So my experiments have confirmed that the binary version of OpenBLAS uses onlt two cores. Should the compiled version use more?
I want figure out which package to utilize mulitiple cores in a UNIX environment. Did some research on this a while back but it's a bit fuzzy right now. My main concern is there's a warning about BLAS and multiple cores in the install docs. Will I run into problems? ----- Original Message ----- From: Michael Rutter <[email protected]> To: Dirk Eddelbuettel <[email protected]> Cc: Scott Raynaud <[email protected]>; "[email protected]" <[email protected]> Sent: Tuesday, February 14, 2012 6:47 PM Subject: Re: [R-sig-Debian] Accessto OpenBLAS On 02/14/2012 06:40 PM, Dirk Eddelbuettel wrote: > > On 14 February 2012 at 18:15, Michael Rutter wrote: > | > | > | On 02/14/2012 04:56 PM, Scott Raynaud wrote: > |> My IT people have set up R on a a Kubuntu box with an RWkard > |> front end. I have OpenBLAS set up as a shared BLAS but I'm not > |> sure how to get R to see it. A.3.1 of the installation docs talks > |> about it but I'm not clear if I need a option on my startup line or > |> if I need to find a config file. The BLAS is is in: > |> > |> /usr/lib/openblas-base > |> > |> on my machine. I'm not sure how to confirm that R is seeing > |> the BLAS. > |> > |> Recommendations? > |> > | > | Scott, > | > | There used to be a good post about this on a blog, but the blog has gone > | under. Luckily, I was able to salvage the post from Google cache. Here > | is the relevant part: > | > | Copy the resulting .so shared object library file > | (libgoto2_penrynp-r1.12.so on my machine) to /usr/lib > | The original BLAS library located there is called libblas.so.3gf.0. > | Back this file up: cp libblas.so.3gf.0 libblas.so.3gf.0.keep > | Make a symbolic link to the new BLAS library: > | ln -s libgoto2_penrynp-r1.12.so libblas.so.3gf.0 > | > | Basically, you need to make sure that the file "libblas.so.3gf.0" links > | to the location of your lib. I would find a benchmark file > | (http://r.research.att.com/benchmarks/) to test R before and after > | creating the link, just to make sure it is working. > > Is that really needed? > > a) We never had Goto in the distro for its licensing issues. But there > always was the goto2helper package from Japan which I and other have > used with great success. > > With it, goto BLAS became a drop-in just like Atlas or MKL. That package is hard to find without Dirk's gcdb vignette. Here is the link: http://prs.ism.ac.jp/~nakama/debian/lenny-ism/ That would work to install GotoBLAS. Reworking the helper package for OpenBLAS would make a nice little project. There is an OpenBLAS package for Ubuntu 11.10, but the binary version only uses two cores, at least that what it used the last time I tried it. > b) I haven't had time play with Openblas but I recall Doug Bates telling me > it worked for him (possibly after one or two manual steps I cannot > recall). My guess is that the manual steps are the ones I described above. Michael > c) I hope to get to OpenBlas myself 'soon' and may follow-up then. > > Lastly, and as always, faster BLAS are nice, but BLAS are rarely your > bottleneck with R. > > Hope this helps, Dirk > > | > | Hope this helps, > | Michael > | > | > | _______________________________________________ > |> R-SIG-Debian mailing list > |> [email protected] > |> https://stat.ethz.ch/mailman/listinfo/r-sig-debian > | > | -- > | Dr. Michael A. Rutter > | School of Science > | Penn State Erie, The Behrend College > | Station Road > | Erie, PA 16563 > | http://math.bd.psu.edu/faculty/rutter > | > | _______________________________________________ > | R-SIG-Debian mailing list > | [email protected] > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian > -- Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
