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Template for using R on a HPC with Slurm

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How to run

Clone git repository

cd ~
git clone https://github.com/ndevln/slurm_template_for_R_Language.git
cd slurm_template_for_R_Language

Optional: Modify files

  1. Modify R library location in example_r_script.R (line 3)
  2. Add your e-mail address to slurm_job.sh (line 11)
  3. Check if QOS medium is avaliable: sacctmgr show qos format=name,priority (slurm_job.sh: line 6)
  4. Load the R module if needed (on CentOS/RHEL) (slurm_job.sh: line 13).

Start Slurm job

sbatch slurm_job.sh

Check job status (replace 'username' with your username on the server):

squeue -u username

This script was tested on the High-Performance-Cluster of the Freie Universität Berlin, Germany

My thanks go to our awesome HPC Team.

High-Performance Computing at ZEDAT

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