[SciPy-user] Problem with scipy on FC5 (PentiumM/PentiumIV)

Grzegorz Koczyk gkoczyk at echostar.pl
Mon Oct 16 04:57:32 CDT 2006


I am not sure whether this an FC5-specific problem, so I am submitting
this here and not as a ticket. 

For Fedora Core 5 running on Pentium4-based servers following scipy
tests fail and I am at a complete loss, at what can be done (and more
importantly to what extent other modules depends on the tested code):  

[ Note: I did try compiling ATLAS (3.6) from source, however then both
numpy and scipy complain about gfortran missing symbols in
lapack_lite.so - so I am unable to verify whether problem stems from
some peculiarity of vanilla FC5 RPMs. ]

======================================================================
FAIL: check_dot (scipy.linalg.tests.test_blas.test_fblas1_simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/usr/lib/python2.4/site-packages/scipy/linalg/tests/test_blas.py", line
75, in check_dot
    assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
  File "/usr/lib/python2.4/site-packages/numpy/testing/utils.py", line
156, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
 ACTUAL: (3.3613915289673437e-35-1.0143136978149414j)
 DESIRED: (-9+2j)
----------------------------------------------------------------------
Scipy configuration:

>>> numpy.__version__
'1.0.dev3341'
>>> scipy.__version__
'0.5.2.dev2288'
>>> scipy.show_config()
umfpack_info:
  NOT AVAILABLE

atlas_threads_info:
  NOT AVAILABLE

blas_opt_info:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib/sse2']
    define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')]
    language = c
    include_dirs = ['/usr/include/atlas']

atlas_blas_threads_info:
  NOT AVAILABLE

djbfft_info:
  NOT AVAILABLE

lapack_opt_info:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib/sse2']
    define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')]
    language = c
    include_dirs = ['/usr/include/atlas']

fftw3_info:
    libraries = ['fftw3']
    library_dirs = ['/usr/lib']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/usr/include']

atlas_info:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib/sse2']
    language = c
    include_dirs = ['/usr/include/atlas']

lapack_mkl_info:
  NOT AVAILABLE

blas_mkl_info:
  NOT AVAILABLE

atlas_blas_info:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/lib/sse2']
    language = c
    include_dirs = ['/usr/include/atlas']

mkl_info:
  NOT AVAILABLE
----------------------------------------------------------------------
Relevant RPMs installed:

atlas-sse2-3.6.0-10.fc5
atlas-sse2-devel-3.6.0-10.fc5
blas-3.0-37.fc5
blas-devel-3.0-37.fc5
fftw-3.1.1-1.fc5
fftw-devel-3.1.1-1.fc5
lapack-3.0-37.fc5
lapack-devel-3.0-37.fc5
python-2.4.3-8.FC5
----------------------------------------------------------------------
/proc/cpuinfo:

processor       : 0
vendor_id       : GenuineIntel
cpu family      : 15
model           : 4
model name      : Intel(R) Pentium(R) 4 CPU 3.00GHz
stepping        : 3
cpu MHz         : 2992.931
cache size      : 2048 KB
physical id     : 0
siblings        : 2
core id         : 0
cpu cores       : 1
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
fpu             : yes
fpu_exception   : yes
cpuid level     : 5
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm
constant_tsc pni monitor ds_cpl est cid cx16 xtpr
bogomips        : 5997.83

processor       : 1
vendor_id       : GenuineIntel
cpu family      : 15
model           : 4
model name      : Intel(R) Pentium(R) 4 CPU 3.00GHz
stepping        : 3
cpu MHz         : 2992.931
cache size      : 2048 KB
physical id     : 0
siblings        : 2
core id         : 0
cpu cores       : 1
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
fpu             : yes
fpu_exception   : yes
cpuid level     : 5
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm
constant_tsc pni monitor ds_cpl est cid cx16 xtpr
bogomips        : 5985.40
----------------------------------------------------------------------

Any help or information concerning the matter would be highly
appreciated.

Best regards,
Grzegorz Koczyk






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