HPC:R
R (programming language)
There are currently several versions of the R programming language installed across all the HPC nodes.
Usage
Currently, the default version of R installed across all the HPC nodes, is version 3.0.1.
[asrini@node062 ~]$ which R /usr/bin/R [asrini@node062 ~]$ R --version R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see http://www.gnu.org/licenses/.
Note: This version (3.0.1) is likely to be removed as the default version and will be made available as module.
Other R versions installed across the HPC nodes can be loaded as a module
[asrini@node062 ~]$ module show R-3.1.1 ------------------------------------------------------------------- /usr/share/Modules/modulefiles/R-3.1.1: module-whatis GNU R prepend-path PATH /opt/software/R/3.1.1/bin prepend-path MANPATH /opt/software/R/3.1.1/share/man ------------------------------------------------------------------- [asrini@node062 ~]$ module load R-3.1.1 [asrini@node062 ~]$ R --version R version 3.1.1 (2014-07-10) -- "Sock it to Me" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see http://www.gnu.org/licenses/. [asrini@node062 ~]$ module show R-3.1.2 ------------------------------------------------------------------- /usr/share/Modules/modulefiles/R-3.1.2: module-whatis GNU R prepend-path PATH /opt/software/R/3.1.2/bin prepend-path MANPATH /opt/software/R/3.1.2/share/man ------------------------------------------------------------------- [asrini@node062 ~]$ module load R-3.1.2 [asrini@node062 ~]$ R --version R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see http://www.gnu.org/licenses/.
R libraries/packages
Several difficult to install R packages/libraries have been installed across all the HPC nodes for every version of R that is installed on the cluster. These typically include various BioConductor packages and some other packages that would otherwise need administrative privileges to install. Users are encouraged to install R packages needed for their work, if the desired package is not already installed. To see a full listing of R packages installed run the following command in an interactive shell:
[asrini@node062 ~]$ echo 'library()' | R --slave
