[SciPy-dev] install problems, SUSE, check_heev

Arnd Baecker arnd.baecker at web.de
Thu Feb 3 05:55:37 CST 2005


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




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