R

There are two R releases available on FLOW and HERO. The actual relase is available by

 module load r/3.2.1

With this command the corresponding Intel compilers and Intel MPI will be automatically loaded.

Additional installed packages

The actual release contains a lot of additional R packages, for example

 abind, ade4, ade4TkGUI, akima, ape, BH, bitops, boot, caTools, chron, cluster,
 coda, codetool, colorspace, DAAG, date, deldir, dichromat, digest, doMC, doMPI, ensembleBMA,
 evaluate, fields, foreach, forecast, foreign, Formula, fracdiff, fts, gdata,
 geosphere, ggplot2, gplots, gtable, gtools, hexbin, Hmisc, ifultools, iterators,
 its, KernSmooth, labeling, lattice, latticeExtra, LearnBayes, mapproj, maps,
 maptools, MASS, Matrix, misc3d, mnormt, mondate, multicore, munsell, mvtnorm,
 ncdf, nlme, nnet, nws, pixmap, plyr, pracma, proto, quadprog, quantreg,
 randomForest, raster, rasterVis, RColorBrewer, Rcpp, RcppArmadillo, RCurl,
 reshape2, rgl, R.matlab, R.methodsS3, Rmpi, R.oo, Rssa, RUnit, R.utils,
 sandwich, sapa, scales, signal, solaR, sp, spam, SparseM, spdep, splancs,
 splus2R, stringr, strucchange, survival, svd, testthat, timeDate,
 timeSeries, tis, tkrplot, tripack, truncnorm, tseries, VGAM, waveslim,
 XML, xts, zoo

and many more...

Usage of R and MPI

For parallelization the packages doMPI and Rmpi are installed. To launch an parallel R script inside an SGE script please use command line

  mpirun -np $NSLOTS R --slave -f SCRIPTNAME SCRIPT_CMDLINE_OPTIONS

to enable SGE to control all processes of your script. Please do not use the batch starting sequence R CMD BATCH.

The corresponding parallel environment in the SGE submission script is specified by

 #$ -pe impi NUMBER_OF_CORES
 #$ -R y

Note (only!) for doMPI:

• Before you start R with the mpirun command you have to unset the environment variable R_PROFILE in your SGE-Script. Otherwise the MPI processes were not spawned. Please add following line to your SGE-script

  unset R_PROFILE

• Please use mpi.quit() at the end of your script. Otherwise it will not end.
• Here a small demo R script for doMPI (it writes in b the current rank of MPI):

 #!/usr/bin/env Rscript
 #
 # file name: test_dompi.R
 #
 
 library(doMPI)
 library("foreach")
 
 # doMPI start
 cl <- startMPIcluster()
 registerDoMPI(cl)
 
 b<-foreach(i=0:1000, .combine="c") %dopar% {
   as.integer(Sys.getenv("PMI_RANK"))
 }
 closeCluster(cl)
 print(b)
 
 mpi.quit()

and he corresponding SGE-script

 #!/bin/bash
 
 #$ -S /bin/bash
 #$ -N test_dompi
 #$ -cwd
 #$ -l h_rt=24:00:0
 #$ -l h_vmem=1800M
 #$ -pe impi 36
 #$ -R y
 #$ -j y
 
 # load modules
 module load r/3.2.1
 
 # unset the environment variable which is needed for Rmpi
 # but makes problems with doMPI
 unset R_PROFILE
 
 # run R in parallel
 mpirun -np $NSLOTS R --slave -f ./test_dompi.R

Note (only!) for Rmpi:

• The MPI processes were spawned by the mpirun command. The Rmpi command mpi.spawn.Rslaves() is not necessary and should not be used within the script!

Usage of NetCDF and R

A package for NetCDF has been installed together with R. In order to use please add the command

module load netcdf/4.3.2/gcc/4.4.7

to your job script before starting R. Your R-script should include a line

library(ncdf)

to load the NetCDF library. Please refer to the documentations of NetCDF and R for more information.

External links

• R project
• R manuals