UMass Boston

R scripts are available for

• Chimera
• GHPCC

Click here to download sample R scripts, also available on chimera at

                      /share/apps/training/sample_scripts/R

hello_world.r

write('Hello, World!',stdout())
write('from',stdout())
write(Sys.info()[["nodename"]],stdout())

Script to submit a job

#!/bin/bash
#$-S /bin/bash
#
#$ -l h_rt=01:00:00
#$-q scavenger.smp
#$ -N r_Hello_World
#$ -P SCAVENGER
#$ -pe smp 1
#$ -cwd
#

# Diagnostic/Logging Information
echo "using $NSLOTS CPUs"
echo `date`

# load the R module; change the version if needed
module load R/3.2.3

# run R
Rscript --vanilla hello_world.r   

#Diagnostic/Logging Information
echo "Finish Run"
echo "end time is `date`"

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R in parallel

hello_parallel.r

library(pbdMPI, quiet = TRUE)
init()
.comm.size <- comm.size()
.comm.rank <- comm.rank()

write(paste('Hello, World! from process ', .comm.rank, 'of', .comm.size) ,stdout())

### Finish
finalize()

Script to submit a parallel job

#!/bin/bash
#$-S /bin/bash
#
#$ -l h_rt=01:00:00
#$-q scavenger.smp
#$ -N r_parallel
#$ -P SCAVENGER
#$ -pe smp 4
#$ -cwd
# Diagnostic/Logging Information
echo "using $NSLOTS CPUs"
echo `date`

# load the R module; change the version if needed
module load R/3.2.3
module load openmpi/1.8.3

# run R under mpi
mpiexec Rscript --vanilla hello_parallel.r  

#Diagnostic/Logging Information
echo "Finish Run"
echo "end time is `date`"

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On GHPCC

Script to submit a job

#!/bin/bash
# Usage:
#BSUB -J "Sample-R"
#BSUB -R rusage[mem=4096]
#BSUB -q short
#BSUB -W 4:00

#BSUB -e samp_r.err

module load R/3.2.2

Rscript  --vanilla hello_world.r   

#Diagnostic/Logging Information
echo "Finish Run"
echo "end time is `date`"

Script to submit a parallel job

#!/bin/bash
# Usage:
#BSUB -J "R-parallel"
#BSUB -R rusage[mem=4096]
#BSUB -q short
#BSUB -W 4:00

#BSUB -e samp_r.err

module load R/3.2.2
module load openmpi/1.6.5

Rscript  --vanilla hello_parallel.r

#Diagnostic/Logging Information
echo "Finish Run"
echo "end time is `date`"

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