====== CLUSTER MANUAL ======


====== Bash files and Batch system ======
What's on this page:\\
  - Dos and don'ts
  - Batch System
  - Creating a job script
  - How to pass command-line parameters to the job script



===== 1. Dos and don'ts =====
  * Never run calculations on the home disk
  * Always use the SLURM queueing system
  * The login via the GUI is only for editing files, submitting jobs and visual inspections
  * Do not run calculations interactively via the GUI
  * Never use spaces for file names, folder names or job process names.


===== 2. Batch System =====

The Psychp01 cluster 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 Psychp01 is [[https://slurm.schedmd.com/|SLURM]] (Simple Linux Utility for Resource Management).


===== 3. Creating a job script =====

To run a job on the batch system you need to create a job script. A job script is a regular shell script (bash) with some directives specifying the number of CPUs, memory, etc., that will be interpreted by the batch system upon submission.\\
After you wrote your job script as shown in the examples, you can start it with:

  sbatch my_job_script_name.sh

You can find job script examples in the [[cluster-jobs|Running jobs]] section. On page 23 of the pdf version of the manual on the [[cluster-guide|main page]], there is a short video on how to run a Python code using a job script. See [[cluster-jobs|here]] for a step-by-step explanation.




===== 4. 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 how to use different parameters and to find a link to a list of possible parameters, see //SLURM Parameters// in the [[cluster-jobs|Running jobs]] section.\\
In SLURM you can do this:

  $ sbatch myscript.sh myinput myoutput 

And then you can pick the parameters up inside the job script:

  #!/bin/bash
  #SBATCH ...
  #SBATCH ...
  ...
  # argument 1 is myinput
  # argument 2 is myoutput
  mybinary.x < ${1} > ${2}

For recommended sets of parameters see also sections [[cluster-advanced_slurm|Advanced SLURM]] and [[cluster-jobs|Running jobs]].


[[{:backward_arrow.png?40|width: 12em}cluster-file_transfer|Transferring files to/from psychp01]][[{:forward_arrow.png?40|width: 12em}cluster-softwares|Softwares on psychp01]]\\
[[{:toc.png?40|width: 12em}cluster-toc|Return to Table of Contents]][[{:main_page.png?40|width: 12em}cluster-guide|Return to main page]]

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