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 > > --- > Mélanie Courtot > MSFHR/PCIRN Ph.D. Candidate, > BCCRC - Terry Fox Laboratory - 12th floor > 675 West 10th Avenue > Vancouver, BC > V5Z 1L3, Canada > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
