Batch system

The Scicluster system is a resource that is shared between many of users and to ensure fair use everyone must do their computations by submitting jobs through a batch system that will execute the applications on the available resources.

The batch system on Scicluster is SLURM (Simple Linux Utility for Resource Management.)

Creating a job script

To run a job on the system you need to create a job script. A job script is a regular shell script (bash) with some directives started by #SBATCH specifying the number of CPUs, memory, etc., that will be interpreted by the batch system upon submission.

You can find job script examples in Job script examples.

After you wrote your job script as shown in the examples, you can start it with:

sbatch jobscript.sh

How to pass command-line parameters to the job script

It is sometimes convenient if you do not have to edit the job script every time you want to change the input file. Or perhaps you want to submit hundreds of jobs and loop over a range of input files. For this it is handy to pass command-line parameters to the job script. For an overview of the different possible parameters, see SLURM Parameter.

In SLURM you can do this:

$ sbatch myscript.sh myinput myoutput

And then you can pick the parameters up inside the job script using ${n} where n is the nth parameter:

#!/bin/bash

#SBATCH ...
#SBATCH ...
...

# argument 1 is myinput
# argument 2 is myoutput
mybinary.x < ${1} > ${2}

Priority

We recommend you to be as precise as you can when specifying the parameters as they will inflict on how fast your jobs will start to run. We generally use fairshare for prioritizing jobs. This means that users with many jobs running will get a decreased priority compared to other users.

To display information for all users, run:

$ sshare -a