This page contains all important information about the batch system Slurm, that you will need to run software on the HLRN. It does not contain every feature that Slurm has to offer. For that, please consult the official documentation and the man pages.
Submission of jobs mainly happens via the
sbatch command using jobscript, but interactive jobs and node allocations are also possible using
salloc. Resource selecttion (e.g. number of nodes or cores) is handled via command parameters, or may be specified in the job script.
To match your job requirements to the hardware you can choose among various partitions. Each partition has its own job queue. All available partitions and their corresponding walltime, core number, memory, CPU/GPU types are listed in Compute node partitions.
|# nodes||-N <#>|
|# tasks||-n <#>|
|# tasks per node||#SBATCH --tasks-per-node <#>||Different defaults between mpirun and srun|
|standard96 (Lise), medium40 (Emmy)|
# CPUs per task
|-c <#>||interesting for OpenMP/Hybrid jobs|
|Wall time limit||-t hh:mm:ss|
|--mail-type=ALL||See sbatch manpage for different types|
|Project/Account||-A <project>||Specify project for NPL accounting|
A job script can be any script that contains special instruction for Slurm. Most commonly used forms are shell scripts, such as
bash or plain
sh. But other scripting languages (e.g. Python, Perl, R) are also possible.
The job scripts have to have a shebang line at the top, followed by the
#SBATCH options. These
#SBATCH comments have to be at the top, as Slurm stops scanning for them after the first non-comment non-whitespace line (e.g. an
echo or variable declaration).
More examples can be found at Examples and Recipes.
Interactive jobs can be started with the additional options
--pty --interactive , e.g.
Important slurm commands
The commands normally used for job control and management are
- Job submission:
srun <arguments> <command>
- Job status of a specific job:
squeue -j jobIDfor queues/running jobs
$ scontrol show job jobIDfor full job information (even after the job finished).
- Job cancellation:
scancel -i -u $USERcancel all your jobs (
-u $USER) but ask for every job (
scancel -9send kill
- Job overview:
$ squeue -l --me
- Job start (estimated):
squeue --start -j jobID
- Workload overview of the whole system:
sinfo --format="%25C %A") ,
Using the Shared Nodes
We provide a varying number of nodes from the large40 and large96 partitions as post processeing nodes in a shared mode, so that multiple jobs can run at once on a single node. You can request CPUs and memory and should take care, that you do not exceed your limits. For each CPU/Hyperthread, there is about 9.6Gb of Memory on large40:shared or 4 on the large96:shared partition.
The maximum walltime on the shared partitions is 2 days.
This is an example for a job script using 10 cores. As this is not a MPI job, srun/mpirun is not needed. This jobs memory usage should not exceed10 * 4096 = 40960Mb
The maximum runtime is set per partition and can be viewed either on the system with
sinfo or here. There is no minimum walltime (we cannot stop your jobs from finishing, obviously), but a walltime of at least 1 hour is encouraged. A large amount of smaller, shorter jobs can cause problems with our accounting system. The occasional short job is fine, but if you submit larger amounts of jobs that finish (or crash) quickly, we might have to intervene and temporarily suspend your account. If you have lots of smaller workloads, please consider combining them into a single job that uses at least 1 hour.
Slurm offers a lot of options for job allocation, process placement, job dependencies and arrays and much more. We cannot exhaustively cover all topics here. As mentioned at the top of the page, please consult the official documentation and the man pages for an in depth description of all parameters.
+48 Hour Jobs & beyond
Most Compute node partitions have a maximal wall time of 12 hours. In contrast, 48 hours is offered per default by all shared partitions and medium40, large40 of Emmy. During normal office hours, one can request the extension of the wall time of any running job (mail with your user and job ID to support[at]hlrn.de). Alternatively - also per mail request (including user and project ID) - permanent access to run 48h jobs on all partitions of Lise and/or Emmy can be granted (by adding
#SBATCH -q 48h). However, we recommend permanent access to the 48h QoS (
#SBATCH -q 48h) only as a last resort: we do not guarantee to refund your NPL on the 48h QoS if something fails. Before, you should exploit all possibilities to parallelize/speed up your code or make it restartable (see below).
Dependent & Restartable Jobs - How to pass the wall time limit
If your simulation is restartable, it might be handy to automatically trigger a follow-up job. Simply provide the ID of the previous job as an additional sbatch argument:
squeue -l -u $USER will mark all your dependent jobs with "(Dependency)" in the column "NODELIST(REASON)".
Please note: As soon as a follow-up jobscript (sbatch file) is submitted, you can not change its content any more. Lines starting with #SBATCH will be evaluated immediately. The remaining content of the jobscript is evaluated as soon as the dependency condition is fulfilled and compute nodes are available. Besides
afterok there exist other dependency types (sbatch man page).
Job arrays are the preferred way to submit many similar job. Jobs, for instance, if you need to run the same program on a number of input files, or with different settings or run them with a range of parameters. Arrays are created with the
-a start-finish sbatch parameter. E.g.
sbatch -a 0-19 will create 20 jobs indexed from 0 to 19. There are different ways to index the arrays, which are described below.
The behavior of the jobs can then be tied to Slurm Environment variables, which tell the program, which part of the array they are.
Job Array Indexing, Stepsize and more
Slurm supports a number of ways to set up the indexing in job arrays.
-a 0-5:2(same as
-a 0-5:2,20(same as
Additionally, you can limit the number of simultaneously running jobs with the
%x parameter in there:
-a 0-11%4only four jobs at once
-a 0-11%1run all jobs sequentially
-a 0-5:2,20%2everything combined. Run IDs 0,2,4,20, but only two at a time.
You can read everything on array indexing in the sbatch man page.
Slurm Array Environment Variables
The most used environment variable in Slurm arrays is
$SLURM_ARRAY_TASK_ID. This contains the index of the job in the array and is different in every Job of the array. Other variables are:
SLURM_ARRAY_TASK_COUNT Total number of tasks in a array. SLURM_ARRAY_TASK_ID Job array ID (index) number. SLURM_ARRAY_TASK_MAX Job array's maximum ID (index) number. SLURM_ARRAY_TASK_MIN Job array's minimum ID (index) number. SLURM_ARRAY_TASK_STEP Job array's index step size. SLURM_ARRAY_JOB_ID Job array's master job ID number.
Example Job Array
This is an example of a a job array, creates a job for every file ending in “.inp” in the current workding directory
In this case, you have to get the number of files beforehand (fill in the X). You can also automatically do that by removing the
#SBATCH -a line and adding that information when submitting the job:
sbatch -a 0-$(($(ls ./*.inp | wc -l)-1)) jobarray.sh
The part in the parenthesis just uses
ls to output all .inp files, counts them with
wc and then subtracts 1, since bash arrays start counting at 0.