General information about R¶

Instructions for using R at PDC¶

R is a programming language and software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing. The R language is widely used among statisticians and data miners for developing statistical software and data analysis. Polls, surveys of data miners, and studies of scholarly literature databases show that R’s popularity has increased substantially in recent years More information can be found at https://cran.r-project.org/

R Packages¶

List Packages¶

To see a list of installed packages, please type:

         > installed.packages()

        

How to install local packages¶

As many packages interfere with each other it is often a good idea to install them locally in your userspace instead. To be able to do that you must first define an R folder for the packages

         export R_LIBS_USER=~/R/library
mkdir -p ~/R/library

Running are you are able to see the local folder:

         $ module add R
$ R
> .libPaths()
[1] "/afs/pdc.kth.se/home/h/hzazzi/R/library"
[2] "/pdc/vol/R/3.2.0/lib64/R/library"

        

To install packages:

         > install.packages("package name",lib=.libPaths()[1])

        

Install global packages¶

Some packages are installed by default by support instructions at http://www.bu.edu/tech/support/research/software-and-programming/common-languages/r-basics/r-faq/ In general we can add new packages directly from within R, but to be globally accessible they must be installed in the global repository rather than your home catalogue.:

         $ module add R
$ R
> .libPaths()
[1] "/afs/pdc.kth.se/home/h/hzazzi/R/library"
[2] "/pdc/vol/R/3.2.0/lib64/R/library"

        

All the packages installed at PDC where installed in the 2nd path, which is globally accessible. To install packages:

         > install.packages("package name",lib=.libPaths()[2])

        

Which will install [package name] in R.

OBS Always try to use the swedish repository for packages. There is a bug in R 3.2.2, meaning you will get a short list of CRAN repositories. In this case choose (HTTP mirrors) and then the swedish respoitory.

Special installation instructions for Tegner and Rmpi¶

To install Rmpi you need to have compile the package using OpenMPI, therefore we need to redirect the compile.:

         $ module add gcc/5.1 openmpi/1.8-gcc-5.1
$ R
$ install.packages("Rmpi", lib = .libPaths()[2], configure.args = "--with-Rmpi-type=OPENMPI --with-Rmpi-libpath=/pdc/vol/openmpi/1.8/gcc/5.1/lib --with-Rmpi-include=/pdc/vol/openmpi/1.8/gcc/5.1/include --with-Rmpi=/pdc/vol/openmpi/1.8/gcc/5.1")

        

Special installation instructions for Beskow and Rmpi¶

To install Rmpi you need to have compile the package using MPI, and also remove dependency of the library opa.

download Rmpi from https://cran.r-project.org/web/packages/Rmpi/index.html
Unpack
Edit configure and create a new entry called CRAY_NOLOPA, which is the same as CRAY without -lopa
pack into tar.gz

           $ MPICH_CRAY=/opt/cray/mpt/7.0.5/gni/mpich2-cray64/83
$ MAKEFLAGS="CC=cc" R CMD INSTALL Rmpi.tar.gz --configure-args="--with-Rmpi-include=$MPICH_CRAY/include --with-Rmpi-libpath=$MPICH_CRAY/lib --with-Rmpi-type=CRAY_NOLOPA CC=cc" --no-test-load

More information can be found in http://www.ahschulz.de/2015/01/02/installing-r-on-hlrn-cray-xc30xc40-and-enabling-rmpi/

Disclaimer¶

PDC takes no responsibility for the correctness of results produced with the binaries. Always evaluate the binaries against known results for the systems and properties you are investigating before using the binaries for production jobs.

Installed software¶

Cluster	How to use	How to build
Dardel	4.1.1.1 4.1.2	4.1.1.1 4.1.2

PDC Center for High Performance Computing