Difference between revisions of "R"
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and many more... | and many more... | ||
== Usage of R | == Usage of R and MPI == | ||
For parallel scripts the R installation contains the package Rmpi. To launch an parallel R script inside an [[SGE Job Management (Queueing) System| SGE]] script please use command line | For parallel scripts the R installation contains the package Rmpi. To launch an parallel R script inside an [[SGE Job Management (Queueing) System| SGE]] script please use command line | ||
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to enable SGE to control all processes of your script. | to enable SGE to control all processes of your script. | ||
The parallel environment is specified by | The corresponding parallel environment in the SGE submission script is specified by | ||
#$ -pe impi41 NUMBER_OF_CORES | #$ -pe impi41 NUMBER_OF_CORES | ||
Revision as of 13:28, 1 July 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, signal, solaR, stringr, timeDate, truncnorm, VGAM, zoo
and many more...
Usage of R and MPI
For parallel scripts the R installation contains the package Rmpi. To launch an parallel R script inside an SGE script please use command line
mpirun -bootstrap sge -np $NSLOTS -env I_MPI_FABRICS shm:ofa R --slave SCRIPTNAME SCRIPT_CMDLINE_OPTIONS
to enable SGE to control all processes of your script.
The corresponding parallel environment in the SGE submission script is specified by
#$ -pe impi41 NUMBER_OF_CORES #$ -R y
