[SciPy-user] Problem with scipy on FC5 (PentiumM/PentiumIV)
Gerard Vermeulen
gerard.vermeulen at grenoble.cnrs.fr
Mon Oct 16 07:55:31 EDT 2006
I have the same unit test failure on Mac OSX where I failed to build ATLAS from
source (it looks like that SciPy falls back on a different BLAS expecting a
different memory layout).
You can try to use something like the following site.cfg when rebuilding NumPy
(put it in the NumPy source tree before building):
cat >site.cfg <<EOF
[atlas]
library_dirs = /usr/lib
atlas_libs = lapack, f77blas, cblas, atlas
EOF
I needed to do this for my home made ATLAS rpm on Mandrake-2005: you have
to adapt it for your system.
Once I had built NumPy with the correct ATLAS settings, SciPy picked it up
and didn't complain about missing symbols anymore.
Gerard
PS: I consider this to be a NumPy bug. Pre-NumPy versions of SciPy could
pick up my lapack, f77blas, cblas, atlas libraries without my intervention
On Mon, 16 Oct 2006 11:57:32 +0200
Grzegorz Koczyk <gkoczyk at echostar.pl> wrote:
> 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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