[Numpy-discussion] numarray and ATLAS

Francesc Alted falted at pytables.org
Fri Oct 15 04:27:55 CDT 2004


Hi,

Perhaps this is a too recurrent subject, but I'm having problems when
making numarray to use ATLAS instead of the mini-lapack included.

I've installed ATLAS 3.6.0 on my pentium IV machine. I've made it a
completely featured LAPACK by following the instructions in:

http://math-atlas.sourceforge.net/errata.html#completelp

and I'm pretty sure that the resulting library works. Now, after exporting
USE_LAPACK and set the appropiate directory for lapack_dirs in addons.py,
the compilation went well (however, I can see that lapack_litemodule.c is
still being compiled, and I don't know if that's normal or not). The command
I've used to install is:

$ python setup.py install --gencode --home=/users/exp/alted/bin-i686

And the error that happens during the test phase follows:

$ python
Python 2.3.4 (#1, Jul 22 2004, 20:47:54)
[GCC 3.3.2 20031022 (Red Hat Linux 3.3.2-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numarray.testall as testall
>>> testall.test()
numarray:                               ((0, 1199), (0, 1199))
numarray.records:                       (0, 48)
numarray.strings:                       (0, 176)
numarray.memmap:                        (0, 82)
numarray.objects:                       (0, 105)
numarray.memorytest:                    (0, 16)
numarray.examples.convolve:             ((0, 20), (0, 20), (0, 20), (0, 20))
numarray.convolve:                      (0, 52)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/users/exp/alted/bin-i686/lib/python/numarray/testall.py", line 24, in test
    result = eval(p+".test()")
  File "<string>", line 0, in ?
  File "/users/exp/alted/bin-i686/lib/python/numarray/fft/FFT.py", line 326, in test
    import dtest
  File "/users/exp/alted/bin-i686/lib/python/numarray/fft/dtest.py", line 238, in ?
    import numarray.random_array as random_array
  File "/users/exp/alted/bin-i686/lib/python/numarray/random_array/__init__.py", line 7, in ?
    from RandomArray2 import *
  File "/users/exp/alted/bin-i686/lib/python/numarray/random_array/RandomArray2.py", line 3, in ?
    import numarray.linear_algebra as linalg
  File "/users/exp/alted/bin-i686/lib/python/numarray/linear_algebra/__init__.py", line 1, in ?
    from LinearAlgebra2 import *
  File "/users/exp/alted/bin-i686/lib/python/numarray/linear_algebra/LinearAlgebra2.py", line 23, in ?
    import lapack_lite2
ImportError:
/users/exp/alted/bin-i686/lib/python/numarray/linear_algebra/lapack_lite2.so:
undefined symbol: dgesdd_

I've checked that dgesdd symbol exists on my liblapack.a:

$ strings ~/bin-i686/lib/atlas/liblapack.a | grep dgesdd
dgesdd.o/       1097832195  2514  515   100644  13788     `

but not a dgesdd_, as you can see. 

I'm missing something?

-- 
Francesc Alted





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