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RMPI installation
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(RMPI installation) |
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==== Rmpi ==== <!--T:16--> | ==== Rmpi ==== <!--T:16--> | ||
Below is the procedure to install [https://cran.r-project.org/web/packages/Rmpi/index.html Rmpi], an interface (wrapper) to MPI routines, which allow R to run in parallel. | |||
First, load the R module. You can find out which are available by running: | |||
module spider r | |||
In this case we choose the latest (as of November, 2017): | |||
module load r/3.4.0 | |||
Next, download the latest version of the software from [https://cran.r-project.org/web/packages/Rmpi/index.html]. Change the version number to whatever is desired. | |||
wget https://cran.r-project.org/src/contrib/Rmpi_0.6-6.tar.gz | |||
Then specify the directory to install the package files in a directory you can write to. The name can be changed as desired. | |||
mkdir -p ~/local/R_libs/ | |||
export R_LIBS=~/local/R_libs/ | |||
Finally, run the install command. | |||
<source lang="bash"> | |||
R CMD INSTALL --configure-args="--with-Rmpi-include=$EBROOTOPENMPI/include --with-Rmpi-libpath=$EBROOTOPENMPI/lib --with-Rmpi-type='OPENMPI' " Rmpi_0.6-6.tar.gz | |||
</source> | |||
This will use the default version of MPI to perform the install, which is currently 2.1.1. | |||
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