Name: lsg-rbuilder
Owner: SURFsara
Description: Scripts to build optimized versions of R on the SURFsara Life Sciences Grid
Created: 2014-08-21 12:13:07.0
Updated: 2017-11-28 17:19:14.0
Pushed: 2014-08-26 10:02:42.0
Homepage: null
Size: 160
Language: Shell
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The Life Sciences Grid has a basic set of packages supplied by Centos. These packages are not optimized for the architecture of the compute nodes of the life-sciences grid. For better performance, you need to compile optimized versions of the software of choice yourself.
OpenBLAS can be optimized for the Bulldozer architecture on the Life Science Grid compute nodes. If R has to be compiled against an optimzied version of OpenBLAS, it must be compiled on the architecture it was optimized for. This means that R cannot be compiled on the user interface machines, because the user interfaces are virtual machines, which have a limited CPU instruction set.
The solution is to compile OpenBLAS and R on the worker nodes, within a job.
This directory contains a script which downloads and compiles OpenBLAS and R. It uses the most recent versions available at the time of writing:
The script should not be run on the user interface machines. Instead, run the script as a grid job:
qsub R-3.1.1-build-job.sh
This will download OpenBLAS and R, and install everything in
$HOME/opt/R-3.1.1
In the 'benchmarks' directory, there are a few R-scrips for running benchmarks mentioned on the sites below. To run the benchmarks, first, downloade the benchmark tests from sites below. Then submit the jobs using
qsub -q express mass-bench-dist.sh
and
qsub -q express mass-bench-openblas.sh
References: