Running R

Taken from Wesleyan Cluster Wiki: https://dokuwiki.wesleyan.edu/doku.php?id=cluster:73#r_r_parallel

R & R/parallel

Native CentOS R is most up to date on node swallowtail for interactive use. IT also has a bunch of packages installed.

Note: All versions were compiled with Blas and Lapack libraries found in the Cluster Math Kernel Libraries.

Set your environment as follows for 3.1.0

 . /share/apps/intel/composerxe/bin/iccvars.sh intel64
 . /share/apps/intel/composerxe/bin/ifortvars.sh intel64
 export MKL_HOME=/share/apps/intel/composerxe/mkl

                                                                                   
export PATH=/share/apps/R/3.1.0/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/R/3.1.0/lib64/R/lib:$LD_LIBRARY_PATH

Set your environment as follows for 2.14.1

  • contains modules: Igraph and Multicore
 . /share/apps/intel/composerxe/bin/iccvars.sh intel64
 . /share/apps/intel/composerxe/bin/ifortvars.sh intel64
 export MKL_HOME=/share/apps/intel/composerxe/mkl

                                                                                   
export PATH=/share/apps/R/2.14.1/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/R/2.14.1/lib64/R/lib:$LD_LIBRARY_PATH

Set your environment as follows for 2.8.1

        . /share/apps/intel/cce/10.0.025/bin/iccvars.sh
        . /share/apps/intel/fce/10.0.025/bin/ifortvars.sh


export PATH=/share/apps/R/2.8.1/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH

Please consult the README file in install dir to set your environment.