[Numpy-discussion] Numpy matrix multiplication slow even though ATLAS linked

Jan-Willem van de Meent vandemeent@damtp.cam.ac...
Thu Oct 30 17:19:01 CDT 2008


On Thursday 30 October 2008 18:41:51 Charles R Harris wrote:
> On Thu, Oct 30, 2008 at 5:19 AM, Jan-Willem van de Meent <
>
> vandemeent@damtp.cam.ac.uk> wrote:
> > Dear all,
> >
> > This is my first post to this list. I am having perfomance issues with
> > with numpy/atlas. Doing dot(a,a) for a 2000x2000 matrix takes  about
> > 1m40s, even though numpy is appears to link to my atlas libraries:
> >
> > I did a quick benchmark by running the following script:
> >
> >    #! /usr/bin/env python
> >    import numpy
> >    import time
> >
> >    try:
> >       import numpy.core._dotblas
> >       print 'Using ATLAS:'
> >    except ImportError:
> >       print 'No ATLAS:'
> >
> >    t = time.time()
> >    x = numpy.random.random((1000,1000))
> >    y = numpy.random.random((1000,1000))
> >    z = numpy.dot(x, y)
> >
> >    print time.time()-t
> >
> > My laptop is a Dell D620 Core Duo T2300 1.66 Ghz, running Archlinux with
> > GCC
> > 4.3.2, atlas 3.8.2, python 2.5.2 and numpy 1.2.1. Output of the script
> > above
> > is:
> >
> >    Using ATLAS:
> >    7.99549412727
> >
> > A department desktop PC, Pentium D 3.00 Ghz, running Scientific Linux,
> > with GCC 4.1.2, atlas 3.7.30, python 2.5.1 and numpy 1.1.0, runs this
> > test 24 times faster:
> >
> >    Using ATLAS:
> >    0.337520122528
>
> About .40 here with numpy from svn.
>
> > So even though _dotblas.so exists, matrix multiplication appears to run
> > at pretty much the same speed as if atlas were not  available. Running
> > ldd on _dotblas.so suggests  that numpy is indeed linking to the atlas
> > libs:
> >
> > ldd /usr/lib/python2.5/site-packages/numpy/core/_dotblas.so
> >        linux-gate.so.1 =>  (0xb7fcf000)
> >        libatlas.so => /usr/lib/libatlas.so (0xb7cb5000)
> >        liblapack.so => /usr/lib/liblapack.so (0xb77ab000)
> >        libcblas.so => /usr/lib/libcblas.so (0xb778b000)
> >        libf77blas.so => /usr/lib/libf77blas.so (0xb776f000)
> >        libpython2.5.so.1.0 => /usr/lib/libpython2.5.so.1.0 (0xb7630000)
> >        libpthread.so.0 => /lib/libpthread.so.0 (0xb7618000)
> >        libc.so.6 => /lib/libc.so.6 (0xb74d6000)
> >        libm.so.6 => /lib/libm.so.6 (0xb74b0000)
> >        libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0xb73ff000)
> >        libdl.so.2 => /lib/libdl.so.2 (0xb73fb000)
> >        libutil.so.1 => /lib/libutil.so.1 (0xb73f6000)
> >        /lib/ld-linux.so.2 (0xb7fd0000)
>
> What's in /usr/local/lib? Do you have a 64 bit system? What does locate
> libatlas return?
>
> Chuck

Thanks for the response. I'm on 32 bit and all ATLAS files are installed 
in /usr/lib (headers are in /usr/include/atlas)

/usr/lib/libatlas.a
/usr/lib/libatlas.so
/usr/lib/libblas.so
/usr/lib/libblas.so.3
/usr/lib/libblas.so.3.0.3
/usr/lib/libcblas.a
/usr/lib/libcblas.so
/usr/lib/libf77blas.a
/usr/lib/libf77blas.so
/usr/lib/liblapack.a
/usr/lib/liblapack.so
/usr/lib/liblapack.so.3
/usr/lib/libptcblas.a
/usr/lib/libptf77blas.a

I posted a full build log earlier today, but I think it is still awaiting 
approval of moderators because of file size limitations.

JW


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