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.
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