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

[Jan-Willem van de Meent]

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

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)

Something appears to be going wrong in the compilation process. In particular, 
the compile process appears unable to determine the version of the atlas libs 
installed (I get NO_ATLAS_INFO). I've pasted some snippets from the build 
output which may be relevant below.

Can anyone help me figure this out? 

Many thanks in advance,
Jan-Willem

-- 
Jan-Willem van de Meent
Research Student
Goldstein Lab, DAMTP
University of Cambridge

--
Snippets from setup.py output
...

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = 
['lapack', 'atlas', 'lapack', 'cblas', 'f77blas', 'ptcblas', 'ptf77blas']
    library_dirs = ['/usr/lib']
    language = f77
    include_dirs = ['/usr/include']

...

customize Gnu95FCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: 
gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=i686 -mtune=generic -O2 -pipe -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread 
_configtest.o -L/usr/lib -llapack -latlas -llapack -lcblas -lf77blas -lptcblas -lptf77blas -o 
_configtest
/usr/bin/ld: _configtest: hidden symbol `__powidf2' 
in /usr/lib/gcc/i686-pc-linux-gnu/4.3.2/libgcc.a(_powidf2.o) is referenced by 
DSO
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: ld returned 1 exit status
/usr/bin/ld: _configtest: hidden symbol `__powidf2' 
in /usr/lib/gcc/i686-pc-linux-gnu/4.3.2/libgcc.a(_powidf2.o) is referenced by 
DSO
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255
Output: 
  FOUND:
    libraries = 
['lapack', 'atlas', 'lapack', 'cblas', 'f77blas', 'ptcblas', 'ptf77blas']
    library_dirs = ['/usr/lib']
    language = f77
    define_macros = [('NO_ATLAS_INFO', 2)]
    include_dirs = ['/usr/include']