Difference between revisions of "R"
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There are two R releases available on FLOW and HERO. The actual relase is available by | There are two R releases available on FLOW and HERO. The actual relase is available by | ||
module load r/3. | module load r/3.1.1 | ||
With this command the corresponding Intel compilers and Intel MPI will be automatically loaded. | With this command the corresponding Intel compilers and Intel MPI will be automatically loaded. | ||
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* Before you start R with the ''mpirun'' command you have to set the environment variable R_PROFILE in your SGE-Script. Otherwise the MPI processes were not spawned. Please add following line to your SGE-script | * Before you start R with the ''mpirun'' command you have to set the environment variable R_PROFILE in your SGE-Script. Otherwise the MPI processes were not spawned. Please add following line to your SGE-script | ||
export R_PROFILE="/cm/shared/apps/ | export R_PROFILE="/cm/shared/uniol/apps/R/3.1.1/lib64/R/library/Rmpi/Rprofile" | ||
* 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! | * 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! | ||
Revision as of 18:51, 22 January 2015
There are two R releases available on FLOW and HERO. The actual relase is available by
module load r/3.1.1
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
chron, abind, ade4, akima, bitops, caTools, circular, doMC, doMPI, ensembleBMA, foreach, gdata, geosphere, gplots, gtools, hht, iterators, lattice, latticeExtra, ncdf, raster, RColorBrewer, RCurl, RMpi, signal, solaR, stringr, timeDate, truncnorm, VGAM, 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 -bootstrap sge -np $NSLOTS -env I_MPI_FABRICS shm:ofa R --slave -f SCRIPTNAME SCRIPT_CMDLINE_OPTIONS
to enable SGE to control all processes of your script. Please do not use the batch starting sequence R CMD BATCH.
The corresponding parallel environment in the SGE submission script is specified by
#$ -pe impi41 NUMBER_OF_CORES #$ -R y
Note (only!) for Rmpi:
- Before you start R with the mpirun command you have to set the environment variable R_PROFILE in your SGE-Script. Otherwise the MPI processes were not spawned. Please add following line to your SGE-script
export R_PROFILE="/cm/shared/uniol/apps/R/3.1.1/lib64/R/library/Rmpi/Rprofile"
- 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!
