single-threaded R, 100% CPU with BLAS, vecLib and ATLAS
Melanie,
On Oct 25, 2012, at 7:16 PM, Melanie Courtot wrote:
Hi, I am trying to run R on my MacBook Pro 2.4 GHz Intel core i5. I am trying to read a csv file, which works fine on my work colleague's machine (under linux) but causes my CPU to go up to 100% and makes the GUI unresponsive and hangs on the command line. Activity monitor indicates there is only one R thread running. I did see that by default R was using the BLAS library, which is single-threaded,
BLAS will have absolutely no effect on read.table() - it will always be single-threaded and it does not use BLAS. The difference between the two machines may be memory - read.table() is not the most efficient way to load a data set and maybe you're running out of memory (but you didn't tell us how you are loading it, really). Cheers, Simon
and that there was an option to use vecLib instead. I did this, and ls -l /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib does return /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib -> libRblas.vecLib.dylib I however still see the same behavior: 100% CPU, single thread. I saw that some MacBook pro (Xeon Nehalem based) had a vecLib bug, so I built the ATLAS library and symlinked R to libtatlas.dylib (unfortunately the pre compiled binairies pointed to in a previous email on the list [1] were not available anymore. Building ATLAS was... fun ;)) I was able to get the shared libraries (using --shared in my config) but still see the same behavior when trying to run my code. I was unsure if I should link to libsatlas.dylib or libtatlas.dylib, so tried both (I guess the latter was the right one though) I tried building R from the source (specifying -arch x86_64 and --enable-BLAS-shlib to be able to switch libraries), but same behavior and it seems it is an identical version to the prepackaged one (I tried with BLAS, vecLib and ATLAS) R info: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows", Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) Any help would be greatly appreciated. Thanks, Melanie [1] https://stat.ethz.ch/pipermail/r-sig-mac/2010-October/007817.html --- M?lanie Courtot MSFHR/PCIRN Ph.D. Candidate, BCCRC - Terry Fox Laboratory - 12th floor 675 West 10th Avenue Vancouver, BC V5Z 1L3, Canada
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