[SciPy-dev] install problems, SUSE, check_heev

Nils Wagner nwagner at mecha.uni-stuttgart.de
Thu Feb 3 06:05:00 CST 2005


Arnd Baecker wrote:

>Hi,
>
>On Thu, 3 Feb 2005, Pearu Peterson wrote:
>
>  
>
>>On Thu, 3 Feb 2005, Arnd Baecker wrote:
>>
>>    
>>
>>>Hi,
>>>
>>>I am going through my yearly torture to install an up-to-date
>>>scipy&Co on SUSE for our computational physics course:
>>>
>>>Installation of scipy works fine, but
>>> import scipy ; scipy.test(1,verbosity=10)
>>>gives
>>> check_heev  (scipy.lib.lapack.test_lapack.test_flapack_complex)
>>> Speicherzugriffsfehler = "memory error"
>>>
>>>I am not quite sure if this is related to the long thread ending with
>>> http://www.scipy.org/mailinglists/mailman?fn=scipy-dev/2004-December/002742.html
>>>
>>>So before I really start digging through all the suggestions
>>>there I would like to hear your advice!
>>>      
>>>
>>Relinking ATLAS libraries with a Fortran LAPACK compiled with -O2 is a
>>(probable) way to fix this segfault.
>>
>>Also (I could not find the corresponding thread at the moment)
>>watch out -fno-f2c flag in LAPACK/make.inc file
>>when compiling LAPACK libraries: someone reported that choosing this
>>flag properly fixed the segfault. Though in my debian sid box -fno-f2c
>>works fine, then see
>>
>>   http://math-atlas.sourceforge.net/errata.html#nof2c
>>
>>that advices not to use -fno-f2c flag with g77.
>>
>>If the combination "use -O2" and "remove -fno-f2c" fixes the issue, then
>>I am curious if also "use -O3" and "remove -fno-f2c" works.
>>    
>>
>
>Thank you very much for the information - I will try
>this out later.
>For the moment I followed Nils Wagner's
>suggestion (which he send off-list) to use
>
>
>   export BLAS_SRC=~/INSTALL_PYTHON_05/CompileDir/blas
>   export LAPACK_SRC=~/INSTALL_PYTHON_05/CompileDir/LAPACK
>   mkdir $BLAS_SRC
>   cd $BLAS_SRC
>   wget http://www.netlib.org/blas/blas.tgz
>   tar xzf blas.tgz
>
>   mkdir $LAPACK_SRC/
>   cd $LAPACK_SRC/..
>   wget http://www.netlib.org/lapack/lapack.tgz
>   tar xzf lapack.tgz
>
>   export BLAS=None
>   export LAPACK=None
>   export ATLAS=None
>
>
>Compilation of scipy works fine, and
>I get much further for scipy.test(1,verbosity=10),
>namely until FAILED (failures=25, errors=2).
>
>The two errors are:
>
>======================================================================
>ERROR: check_defective1 (scipy.linalg.matfuncs.test_matfuncs.test_signm)
>----------------------------------------------------------------------
>Traceback (most recent call last):
>  File
>"/opt/python/lib/python2.3/site-packages/scipy/linalg/tests/test_matfuncs.py",
>line 48, in check_defective1
>    r = signm(a)
>  File "/opt/python/lib/python2.3/site-packages/scipy/linalg/matfuncs.py",
>line 267, in signm
>    iS0 = inv(S0)
>  File "/opt/python/lib/python2.3/site-packages/scipy/linalg/basic.py",
>line 176, in inv
>    a1 = asarray_chkfinite(a)
>  File
>"/opt/python/lib/python2.3/site-packages/scipy_base/function_base.py",
>line 27, in asarray_chkfinite
>    raise ValueError, "Array must not contain infs or nans."
>ValueError: Array must not contain infs or nans.
>
>======================================================================
>ERROR: check_defective3 (scipy.linalg.matfuncs.test_matfuncs.test_signm)
>----------------------------------------------------------------------
>Traceback (most recent call last):
>  File
>"/opt/python/lib/python2.3/site-packages/scipy/linalg/tests/test_matfuncs.py",
>line 69, in check_defective3
>    r = signm(a)
>  File "/opt/python/lib/python2.3/site-packages/scipy/linalg/matfuncs.py",
>line 267, in signm
>    iS0 = inv(S0)
>  File "/opt/python/lib/python2.3/site-packages/scipy/linalg/basic.py",
>line 176, in inv
>    a1 = asarray_chkfinite(a)
>  File
>"/opt/python/lib/python2.3/site-packages/scipy_base/function_base.py",
>line 27, in asarray_chkfinite
>    raise ValueError, "Array must not contain infs or nans."
>ValueError: Array must not contain infs or nans.
>
>
>
>
>And the failures are all of the type of the first one:
>
>======================================================================
>FAIL: check_heevr_complex
>(scipy.lib.lapack.test_lapack.test_flapack_complex)
>----------------------------------------------------------------------
>Traceback (most recent call last):
>  File
>"/opt/python/lib/python2.3/site-packages/scipy/lib/lapack/tests/esv_tests.py",
>line 53, in check_heevr_complex
>    assert_array_almost_equal(dot(a,v[:,i]),w[i]*v[:,i])
>  File "/opt/python/lib/python2.3/site-packages/scipy_test/testing.py",
>line 740, in assert_array_almost_equal
>    assert cond,\
>AssertionError:
>Arrays are not almost equal (mismatch 33.3333333333%):
>        Array 1: [ 3.3270837 +5.8356678e+00j  2.2669436 +1.9275274e+00j
>       8.8565315 +1.4901161e-08j]
>        Array 2: [ 3.3270836+5.8356678j  2.2669436+1.9275274j
>8.8565297+0.j       ]
>
>
>So it is again (still) heevr
>(though the memory error came with
>check_heevr and not check_heevr_complex if
>this is of any relevance or difference).
>
>All failures are from
>- scipy.lib.lapack.test_lapack.test_flapack_complex (check_heevr_XXX)
>- scipy.lib.lapack.test_lapack.test_flapack_double (check_syevr_XXX)
>- scipy.lib.lapack.test_lapack.test_flapack_double_complex
>  (check_heevr_XXX)
>-  scipy.lib.lapack.test_lapack.test_flapack_float (check_syevr_XXX)
>
>
>Is any of the above expected when not using the full atlas/lapack
>combo and just blas/lapack?
>
>Best,
>
>Arnd
>
>_______________________________________________
>Scipy-dev mailing list
>Scipy-dev at scipy.net
>http://www.scipy.net/mailman/listinfo/scipy-dev
>  
>


 Hi Arnd,

I cannot reproduce your errors
check_nils (scipy.linalg.matfuncs.test_matfuncs.test_logm)Result may be inaccurate, approximate err = 4.39192767776e-09
 ... ok
check_defective1 (scipy.linalg.matfuncs.test_matfuncs.test_signm) ... ok
check_defective2 (scipy.linalg.matfuncs.test_matfuncs.test_signm) ... ok
check_defective3 (scipy.linalg.matfuncs.test_matfuncs.test_signm) ... ok
check_nils (scipy.linalg.matfuncs.test_matfuncs.test_signm) ... ok


>>> scipy.__version__
'0.3.3_302.4564'

>>> Numeric.__version__
'23.7'

f2py -v
2.45.241_1926

Python 2.3.3 (#1, Apr  6 2004, 01:47:39)
[GCC 3.3.3 (SuSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.


Cheers,

            Nils






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