Difference: R ( vs. 1)

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About this wiki

The following best practices document aims to provide some hints and examples on how to install and configure R on a grid based infrastructure.

About R

  • R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.
  • To download R, please choose your preferred CRAN mirror.
  • If you have questions about R like how to download and install the software, or what the license terms are, please read the FAQs.

Source Pack

The following source packs are available for download.

Pack File
<-- -->
Sorted descending
rpm xdg-utils-1.0.2-2.el5.noarch.rpm
rpm R-devel-2.14.1-1.el5.x86_64.rpm
rpm R-core-2.14.1-1.el5.x86_64.rpm
rpm R-2.14.1-1.el5.x86_64.rpm
rpm libRmath-devel-2.14.1-1.el5.x86_64.rpm
rpm libRmath-2.14.1-1.el5.x86_64.rpm

System requirements

The instructions from this best practice have been tested on a:
  • OS: Scientific Linux SL release 5.4 (Boron)
  • Compiler: any
  • Arch: x86_64

Before to install R, please install from repo the following list of packages:

$ yum install -y tk-devel 
$ yum install -y tetex-latex 
$ yum install -y tcl-devel 
$ yum install -y pcre-devel 
$ yum install -y bzip2-devel 
$ yum install -y texinfo-tex

Create and deploy the SW tar in grid

By using the rpm2cpio command extract the rpm files and create the SW tar-ball to be deployed

rpm2cpio *.rpm | cpio -idmv

$ tree R-2.14.1-1.el5.x86_64 -L 3
R-2.14.1-1.el5.x86_64
|-- etc
|   |-- ld.so.conf.d
|   |   `-- R-x86_64.conf
|   `-- rpm
|       `-- macros.R
`-- usr
    |-- bin
    |   |-- R
    |   |-- Rscript
    |   |-- xdg-desktop-icon
    |   |-- xdg-desktop-menu
    |   |-- xdg-email
    |   |-- xdg-icon-resource
    |   |-- xdg-mime
    |   |-- xdg-open
    |   `-- xdg-screensaver
    |-- include
    |   |-- R
    |   `-- Rmath.h
    |-- lib
    |   `-- rpm
    |-- lib64
    |   |-- R
    |   |-- libRmath.so
    |   `-- pkgconfig
    `-- share
        |-- R
        |-- doc
        |-- info
        |-- man
        `-- texmf

18 directories, 13 files

Testing the R Project for Statistical Computing in grid

This is an example of JDL file that can be used for testing:

$ cat R.jdl 
[
Executable = "/bin/sh";
Arguments = "start_R_macro.sh macro.r";

StdOutput = "std.out";
StdError = "std.err";

InputSandbox = {"start_R_macro.sh","macro.r"};
OutputSandbox = {"std.out", "std.err", "out.ps"};

Requirements   = Member("VO-gridit-prod-R-2.14.1-1-SL5-x86_64-gccany", other.GlueHostApplicationSoftwareRunTimeEnvironment);
]

This is the bash script and the macro sent in InputSandbox with the JDL file:

$ cat start_R_macro.sh 
#!/bin/sh
${VO_GRIDIT_SW_DIR}/R-2.14.1-1.el5.x86_64/usr/bin/R --vanilla < $1 > std.out

$ cat macro.r 
postscript("out.ps")
x<-c(1,2,3,4,5,6,7,8)
y<-c(1,2,3,4,5,6,7,8)
plot(x,y,xlim=range(0:10),ylim=range(0:10),type='b',main="X vs Y")
text(4,6,label="Slope=1")
title("X vs Y")
lines(x,y)
dev.off()
q()

References

The R Project for Statistical Computing

Manual

-- GiuseppeLaRocca - 2012-02-07

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