From ALICE Documentation

Revision as of 08:36, 29 June 2020 by Deuler (talk | contribs)

Running R from bacth scripts is a programming language and software environment for statistical computing and graphics.

For use on the kingspeak, ember, and ash clusters, and on Linux desktops, we have installed R from the source code. We also installed a number of external R libraries. If there is another library that you want to use, please try to install the library in your own environment. If you run into trouble, feel free to ask us to perform the installation.

The currently supported version is 3.3.2 (Centos7). It was built with the Intel compilers and its threaded Math Kernel Library (MKL). The presence of MKL may result in a considerable speed-up when compared to R builds which rely solely on non-optimized mathematical libraries. As a rule of thumb, programs that use a lot of floating point numerical calculations should benefit from multi-threading the most.

By default we have turned off multi-threading by setting the environmental variable OMP_NUM_THREADS to 1, i.e.

setenv OMP_NUM_THREADS 1 # Tcsh/Csh Shell export OMP_NUM_THREADS=1 # Bash Shell

to facilitate easier use of parallel independent calculations. If you want to run R in a multithreaded fashion (e.g. on a compute node), we strongly recommend not to use more threads than there are physical cores on the node.