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Notes on using Atlas libs with GNU Octave and GNU R
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As of the Debian releases 2.1.34-6 (for GNU Octave) and 1.3.0-3 (for GNU R),
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both Octave and R can be used with Atlas, the Automatically Tuned Linear
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Algebra Software, in order to obtain much faster linear algebra operations.
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To make use of Atlas, Debian users need to install the Atlas libraries for
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their given cpu architecture. Concretely, one of
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atlas2-base - Automatically Tuned Linear Algebra Software
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atlas2-p3 - Automatically Tuned Linear Algebra Software
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atlas2-p4 - Automatically Tuned Linear Algebra Software
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atlas2-athlon - Automatically Tuned Linear Algebra Software
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must be installed. Here, 'base' provides generic libraries which run on all
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platforms whereas 'p3', 'p4' and 'athlon' stand for the Pentium III and IV as
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well as the AMD Athlon, respectively. The actual libraries are installed in
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/usr/lib/atlas (in the case of 'base') and in /usr/lib/$arch/atlas for the
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cpu-specific versions. Here $arch stands for the cpu code used by the kernel
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and shown in /proc/cpuinfo.
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The Atlas libraries can be loaded dynamically instead of the (non-optimised)
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blas libraries against which both Octave and R are compiled.
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Section III below briefly describes how Atlas libraries can be compiled for
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your specific machine to further optimise performance.
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II. Using the Atlas libraries
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II.A New default behaviour with automatic loading of the Atlas libraries
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In order to have the libraries loaded at run-time, the location needs to be
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communicated to the dynamic linker/loader. As of the Debian release
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libc6_2.2.4-5 of the glibc library, a patch to ldconfig automates the use of
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the Atlas library. If an Atlas package is installed, and correctly registered
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in /etc/ld.so.conf as done by its postinst script, ldconfig will
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automatically load the Atlas' version of the Blas instead of the (slower)
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The following text is hence only relevant for systems which have not yet
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upgraded to libc6_2.2.4-5 or later.
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II.B Old behaviour requiring LD_LIBRARY_PATH for Octave
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For Octave, use the variable LD_LIBRARY_PATH. On a computer with the
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$ LD_LIBRARY_PATH=/usr/lib/atlas octave2.1 -q
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octave2.1:1> X=randn(1000,1000);t=cputime();Y=X'*X;cputime-t
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$ edd@homebud:~> octave2.1 -q
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octave2.1:1> X=randn(1000,1000);t=cputime();Y=X'*X;cputime-t
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For R version 1.3.0-4, the R_LD_LIBRARY_PATH variable has to be used, and its
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value needs to be copied out of /usr/bin/R (or edited therein). For R version
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1.3.1 or later this is done automatically in the R startup shell script. For
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an Athlon machine, and with the explicit definition which is no longer needed
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as of R 1.3.1, the example becomes
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$ R_LD_LIBRARY_PATH=/usr/lib/R/bin:/usr/local/lib:/usr/X11R6/lib:/usr/lib/3dnow/atlas:/usr/lib:/usr/X11R6/lib:/usr/lib/gcc-lib/i386-linux/2.95.4:. R --vanilla -q
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> mm <- matrix(rnorm(10^6), ncol = 10^3)
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> system.time(crossprod(mm))
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[1] 2.38 0.04 2.84 0.00 0.00
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> mm <- matrix(rnorm(10^6), ncol = 10^3)
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> system.time(crossprod(mm))
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[1] 28.28 0.08 33.54 0.00 0.00
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Running such a small example is highly recommded to ascertain that the
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libraries are indeed found, and to "prove" that the speed gain is real (and
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significant) for problems of at least a medium size as the 1000x1000 examples
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Note that the example use "/usr/lib/atlas" for the atlas2-base package;
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Athlon users should employ "/usr/lib/3dnow/atlas", Pentium III users should
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employ "/usr/lib/xmm/atlas" and Pentium IV users should employ
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Lastly, it should be pointed out that it is probably worthwhile to locally
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compile, and thereby optimise, the Atlas libraries if at least a moderately
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intensive load is expected. This is described in the next section.
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III. Locally compiling the Atlas libraries
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The Debian Atlas packages have been setup to allow for local recompilation of
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the Atlas libraries. This way the behaviour will be tuned exactly to the
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specific CPU rather than the broader class of CPUs. It has been reported that
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this can increase performance by a further 12% on the examples above.
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Detailed instructions are in /usr/share/doc/atlas2-base/README.debian.gz but
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the process is essentially the following [ courtesy of Doug Bates ]
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apt-get source atlas2-base
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fakeroot debian/rules/custom
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# wait for a *very* long time
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dpkg -i ../atlas2-base*.deb
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The Atlas packages have a very detailed README.Debian file which should be
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consulted; it also details local recompilation. Sources and documentation for
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Atlas are at http://www.netlib.org/atlas.
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Camm Maguire developed the scheme of overloading Atlas over the default blas
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libraries and deserves all the credit. Many thanks to John Eaton for helping
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debug some errors in the initial setup, and to Doug Bates for work on the R
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package. Special thanks to Ben Collins for providing a patched ldconfig as
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part of the libc6 package.
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-- Dirk Eddelbuettel <edd@debian.org> Tue, 21 Aug 2001 21:37:15 -0500
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-- Dirk Eddelbuettel <edd@debian.org> Sun, 11 Nov 2001 11:03:19 -0600
added
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debian/README.Atlas
