Basic Commands | crc.pitt.edu | University of Pittsburgh

These are some of the basic commands:

sinfo – Quick view of hardware allocated and free
smap – More visual version of sinfo using ncurses
sview – Graphical interface of hardware (requires X11).
sbatch <job_script> – Submit a job file
squeue – View all running jobs
squeue -u <user> – View particular <user>’s jobs (could be you)
sshare – View fairshare information
sprio – View queued job’s priority

If you are a PBS Torque user and want to migrate to Slurm, you can find the equivalent examples for PBS and Slurm job scripts in the following table.

Command	PBS/Torque	Slurm
Job submission	qsub job_script	sbatch job_script
Job submission	qsub -q queue -l nodes=1:ppn=16 -l mem=64g job_script	sbatch --partition=queue --nodes=1 --cpus-per-node=16 --mem=64g job_script
Node count	-l nodes=count	--nodes=1
Cores per node	-l ppn=count	--cpus-per-node=count
Memory size	-l mem=16384	--mem=16g
Wall clock limit	-N name	--job-name=name

The sbatch arguments here are the minimal subset required to accurately specify a job on the h2p cluster. Please refer to man sbatch for more options.

SBATCH ARGUMENT	DESCRIPTION
--nodes	Maximum number of nodes to be used by each Job Step.
--tasks-per-node	Specify the number of tasks to be launched per node.
--cpus-per-task	Advise the Slurm controller that ensuing job steps will require a certain number of processors per task.
--error	File to redirect standard error.
--job-name	The job name.
--time	Define the total time required for the job The format is days-hh:mm:ss.
--cluster	Select the cluster to submit the job to. smp, mpi and gpu are the available partition in the H2P
--partition	Select the partition to submit the job to. smp, high-mem for smp cluster, opa, legacy for mpi cluster, gtx1080, titan, titanx and k40 for gpu cluster.
--account	Charge resources used by this job to specified account. This is only relevant for users who are in multiple SLURM accounts because he/she is in groups that are collaborating.

srun also takes the --nodes,--tasks-per-node and --cpus-per-task arguments to allow each job step to change the utilized resources but they cannot exceed those given to sbatch. The above arguments can be provided in a batch script by preceding them with #SBATCH. Note that the shebang (#!) line must be present. The shebang line can call any shell or scripting language available on the cluster. For example, #!/usr/bin/env bash.

Slurm is very explicit in how one requests cores and nodes. While extremely powerful, the three flags,--nodes, --ntasks, and --cpus-per-task can be a bit confusing at first.

--ntasks vs. --cpus-per-task

The term “task” in this context can be thought of as a “process”. Therefore, a multi-process program (e.g. MPI) is comprised of multiple tasks. In Slurm, tasks are requested with the --ntasks flag. A multi-threaded program is comprised of a single task, which can in turn use multiple CPUs. CPUs, for the multithreaded programs, are requested with the --cpus-per-task flag. Individual tasks cannot be split across multiple compute nodes, so requesting a number of CPUs with --cpus-per-task flag will always result in all your CPUs allocated on the same compute node.