[SciPy-dev] Building newscipy against non-atlas blas/lapack libraries

Nils Wagner nwagner at mecha.uni-stuttgart.de
Mon Nov 7 02:40:48 CST 2005


Pearu Peterson wrote:
>On Sun, 6 Nov 2005, Nils Wagner wrote:
>
>  
>>Hi Pearu,
>>
>>Which tests will exactly fail ?
>>
>>I have used
>>
>>   export BLAS_SRC=~/src/blas
>>   export LAPACK_SRC=~/src/lapack
>>   mkdir $BLAS_SRC
>>   cd $BLAS_SRC
>>   wget http://www.netlib.org/blas/blas.tgz
>>   tar xzf blas.tgz
>>
>>   cd $LAPACK_SRC/..
>>   wget http://www.netlib.org/lapack/lapack.tgz
>>   tar xzf lapack.tgz
>>
>>   export BLAS=None
>>   export LAPACK=None
>>   export ATLAS=None
>>
>>I have already reported the bugs with respect to this approach.
>>    
>
>Using LAPACK_SRC approuch will not work as some LAPACK source files need 
>to be compiled without optimization flags but currently scipy.distutils 
>does not support switching off optimization for certain files. Using
>`config_fc --noopt` would switch off optimization for all Fortran sources.
>
>So, you need to build at least LAPACK library manually, see `Building 
>the LAPACK library` section in
>
>   http://www.scipy.org/documentation/buildatlas4scipy.txt
>
>Pearu
>
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>Scipy-dev mailing list
>Scipy-dev at scipy.net
>http://www.scipy.net/mailman/listinfo/scipy-dev
>  

Pearu,

Following your advice, I have build the LAPACK library from scratch
using OPTS     = -O2.

/home/nwagner> echo $LAPACK
/var/tmp/LAPACK/lapack_LINUX.a
/home/nwagner> echo $LAPACK_SRC
LAPACK_SRC: Undefined variable.
/home/nwagner> echo $BLAS_SRC
/var/tmp/src/blas

Now scipy.test(10,10) yields one error

======================================================================
FAIL: check_nils (scipy.linalg.matfuncs.test_matfuncs.test_signm)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/usr/local/lib/python2.4/site-packages/scipy/linalg/tests/test_matfuncs.py",
line 44, in check_nils
    assert_array_almost_equal(r,cr)
  File "/usr/local/lib/python2.4/site-packages/scipy/test/testing.py",
line 735, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[ -5.2848319e-01 +3.8543597e+00j  -6.2440787e+01
+6.0410538e+00j
    2.7508638e+01 +1.3623836e+01j   5.9339443e+00 +3.4...
        Array 2: [[ 11.9493333  -2.2453333  15.3173333  21.6533333 
-2.2453333]
 [ -3.8426667   0.4986667  -4.5906667  -7.1866667   0.498...


----------------------------------------------------------------------
Ran 1331 tests in 179.443s

FAILED (failures=1)

0.4.3.1440
0.4.2_1422


The repeated computation of logm(A) yields different results, but for
what reason ?
See the imaginary part  -9.91687203e+00j in the last loop.

>>> A
array([[ 3.1,  0. ],
       [ 0. ,  3.1]])

>>> linalg.logm(A)
array([[  1.13140211e+000,   1.49230383e-269],
       [  0.00000000e+000,   1.13140211e+000]])
>>> linalg.logm(A)
array([[  1.13140211e+000,   1.33902098e-270],
       [  0.00000000e+000,   1.13140211e+000]])
>>> linalg.logm(A)
array([[  1.13140211e+000,   1.62403951e-270],
       [  0.00000000e+000,   1.13140211e+000]])
>>> linalg.logm(A)
array([[  1.13140211e+000,  -2.19984796e-269],
       [  0.00000000e+000,   1.13140211e+000]])
>>> linalg.logm(A)
array([[ 1.13140211 +0.00000000e+00j,  0.         -9.91687203e+00j],
       [ 0.         +0.00000000e+00j,  1.13140211 +0.00000000e+00j]])

Any pointer how to resolve these problems ?

Newscipy should work without ATLAS.

Nils







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