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submit.sh
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submit.sh
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#!/bin/bash -l
# R MPI parallel job
# Request wallclock time (format hours:minutes:seconds).
#$ -l h_rt=3:00:0
# Request 1 gigabyte of RAM per process.
#$ -l mem=300M
# Set the name of the job.
#$ -N vs_ew
# Select the MPI parallel environment with 32 processes
#$ -pe mpi 30
# Load R/GRASS environment
echo "running init.sh script..."
source /home/tcrnbgh/Scratch/rmal_vs/init.sh
echo "done!"
# Set the working directory to somewhere in your scratch space. This is
# necessary because the compute nodes cannot write to your $HOME
# NOTE: this directory must exist.
# set working dir
#$ -wd /home/tcrnbgh/Scratch/rmal_vs
# Run our MPI job. GERun is our wrapper for mpirun, which launches MPI jobs
echo "running gerun..."
gerun /home/tcrnbgh/RMPISNOW_bgh < /home/tcrnbgh/Scratch/rmal_vs/rscript/analysis.R
echo "done!"