Difference between revisions of "R"
From HPC users
Jump to navigationJump to search
Albensoeder (talk | contribs) |
Albensoeder (talk | contribs) |
||
| Line 19: | Line 19: | ||
== Usage of R and MPI == | == Usage of R and MPI == | ||
For | For parallelization the packages doMPI and Rmpi are installed. To launch an parallel R script inside an [[SGE Job Management (Queueing) System| SGE]] script please use command line | ||
mpirun -bootstrap sge -np $NSLOTS -env I_MPI_FABRICS shm:ofa R --slave | mpirun -bootstrap sge -np $NSLOTS -env I_MPI_FABRICS shm:ofa R --slave -f ''SCRIPTNAME'' ''SCRIPT_CMDLINE_OPTIONS'' | ||
to enable SGE to control all processes of your script. | to enable SGE to control all processes of your script. Please do not use the batch starting sequence ''R CMD BATCH''. | ||
The corresponding parallel environment in the SGE submission script is specified by | The corresponding parallel environment in the SGE submission script is specified by | ||
| Line 29: | Line 29: | ||
#$ -pe impi41 NUMBER_OF_CORES | #$ -pe impi41 NUMBER_OF_CORES | ||
#$ -R y | #$ -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/apps/r/3.0.1/intel/64/2013.0.028/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! | |||
== External links == | == External links == | ||
* [http://www.r-project.org/ R project] | * [http://www.r-project.org/ R project] | ||
* [http://cran.r-project.org/manuals.html R manuals] | * [http://cran.r-project.org/manuals.html R manuals] | ||
Revision as of 12:51, 9 September 2013
There are two R releases available on FLOW and HERO. The actual relase is available by
module load r/3.0.1
With this command the corresponding Intel compilers and Intel MPI will be automatically loaded.
Note: The release 2.15.2 is deprecated and only for legacy on the system.
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/apps/r/3.0.1/intel/64/2013.0.028/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!
