Difference between revisions of "Submit R jobs on Abel"

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(Created page with "<div class="vrtx-introduction"> This is an example of a Matlab submit script for use on the Abel cluster. Abel usage is documented at [http://www.uio.no/english/services/it/re...")
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Revision as of 11:00, 27 April 2015

This is an example of a Matlab submit script for use on the Abel cluster. Abel usage is documented at UiOs HPC pages


For normal off-line non-parallell R running on any Linux server, you can simply do e.g. 

module load R

R CMD BATCH R_program.r

For large jobs, this script should set you up OK at the Abel cluster:

  1. !/bin/bash
    # Job name:
    #SBATCH --job-name=R
    #
    # Project (change to your :
    #SBATCH --account=geofag
    #
    # Wall clock limit:
    #SBATCH --time=1000:0:0
    #
    # Max memory usage per core (MB):
    #SBATCH --mem-per-cpu=2000M
    #
    # Number of tasks (cores):
    #SBATCH --ntasks-per-cpu=12
    #
    1. Setup job environment
      source /cluster/bin/jobsetup
  1. Load R module

module load R

#Set variable with number of processors and load mpi

export OMP_NUM_THREADS=12 

module load R openmpi.gnu
mpirun -np 1 R CMD BATCH --no-save --no-restore R_program.r

  1. End of script



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