My R with Atlas configured to use 4 cores uses 4 cores. Note however that you only get the 4 cores for the actual multiplication, not the matrix generation.
I'm probably several years behind the curve, but my experience is that if you download source R and do the standard ./configure make make install sequence, R will not use an external BLAS. The manual basically states as much: The linear algebra routines in R can make use of enhanced BLAS (Basic Linear Algebra Subprograms, http://www.netlib.org/blas/faq.html) routines. However, these have to be explicitly requested at configure time: R provides an internal BLAS which is well-tested and will be adequate for most uses of R. Unless the manual is out of date, I suspect that despite the apparent linking of the dynamic ATLAS library R still uses its own internal, single-threaded, BLAS. Peter On Wed, May 26, 2010 at 8:29 PM, Jonathan Greenberg <greenb...@ucdavis.edu> wrote: > > Peter and Dirk: > > Thanks for the quick response -- I'm trying to get multiple CPU > responses as Peter indicated should happen, but those R commands only > illicit a single CPU response. > > When I check the libraries: > > ldd /usr/lib/R/bin/exec/R > linux-vdso.so.1 => (0x00007fffd05ff000) > libR.so => /usr/lib/R/lib/libR.so (0x00007f5f3b667000) > libc.so.6 => /lib/libc.so.6 (0x00007f5f3b313000) > libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007f5f3a7fe000) > libg fortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f5f3a512000) > libm.so.6 => /lib/libm.so.6 (0x00007f5f3a290000) > libreadline.so.6 => /lib/libreadline.so.6 (0x00007f5f3a04b000) > libpcre.so.3 => /lib/libpcre.so.3 (0x00007f5f39e1c000) > libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00007f5f39c0c000) > libz.so.1 => /usr/lib/libz.so.1 (0x00007f5f399f4000) > libdl.so.2 => /lib/libdl.so.2 (0x00007f5f397f0000) > /lib64/ld-linux-x86-64.so.2 (0x00007f5f3bbec000) > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f5f395da000) > libpthread.so.0 => /lib/libpthread.so.0 (0x00007f5f393bd000) > libncurses.so.5 => /lib/libncurses.so.5 (0x00007f5f39177000) > > Following /usr/lib/libblas.so.3gf : > ls -l /usr/lib/libblas.so.3gf > /usr/lib/libblas.so.3gf -> /etc/alternatives/libblas.so.3gf > > And again following this: > ls -l /etc/alternatives/libblas.so.3gf > /etc/alternatives/libblas.so.3gf -> /usr/lib/atlas-base/atlas/libblas.so.3gf > > So it appears to be properly linked to Atlas. Note that I got this > same response from both the binary install of r-base (apt-get install > r-base) and the source build of r-base-dev (apt-get source -b > r-base-dev). Also, I did a "tuned" install of ATLAS 3.8.3 using: > > apt-get source atlas -t unstable > cd atlas-3.8.3 > DEFAULTS=n fakeroot debian/rules custom > > I did notice during the VERY long compilation that it seemed to > correctly identify that I have 4 CPUs. > > Can someone confirm that the test: > > a = matrix(rnorm(5000*5000), 5000, 5000) > b = matrix(rnorm(5000*5000), 5000, 5000) > c = a%*%b > > Should illicit a multi-CPU response with R/ATLAS? If so, any > suggestions on how to tweak my install to get it working? Thanks! > > --j > > On Wed, May 26, 2010 at 3:17 PM, Peter Langfelder > <peter.langfel...@gmail.com> wrote: > > If you didn't specify an external BLAS when you ran R configure > > script, you are not using ATLAS. If you're not sure and you still have > > the output of the configure script, at the end it'll say whether it > > uses an external BLAS. > > > > Alternatively, you may also want to generate two random 5000x5000 > > matrices and do their multiplication > > > > a = matrix(rnorm(5000*5000), 5000, 5000) > > b = matrix(rnorm(5000*5000), 5000, 5000) > > c = a%*%b > > > > While the calculation is running, in a separate terminal, run top and > > watch how much CPU R takes. AFAIK standard installation of R is single > > threaded and will only use one CPU (up to 100%). ATLAS is > > multithreaded and (unless you configured it otherwise) it will use all > > available processors, so if you have a 4-core machine, you will see > > CPU usage of nearly 400%. Note though that this will not discriminate > > ATLAS from other multi-threaded BLASes. > > > > HTH, > > > > Peter > > > > > > On Wed, May 26, 2010 at 2:16 PM, Jonathan Greenberg > > <greenb...@ucdavis.edu> wrote: > >> Rhelpers: > >> > >> I recently installed the 64-bit version of R on my Debian system, and > >> afterwards was asked if it was compiled using ATLAS. Is there a way > >> to test to see if R is using ATLAS? > >> > >> --j > >> > >> ______________________________________________ > >> R-help@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> PLEASE do read the posting guide > >> http://www.R-project.org/posting-guide.html > >> and provide commented, minimal, self-contained, reproducible code. > >> > > > > ______________________________________________ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
