodesscontrol show nodes
Table 1.1: System commands for Torque and SLURM
Command Description MoabSLURM
Job start timeshowstart <Job ID>squeue –start -j <Job ID>
Status of nodesmdiag -nsinfo -N -l
User’s accountmdiag -u <User Name>sacctmgr show association user=<User Name>
Account membersmdiag -a <Account Name>sacctmgr show assoc account=<Account Name>
Nodes of accountsmdiag -ssinfo -a
Table 1.2: System commands for Moab and SLURM
Command DescriptionOpenMPISLURM
Parallel wrappermpirunsrun
Table 1.3: System Commands for Parallel Processing with OpenMPI and SLURM

Directive Differences (in Job script or command line)

Notice: There are important differences between SLURM and PBS. Please be careful when using the specifications –ntask= (-n) and –cpus-per-task= (-c) in SLURM because they are not PBS specifications, and there are no CPUs per node or ppn options in SLURM. The number of tasks (-n) is the specified number of parallel processes in the distributed memory (such as MPI model).

Torque DirectiveSLURM DirectiveDescriptionTorque ExampleSLURM Example
#PBS#SBATCHHead of each lineN/AN/A
-A-A, –account=<account>This option tells Torque to use the Account (not the User Name) specified for the credential.#PBS -A <Account Name>#SBatch -A <Account Name>

#SBATCH –account=<Account Name>
-a-begin=<time>This option tells PBS to run a job at the given time#PBS -a <0001>#SBATCH –begin=00:01


-e, –error=<filename pattern>

-o, –output=<filename pattern>

*NOTE: this command requires a file name pattern, and the file name pattern cannot be a directory. To find the details on valid filename patterns, check the sbatch manual by typing “man sbatch” into a CLI terminal and looking at the filename pattern section of the sbatch manual.
The location for the error_path and output_path attributes.

Users only need to use one of these two options if the -j option is also in use.

Combining the -e and -o options (to create “eo” or “oe”) will combine the STDOUT and STDERR together into a single file that the user specifies. “eo” will place the information into the error_path file, and “oe” will place the information into the output_path file.
#PBS -e ~/ErrorFile

#PBS -j oe

#PBS -j eo
#SBATCH -e ~/ErrorFile_%j_%u

*NOTE: Both standard output and standard error information for the job are directed into the same file.
qsub -l salloc

srun –pty /bin/bash
Declares that the job is to be run interactively.qsub -l

qsub -l -X
srun –pty /bin/bash

salloc –x11
-l-N, –nodes=<minnodes[-maxnodes]> -n, –ntasks=<number> –ntasks-per-node=<ntasks>

-c, –cpus-per-task=<ncpus>


-t, –time=<time>


-C, –constraint=<list>

Remember to separate options with a comma ( , ).

Nodes=# : gives the number and/or type of nodes desired.

ppn=# : gives the number of processors per node desired.

gpus=# : gives the number of GPUs desired.

walltime= : total runtime desired in the format DD:HH:MM:SS or HH:MM:SS

mem= : maximum amount of memory required by the job.

feature= : states name of type of compute node required.

file= : states the maximum amount of local disk space required by the job.

#PBS -l nodes=5:ppn=2:gpus=3

#PBS -l walltime=01:30:00

#PBS -l mem=5gb

#PBS -l feature=intel14|intel16

#PBS -l file=50GB
#SBATCH -n 5 -c 2 –gres=gpu:3

#SBATCH –time=01:30:00

#SBATCH –mem=5G

#SBATCH -C NOAUTO:intel14|intel16

#SBATCH –tmp=50G
-M–mail-user=<User Name>Emails email accounts(s) that are listed to notify users once a job changes states.#PBS -M <username> –mail-user=<username>
-m–mail-type=<type>a- this option sends a mail notification when the job is aborted.

b- this option sends a mail notification when the job execution begins.

e- this option sends a mail notification when the job ends.

n- this option does not send mail.

#PBS -m abe#SBATCH –mail-type=FAIL/BEGIN/END

if NONE option is used, no mail will be sent.
-N-J, –job-name=<jobname>Names a job#PBS -N <Desired Name of Job>#SBATCH -J <Desired Name of Job>
-t-a, –array=<indexes>Submits an array job with “n” number of identical tasks.

Remember: each job that is part of an array job will have the same JOBID, but a different ARRAYID.
#PBS -t 7

#PBS -t 2-13

#SBATCH -a 7

#SBATCH –array=2-13
-V–export=<environment variables [all] | none>Passes all current environmental variables to the job.#PBS -V#SBATCH –export=ALL
-v–export=<environment variables [all] | none>Defines any additional environmental variables for the job.#PBS -v ev1=ph5,ev2=43#SBATCH –export=’ev1=ph5,ev2=43′
-W-L, –licenses=<license>Special Generic Resources (i.e., software licenses) can be requested by using the -W option. #PBS -W gres:<Name of Software>#SBATCH -L <name of software>@<specified by license>@<specified by license>
Table 1.4: Job Submission Specification Options
DescriptionTorqueSLURM Variables
Directory where the submission command was executedPBS_O_WORKDIRSLURM_SUBMIT_DIR
List of nodes allocated to the jobPBS_NODEFILESLURM_JOB_NODELIST
Number of Processors Per Node (ppn) requestedPBS_NUM_PPNSLURM_JOB_CPUS_PER_NODE
Total number of cores requestedPBS_NPSLURM_NTASKS*
Total number of nodes requestedPBS_NUM_NODESSLURM_NTASKS
Table 1.5: Environment Variables for Torque and SLURM