Basic Commands
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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.