Compile R with GotoBLAS

I want to share my experience to use GotoBLAS as an external multithread library of R. I didn’t make through performance test with other libraries (such as ATLAS) but I did got lot of performance gains with GotoBLAS in using R.

1. GotoBLAS from http://www.tacc.utexas.edu/resources/software
Follow instructions in 02QuickInstall.txt.

2. CBLAS from http://www.netlib.org/blas/blast-forum/cblas.tgz
This is not required for using R but you may need this for using GSL(GNU Scientific Library)
a. If the architecture is Linux, type
$ ln –s Make.LINUX Make.in
b. In Make.in, Modify BLLIB, CBDIR and –fPIC –lpthread to LOADER option.
c. Type make all for building libraries and testing
d. After completing, go to lib/LINUX and type
$ ld -melf_x86_64 -shared -soname libgotocblas.so -o libgotocblas.so cblas_LINUX.a

Note. try to use –m64 or –m32 if you are working with powerpc

3. R from http://cran.r-project.org/
Run configure as follows:
$ export GOTOBLAS_LIB=PATH/TO/GOTOBLAS_LIB
$ mkdir build_goto; cd build_goto;
$ ../configure --prefix=$HOME/usr/R/ --with-blas="-L$GOTOBLAS_LIB -lgotoblas -lpthread" --enable-R-shlib --enable-R-static-lib --enable-BLAS-shlib

Create AVI from R plot

1. In R, save plots as postscript (or png) files by adding sequence number. For example,

postscript(sprintf("%04d.eps", i))

2. By using ImageMagick’s convert command line tool, convert images from eps to png (You may skip if you have png files)

for f in *.eps; do convert -rotate 90 $f png32:$f.png; done

You may want to add the following options:

-resize 1280x720 : change image size
-bordercolor white -border 0x0 : add white background

3. Create AVI by using ffmpeg

ffmpeg -r 15 -sameq -i %04d.eps.png out.avi

You can control frame rate (-r rate) and quality (-sameq or –b bitrate)

 

Note:

If you need speed-up in conversion, you may try to use a bash script parallel.sh in http://pebblesinthesand.wordpress.com/2008/05/22/a-srcipt-for-running-processes-in-parallel-in-bash/