Hi, Although I should, I don't follow too closely in the places I should (I don't know where those places are) to know if Apple is aware of this vecLib breakdown issue ... are they? Where can we go to add our voices/votes for them to fix it?
Apple still has their apple.com/science section, so I guess this should be (somehow) important to them ... maybe we can make an R-SIG-Mac 20-person-strong tidal wave to help force their hand? ;-) -steve On Thu, Oct 21, 2010 at 12:36 PM, Simon Urbanek <simon.urba...@r-project.org> wrote: > On Oct 21, 2010, at 7:47 AM, Stefan Evert wrote: > >> >> On 21 Oct 2010, at 03:28, Simon Urbanek wrote: >> >>> It's not vague at all, it's MacPro4,1 and MacPro5,1 models (you can use use >>> "sysctl hw.model" to find out what you have). If in doubt, check on >>> Wikipedia ;) >>> >>> The latter uses the Nehalem architecture but I don't have a specimen of >>> those so I can't confirm that the bug still holds true for those. >> >> Not just those ... I'm plagued by the same problem on my Penryn-based >> MacBookPro4,1. In 64-bit mode, BLAS performance breaks down to single core >> levels, whereas in 32-bit mode (i.e. R --arch=i386) it uses both cores. I >> posted some benchmark results to this list a few weeks ago. >> > > Well, given that it is only a two-thread CPU there is not much you can gain > so I wouldn't lose my sleep over it. If you have 16-theads CPU it's a while > different story ;). For illustration, those are the timings from your > benchmarks (only those that use BLAS) for 64-bit R 2.1...@10.6.4 on a 2.66GHz > MacPro4,1: > > test R BLAS vecLib ATLAS MKL > inner M %*% t(M) D 19.961 3.470 0.519 0.662 > inner tcrossprod D 0.658 1.867 0.243 0.235 > inner crossprod t(M) D 9.574 1.849 0.242 0.256 > cosine normalised D 0.798 2.009 0.385 0.411 > cosine general D 0.770 1.993 0.380 0.352 > euclid() D 2.072 3.271 1.637 1.635 > euclid() small D 0.515 0.821 0.421 0.395 > > As you can see both MKL and ATLAS outperform vecLib and R BLAS by an order of > magnitude. It's sad, because vecLib used to be fairly well optimized ... (in > fact it is actually some version of ATLAS which is even more strange ...). > > >> My solution has also been to switch to the reference BLAS, which outperforms >> vecLib on most of the operations I benchmarked, except for crossprod(), >> which is terribly slow (more than 10x slower than tcrossprod()). I've just >> tested again with R 2.12.0, and the situation has become even worse: now an >> explicit matrix multiplication M %*% t(M) -- which used to be fast -- >> performs as poorly as crossprod(). >> >> Any ideas about this? The crossprod() slowdown isn't a Mac problem: I got >> similar results on a Pentium Dual Core laptop running Ubuntu. If this is a >> known problem of the reference BLAS, is there any way to work around it? >> >> Apart from the speed hiccups, in my benchmarks vecLib BLAS performed >> consistently slower than the reference BLAS. Is there evidence from other >> benchmarks / hardware architectures that vecLib can be faster? If not, >> perhaps the default should be _not_ to use vecLib on Mac? Or perhaps it >> would be possible to autodetect hardware in the R startup wrapper and select >> the BLAS that's known to run faster on this setup? >> > > I don't think we would want to do that since that would prevent the user from > choosing the BLAS they want to use. We will probably abandon vecLib as the > default for the next release (more due to its numerical instability issues) > and maybe provide all three options (vecLib, R BLAS, ATLAS) for the user to > choose from in case they have a machine that can take advantage of it. > > Cheers, > Simon > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
