Helix/Slurm
Contents
1 General information about Slurm
The bwForCluster Helix uses Slurm as batch system.
- Slurm documentation: https://slurm.schedmd.com/documentation.html
- Slurm cheat sheet: https://slurm.schedmd.com/pdfs/summary.pdf
- Slurm tutorials: https://slurm.schedmd.com/tutorials.html
2 Slurm Command Overview
| Slurm commands | Brief explanation |
|---|---|
| sbatch | Submits a job and queues it in an input queue |
| squeue | Displays information about active, eligible, blocked, and/or recently completed jobs |
| scontrol | Displays detailed job state information |
| scancel | Cancels a job |
3 Job Submission
Batch jobs are submitted with the command:
$ sbatch <job-script>
A job script contains options for Slurm in lines beginning with #SBATCH as well as your commands which you want to execute on the compute nodes. For example:
#!/bin/bash
#SBATCH --partition=single
#SBATCH --ntasks=1
#SBATCH --time=00:20:00
#SBATCH --mem=1gb
#SBATCH --export=NONE
echo 'Hello world'
This jobs requests one core (--ntasks=1) and 1 GB memory (--mem=1gb) for 20 minutes (--time=00:20:00) on nodes provided by the partition 'single'.
For the sake of a better reproducibility of jobs it is recommended to use the option --export=NONE to prevent the propagation of environment variables from the submit session into the job environment and to load required software modules in the job script.
4 Partitions
On bwForCluster Helix Production it is necessary to request a partition with '--partition=<partition_name>' on job submission. Within a partition job allocations are routed automatically to the most suitable compute node(s) for the requested resources (e.g. amount of nodes and cores, memory, number of GPUs). The devel partition is the default partition, if no partition is requested.
The partitions devel and single are operated in shared mode, i.e. jobs from different users can run on the same node. Jobs can get exclusive access to compute nodes in these partitions with the "--exclusive" option. The partitions multi is operated in exclusive mode. Jobs in these partitions automatically get exclusive access to the requested compute nodes.
GPUs are requested with the option "--gres=gpu:<number-of-gpus>".
| Partition | Node Access Policy | Node Types | Default | Limits |
|---|---|---|---|---|
| devel | shared | cpu, gpu | ntasks=1, time=00:10:00, mem-per-cpu=1gb | nodes=1, time=00:30:00 |
| single | shared | cpu, gpu | ntasks=1, time=00:30:00, mem-per-cpu=2gb | nodes=1, time=120:00:00 |
| multi | job exclusive | cpu, gpu | nodes=2, time=00:30:00 | nodes=16, time=48:00:00 |
5 Examples
Here you can find some examples for resource requests in batch jobs.
5.1 Serial Programs
#SBATCH --partition=single
#SBATCH --ntasks=1
#SBATCH --time=120:00:00
#SBATCH --mem=4gb
Notes:
- Jobs with "--mem" below 240gb can run on all node types associated with the single partition.
5.2 Multi-threaded Programs
#SBATCH --partition=single
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --time=01:30:00
#SBATCH --mem=50gb
Notes:
- Jobs with "--ntasks-per-node" up to 64 and "--mem" below 240gb can run on all node types associated with the single partition.
5.3 MPI Programs
#SBATCH --partition=multi
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=64
#SBATCH --time=12:00:00
#SBATCH --mem=50gb
Notes:
- "--mem" requests the memory per node. Jobs with "--mem" below 240gb can run on all node types associated with the multi partition.
5.4 GPU Programs
#SBATCH --partition=single
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
#SBATCH --gres=gpu:4
#SBATCH --time=12:00:00
#SBATCH --mem=200gb
Notes:
- The number of GPUs per node is requested with the option "--gres=gpu:<number-of-gpus>"
- It is possible to request a certain GPU type with the option "--gres=gpu:<gpu-type>:<number-of-gpus>". For <gpu-type> put the 'GPU Type' listed in the last line of the GPU Nodes Hardware table.
6 Interactive Jobs
Interactive jobs must NOT run on the logins nodes, however resources for interactive jobs can be requested using srun. The following example requests an interactive session on 1 core for 2 hours:
$ salloc --partition=single --ntasks=1 --time=2:00:00
After execution of this command wait until the queueing system has granted you the requested resources. Once granted you will be automatically logged on the allocated compute node.
If you use applications or tools which provide a GUI, enable X-forwarding for your interactive session with:
$ salloc --partition=single --ntasks=1 --time=2:00:00 --x11
Once the walltime limit has been reached you will be automatically logged out from the compute node.
