Difference between revisions of "R"
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== General remarks == | == General remarks == | ||
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| − | + | You may want to install R locally in your home directory. This puts you in control of the version installed, the packages installed and you can tweak the installation according to your needs. Consequently, before you can use R, you have to do the following: | |
| − | + | * [[Install R]] and the relevant packages | |
| − | + | * Write the code to be executed on the cluster | |
| − | + | * Write the submit script to be submitted via qsub | |
Below each of these steps is documented in detail. | Below each of these steps is documented in detail. | ||
| Line 25: | Line 21: | ||
== Example == | == Example == | ||
| + | == System-wide install == | ||
| + | |||
| + | Available in '''/apps/R-3.0.1'''. The system-wide install of R has been compiled and installed with the commands given below. If this is sufficient for your purposes, you don't have to install your own version in your home directory. | ||
| + | <pre> | ||
| + | $ ./configure --prefix=/apps/R-3.0.1 --enable-R-shlib --with-blas --with-lapack --with-system-zlib --with-system-bzlib --with-system-pcre --with-x=no | ||
| + | $ make | ||
| + | $ make check | ||
| + | $ make install | ||
| + | </pre> | ||
| − | - | + | === Rmpi 0.6-3 === |
| − | -- | + | <pre> |
| + | /apps/R-3.0.1/bin/R CMD INSTALL \ | ||
| + | -l /apps/R-3.0.1/lib64/R/library/ \ | ||
| + | --configure-args=" \ | ||
| + | --with-mpi=/usr/lib64/openmpi/ \ | ||
| + | --with-Rmpi-libpath=/usr/lib64/openmpi/lib/ \ | ||
| + | --with-Rmpi-include=/usr/include/openmpi-x86_64/ \ | ||
| + | --with-Rmpi-type=OPENMPI" \ | ||
| + | /usr/local/src/shared/Rmpi_0.6-3.tar.gz | ||
| + | </pre> | ||
Revision as of 12:11, 4 July 2013
Contents
General remarks
You may want to install R locally in your home directory. This puts you in control of the version installed, the packages installed and you can tweak the installation according to your needs. Consequently, before you can use R, you have to do the following:
- Install R and the relevant packages
- Write the code to be executed on the cluster
- Write the submit script to be submitted via qsub
Below each of these steps is documented in detail.
Installation of R and necessary packages
Submit script
Example
System-wide install
Available in /apps/R-3.0.1. The system-wide install of R has been compiled and installed with the commands given below. If this is sufficient for your purposes, you don't have to install your own version in your home directory.
$ ./configure --prefix=/apps/R-3.0.1 --enable-R-shlib --with-blas --with-lapack --with-system-zlib --with-system-bzlib --with-system-pcre --with-x=no $ make $ make check $ make install
Rmpi 0.6-3
/apps/R-3.0.1/bin/R CMD INSTALL \
-l /apps/R-3.0.1/lib64/R/library/ \
--configure-args=" \
--with-mpi=/usr/lib64/openmpi/ \
--with-Rmpi-libpath=/usr/lib64/openmpi/lib/ \
--with-Rmpi-include=/usr/include/openmpi-x86_64/ \
--with-Rmpi-type=OPENMPI" \
/usr/local/src/shared/Rmpi_0.6-3.tar.gz
