I'm trying to build SciPy for Python 2.5.1 on CentOS 5, and am having quite a few problems. First, I uninstalled any existing blas and lapack RPMs, since the existing RPMs are pretty old. I've built and installed refblas3, lapack3, and atlas, using the source RPMS from http://download.opensuse.org/repositories/home:/ashigabou/Fedora_7/src/ When I install the RPMS, I use the '--relocate' option to install the files in /usr/local, rather than /usr. (Our system admins prefer we not install 'unoffical' RPMS into /usr) I've installed numpy, using easy_install. I've edited site-packages/numpy/distutils/site.cfg to match where the blas and lapack libraries got installed. When I try to build scipy, it complains about various missing packages, but still builds, and installs files into <PYTHON>/site-packages. (I've attached the log file). However, scipy doesn't work: import scipy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "scipy/__init__.py", line 54, in <module> from __config__ import show as show_config ImportError: No module named __config__ I'm an experienced programmer, and I've already invested 10+ hours in trying to install scipy. I'm a bit frustrated with the documentation and the build/install procedures - it just shouldn't be this hard to install scipy! I'd be happy to contribute detailed documentation (and RPMS) for build with CentOS 5, once I get a working system. mkl_info: libraries mkl,vml,guide not found in /usr/local/lib64/atlas/sse2 libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE fftw3_info: libraries fftw3 not found in /usr/local/lib64/atlas/sse2 libraries fftw3 not found in /usr/local/lib64 FOUND: libraries = ['fftw3'] library_dirs = ['/usr/lib64'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/usr/include'] djbfft_info: NOT AVAILABLE blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/lib64/atlas/sse2 libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64/atlas/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib64/atlas/sse2 libraries f77blas,cblas,atlas not found in /usr/local/lib64/atlas libraries f77blas,cblas,atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/lib64/sse2 libraries f77blas,cblas,atlas not found in /usr/lib64 libraries f77blas,cblas,atlas not found in /usr/lib/sse2 libraries f77blas,cblas,atlas not found in /usr/lib NOT AVAILABLE /net/opt_lnx/local_el5_64/lib/python2.5/site-packages/numpy/distutils/system_info.py:1314: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in /usr/local/lib64/atlas/sse2 FOUND: libraries = ['blas'] library_dirs = ['/usr/local/lib64'] language = f77 FOUND: libraries = ['blas'] library_dirs = ['/usr/local/lib64'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 lapack_opt_info: lapack_mkl_info: NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64/atlas/sse2 libraries lapack_atlas not found in /usr/local/lib64/atlas/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64/atlas libraries lapack_atlas not found in /usr/local/lib64/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries lapack_atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2 libraries lapack_atlas not found in /usr/lib64/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64 libraries lapack_atlas not found in /usr/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2 libraries lapack_atlas not found in /usr/lib/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib64/atlas/sse2 libraries lapack_atlas not found in /usr/local/lib64/atlas/sse2 libraries f77blas,cblas,atlas not found in /usr/local/lib64/atlas libraries lapack_atlas not found in /usr/local/lib64/atlas libraries f77blas,cblas,atlas not found in /usr/local/lib64 libraries lapack_atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/lib64/sse2 libraries lapack_atlas not found in /usr/lib64/sse2 libraries f77blas,cblas,atlas not found in /usr/lib64 libraries lapack_atlas not found in /usr/lib64 libraries f77blas,cblas,atlas not found in /usr/lib/sse2 libraries lapack_atlas not found in /usr/lib/sse2 libraries f77blas,cblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_info NOT AVAILABLE /net/opt_lnx/local_el5_64/lib/python2.5/site-packages/numpy/distutils/system_info.py:1221: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: libraries lapack not found in /usr/local/lib64/atlas/sse2 FOUND: libraries = ['lapack'] library_dirs = ['/usr/local/lib64'] language = f77 FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/local/lib64'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 non-existing path in 'scipy/linsolve': 'tests' umfpack_info: libraries umfpack not found in /usr/local/lib64/atlas/sse2 libraries umfpack not found in /usr/local/lib64 libraries umfpack not found in /usr/lib64 libraries umfpack not found in /usr/lib /net/opt_lnx/local_el5_64/lib/python2.5/site-packages/numpy/distutils/system_info.py:403: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src building py_modules sources building library "dfftpack" sources building library "linpack_lite" sources building library "mach" sources building library "quadpack" sources building library "odepack" sources building library "fitpack" sources building library "superlu_src" sources building library "odrpack" sources building library "minpack" sources building library "rootfind" sources building library "c_misc" sources building library "cephes" sources building library "mach" sources building library "toms" sources building library "amos" sources building library "cdf" sources building library "specfun" sources building library "statlib" sources building extension "scipy.cluster._vq" sources building extension "scipy.fftpack._fftpack" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.fftpack.convolve" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.integrate._quadpack" sources building extension "scipy.integrate._odepack" sources building extension "scipy.integrate.vode" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.interpolate._fitpack" sources building extension "scipy.interpolate.dfitpack" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/scipy/interpolate/dfitpack-f2pywrappers.f' to sources. building extension "scipy.io.numpyio" sources building extension "scipy.lib.blas.fblas" sources f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/build/src.linux-x86_64-2.5/scipy/lib/blas/fblas-f2pywrappers.f' to sources. building extension "scipy.lib.blas.cblas" sources adding 'build/src.linux-x86_64-2.5/scipy/lib/blas/cblas.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.lib.lapack.flapack" sources f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.lib.lapack.clapack" sources adding 'build/src.linux-x86_64-2.5/scipy/lib/lapack/clapack.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.lib.lapack.calc_lwork" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.lib.lapack.atlas_version" sources building extension "scipy.linalg.fblas" sources adding 'build/src.linux-x86_64-2.5/scipy/linalg/fblas.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/build/src.linux-x86_64-2.5/scipy/linalg/fblas-f2pywrappers.f' to sources. building extension "scipy.linalg.cblas" sources adding 'build/src.linux-x86_64-2.5/scipy/linalg/cblas.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linalg.flapack" sources adding 'build/src.linux-x86_64-2.5/scipy/linalg/flapack.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/build/src.linux-x86_64-2.5/scipy/linalg/flapack-f2pywrappers.f' to sources. building extension "scipy.linalg.clapack" sources adding 'build/src.linux-x86_64-2.5/scipy/linalg/clapack.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linalg._flinalg" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linalg.calc_lwork" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linalg.atlas_version" sources building extension "scipy.linalg._iterative" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linsolve._zsuperlu" sources building extension "scipy.linsolve._dsuperlu" sources building extension "scipy.linsolve._csuperlu" sources building extension "scipy.linsolve._ssuperlu" sources building extension "scipy.linsolve.umfpack.__umfpack" sources building extension "scipy.odr.__odrpack" sources building extension "scipy.optimize._minpack" sources building extension "scipy.optimize._zeros" sources building extension "scipy.optimize._lbfgsb" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.optimize.moduleTNC" sources building extension "scipy.optimize._cobyla" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.optimize.minpack2" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.signal.sigtools" sources building extension "scipy.signal.spline" sources building extension "scipy.sparse._sparsetools" sources building extension "scipy.special._cephes" sources building extension "scipy.special.specfun" sources f2py options: ['--no-wrap-functions'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.stats.statlib" sources f2py options: ['--no-wrap-functions'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.stats.futil" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.stats.mvn" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/scipy/stats/mvn-f2pywrappers.f' to sources. building extension "scipy.ndimage._nd_image" sources building data_files sources running build_py copying build/src.linux-x86_64-2.5/scipy/__config__.py -> build/lib.linux-x86_64-2.5/scipy running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_clib running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext library 'mach' defined more than once, overwriting build_info {'sources': ['scipy/integrate/mach/r1mach.f', 'scipy/integrate/mach/i1mach.f', 'scipy/integrate/mach/xerror.f', 'scipy/integrate/mach/d1mach.f'], 'config_fc': {'noopt': ('scipy/integrate/setup.pyc', 1)}, 'source_languages': ['f77']} with {'sources': ['scipy/special/mach/r1mach.f', 'scipy/special/mach/i1mach.f', 'scipy/special/mach/xerror.f', 'scipy/special/mach/d1mach.f'], 'config_fc': {'noopt': ('scipy/special/setup.pyc', 1)}, 'source_languages': ['f77']}. extending extension 'scipy.linsolve._zsuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] extending extension 'scipy.linsolve._dsuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] extending extension 'scipy.linsolve._csuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] extending extension 'scipy.linsolve._ssuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext running install_lib copying build/lib.linux-x86_64-2.5/scipy/__config__.py -> /opt/local/lib/python2.5/site-packages/scipy byte-compiling /opt/local/lib/python2.5/site-packages/scipy/__config__.py to __config__.pyc running install_data running install_egg_info Removing /opt/local/lib/python2.5/site-packages/scipy-0.6.0-py2.5.egg-info Writing /opt/local/lib/python2.5/site-packages/scipy-0.6.0-py2.5.egg-info
On Mon, Mar 10, 2008 at 4:40 PM, Joseph VanAndel <vanandel@ucar.edu> wrote:
I'm trying to build SciPy for Python 2.5.1 on CentOS 5, and am having quite a few problems.
First, I uninstalled any existing blas and lapack RPMs, since the existing RPMs are pretty old.
I've built and installed refblas3, lapack3, and atlas, using the source RPMS from
http://download.opensuse.org/repositories/home:/ashigabou/Fedora_7/src/
When I install the RPMS, I use the '--relocate' option to install the files in /usr/local, rather than /usr. (Our system admins prefer we not install 'unoffical' RPMS into /usr)
I've installed numpy, using easy_install.
I've edited site-packages/numpy/distutils/site.cfg to match where the blas and lapack libraries got installed.
When I try to build scipy, it complains about various missing packages, but still builds, and installs files into <PYTHON>/site-packages. (I've attached the log file).
However, scipy doesn't work:
import scipy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "scipy/__init__.py", line 54, in <module> from __config__ import show as show_config ImportError: No module named __config__
Change to another directory. Python looks in the current directory for modules and packages before it looks in site-packages, so you are seeing the incomplete source tree rather than the installed scipy. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
Robert, thanks for your help. Now, when I run python2.5
import scipy scipy.test(level=1, verbosity=2)
======================================= Error 1: I get the message: WARNING: cblas module is empty As I mentioned earlier, I build Atlas from the source RPMS found here: http://download.opensuse.org/repositories/home:/ashigabou/Fedora_7/src/ There is no mention of cblas in the atlas.spec file, so I don't see how the Atlas SRPM could supply cblas . ====================================== Error 2: python2.5.1 crashes : check_complex_dotc (scipy.linalg.tests.test_blas.test_fblas1_simple)Segmentation fault Robert Kern wrote:
Change to another directory. Python looks in the current directory for modules and packages before it looks in site-packages, so you are seeing the incomplete source tree rather than the installed scipy.
Joseph VanAndel wrote:
Robert, thanks for your help.
Now, when I run python2.5
import scipy scipy.test(level=1, verbosity=2)
=======================================
Error 1: I get the message: WARNING: cblas module is empty
As I mentioned earlier, I build Atlas from the source RPMS found here: http://download.opensuse.org/repositories/home:/ashigabou/Fedora_7/src/
There is no mention of cblas in the atlas.spec file, so I don't see how the Atlas SRPM could supply cblas .
======================================
Error 2: python2.5.1 crashes :
check_complex_dotc (scipy.linalg.tests.test_blas.test_fblas1_simple)
What is the fortran compiler on CENTOS 5 ? I bet you built scipy with g77, but ATLAS for FC 7 are built with gfortran. Could you provide the scipy build log ? cheers, David
I built ATLAS from source (using the ashigabou FC 7 SRPMS), using gfortran 4.1.2 Is the ashigabou SRPM supposed to provide 'cblas'? Should I use http://math-atlas.sourceforge.net instead? How do I specify which fortran compiler is used to build scipy? I've attached the scipy log file. David Cournapeau wrote:
Joseph VanAndel wrote:
Robert, thanks for your help.
Now, when I run python2.5
import scipy scipy.test(level=1, verbosity=2)
=======================================
Error 1: I get the message: WARNING: cblas module is empty
As I mentioned earlier, I build Atlas from the source RPMS found here: http://download.opensuse.org/repositories/home:/ashigabou/Fedora_7/src/
There is no mention of cblas in the atlas.spec file, so I don't see how the Atlas SRPM could supply cblas .
======================================
Error 2: python2.5.1 crashes :
check_complex_dotc (scipy.linalg.tests.test_blas.test_fblas1_simple)
What is the fortran compiler on CENTOS 5 ? I bet you built scipy with g77, but ATLAS for FC 7 are built with gfortran. Could you provide the scipy build log ?
cheers,
David _______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
mkl_info: libraries mkl,vml,guide not found in /usr/local/lib64/atlas/sse2 libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE fftw3_info: libraries fftw3 not found in /usr/local/lib64/atlas/sse2 libraries fftw3 not found in /usr/local/lib64 FOUND: libraries = ['fftw3'] library_dirs = ['/usr/lib64'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/usr/include'] djbfft_info: NOT AVAILABLE blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/lib64/atlas/sse2 libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64/atlas/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib64/atlas/sse2 libraries f77blas,cblas,atlas not found in /usr/local/lib64/atlas libraries f77blas,cblas,atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/lib64/sse2 libraries f77blas,cblas,atlas not found in /usr/lib64 libraries f77blas,cblas,atlas not found in /usr/lib/sse2 libraries f77blas,cblas,atlas not found in /usr/lib NOT AVAILABLE /net/opt_lnx/local_el5_64/lib/python2.5/site-packages/numpy/distutils/system_info.py:1314: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in /usr/local/lib64/atlas/sse2 FOUND: libraries = ['blas'] library_dirs = ['/usr/local/lib64'] language = f77 FOUND: libraries = ['blas'] library_dirs = ['/usr/local/lib64'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 lapack_opt_info: lapack_mkl_info: NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64/atlas/sse2 libraries lapack_atlas not found in /usr/local/lib64/atlas/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64/atlas libraries lapack_atlas not found in /usr/local/lib64/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries lapack_atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2 libraries lapack_atlas not found in /usr/lib64/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64 libraries lapack_atlas not found in /usr/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2 libraries lapack_atlas not found in /usr/lib/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib64/atlas/sse2 libraries lapack_atlas not found in /usr/local/lib64/atlas/sse2 libraries f77blas,cblas,atlas not found in /usr/local/lib64/atlas libraries lapack_atlas not found in /usr/local/lib64/atlas libraries f77blas,cblas,atlas not found in /usr/local/lib64 libraries lapack_atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/lib64/sse2 libraries lapack_atlas not found in /usr/lib64/sse2 libraries f77blas,cblas,atlas not found in /usr/lib64 libraries lapack_atlas not found in /usr/lib64 libraries f77blas,cblas,atlas not found in /usr/lib/sse2 libraries lapack_atlas not found in /usr/lib/sse2 libraries f77blas,cblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_info NOT AVAILABLE /net/opt_lnx/local_el5_64/lib/python2.5/site-packages/numpy/distutils/system_info.py:1221: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: libraries lapack not found in /usr/local/lib64/atlas/sse2 FOUND: libraries = ['lapack'] library_dirs = ['/usr/local/lib64'] language = f77 FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/local/lib64'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 non-existing path in 'scipy/linsolve': 'tests' umfpack_info: libraries umfpack not found in /usr/local/lib64/atlas/sse2 libraries umfpack not found in /usr/local/lib64 libraries umfpack not found in /usr/lib64 libraries umfpack not found in /usr/lib /net/opt_lnx/local_el5_64/lib/python2.5/site-packages/numpy/distutils/system_info.py:403: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src building py_modules sources building library "dfftpack" sources building library "linpack_lite" sources building library "mach" sources building library "quadpack" sources building library "odepack" sources building library "fitpack" sources building library "superlu_src" sources building library "odrpack" sources building library "minpack" sources building library "rootfind" sources building library "c_misc" sources building library "cephes" sources building library "mach" sources building library "toms" sources building library "amos" sources building library "cdf" sources building library "specfun" sources building library "statlib" sources building extension "scipy.cluster._vq" sources building extension "scipy.fftpack._fftpack" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.fftpack.convolve" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.integrate._quadpack" sources building extension "scipy.integrate._odepack" sources building extension "scipy.integrate.vode" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.interpolate._fitpack" sources building extension "scipy.interpolate.dfitpack" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/scipy/interpolate/dfitpack-f2pywrappers.f' to sources. building extension "scipy.io.numpyio" sources building extension "scipy.lib.blas.fblas" sources f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/build/src.linux-x86_64-2.5/scipy/lib/blas/fblas-f2pywrappers.f' to sources. building extension "scipy.lib.blas.cblas" sources adding 'build/src.linux-x86_64-2.5/scipy/lib/blas/cblas.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.lib.lapack.flapack" sources f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.lib.lapack.clapack" sources adding 'build/src.linux-x86_64-2.5/scipy/lib/lapack/clapack.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.lib.lapack.calc_lwork" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.lib.lapack.atlas_version" sources building extension "scipy.linalg.fblas" sources adding 'build/src.linux-x86_64-2.5/scipy/linalg/fblas.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/build/src.linux-x86_64-2.5/scipy/linalg/fblas-f2pywrappers.f' to sources. building extension "scipy.linalg.cblas" sources adding 'build/src.linux-x86_64-2.5/scipy/linalg/cblas.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linalg.flapack" sources adding 'build/src.linux-x86_64-2.5/scipy/linalg/flapack.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/build/src.linux-x86_64-2.5/scipy/linalg/flapack-f2pywrappers.f' to sources. building extension "scipy.linalg.clapack" sources adding 'build/src.linux-x86_64-2.5/scipy/linalg/clapack.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linalg._flinalg" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linalg.calc_lwork" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linalg.atlas_version" sources building extension "scipy.linalg._iterative" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.linsolve._zsuperlu" sources building extension "scipy.linsolve._dsuperlu" sources building extension "scipy.linsolve._csuperlu" sources building extension "scipy.linsolve._ssuperlu" sources building extension "scipy.linsolve.umfpack.__umfpack" sources building extension "scipy.odr.__odrpack" sources building extension "scipy.optimize._minpack" sources building extension "scipy.optimize._zeros" sources building extension "scipy.optimize._lbfgsb" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.optimize.moduleTNC" sources building extension "scipy.optimize._cobyla" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.optimize.minpack2" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.signal.sigtools" sources building extension "scipy.signal.spline" sources building extension "scipy.sparse._sparsetools" sources building extension "scipy.special._cephes" sources building extension "scipy.special.specfun" sources f2py options: ['--no-wrap-functions'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.stats.statlib" sources f2py options: ['--no-wrap-functions'] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.stats.futil" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. building extension "scipy.stats.mvn" sources f2py options: [] adding 'build/src.linux-x86_64-2.5/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.5' to include_dirs. adding 'build/src.linux-x86_64-2.5/scipy/stats/mvn-f2pywrappers.f' to sources. building extension "scipy.ndimage._nd_image" sources building data_files sources running build_py copying build/src.linux-x86_64-2.5/scipy/__config__.py -> build/lib.linux-x86_64-2.5/scipy running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_clib running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext library 'mach' defined more than once, overwriting build_info {'sources': ['scipy/integrate/mach/r1mach.f', 'scipy/integrate/mach/i1mach.f', 'scipy/integrate/mach/xerror.f', 'scipy/integrate/mach/d1mach.f'], 'config_fc': {'noopt': ('scipy/integrate/setup.pyc', 1)}, 'source_languages': ['f77']} with {'sources': ['scipy/special/mach/r1mach.f', 'scipy/special/mach/i1mach.f', 'scipy/special/mach/xerror.f', 'scipy/special/mach/d1mach.f'], 'config_fc': {'noopt': ('scipy/special/setup.pyc', 1)}, 'source_languages': ['f77']}. extending extension 'scipy.linsolve._zsuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] extending extension 'scipy.linsolve._dsuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] extending extension 'scipy.linsolve._csuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] extending extension 'scipy.linsolve._ssuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext running install_lib copying build/lib.linux-x86_64-2.5/scipy/__config__.py -> /opt/local/lib/python2.5/site-packages/scipy byte-compiling /opt/local/lib/python2.5/site-packages/scipy/__config__.py to __config__.pyc running install_data running install_egg_info Removing /opt/local/lib/python2.5/site-packages/scipy-0.6.0-py2.5.egg-info Writing /opt/local/lib/python2.5/site-packages/scipy-0.6.0-py2.5.egg-info
Joseph VanAndel wrote:
I built ATLAS from source (using the ashigabou FC 7 SRPMS), using gfortran 4.1.2
If I remember well, I forced using gfortran for FC 7.
Is the ashigabou SRPM supposed to provide 'cblas'? Not really, because it is not needed. The problem is that ATLAS is basically impossible to build in a reproducible way, so I do not provide binary rpm. The idea was that you install RPM for scipy, and then build ATLAS from the SRPM on your machine, which can be used as a drop-in by scipy (ATLAS is picked up instead of BLAS/LAPACK at runtime).
Should I use http://math-atlas.sourceforge.net instead?
It is your choice, but using the rpms is way easier. I have not tested on CENTOS, what is the difference between FC and CENTOS ? I built those rpms, but I do not use those distributions, so I do not necessarily know how to do thing the right way.
How do I specify which fortran compiler is used to build scipy?
This will force using gfortran: python setup.py build --fcompiler=gnu95 But this is taken care of by the scipy RPMS on ashigabou....
I've attached the scipy log file.
The log is incomplete: you should give us a complete log (that is, with the build directory deleted first), because otherwise, most info are not there. cheers, David
I rebuilt scipy, using g95 (thanks David!). Now, the scipy test doesn't crash, but has two failures. Any ideas on why these Orthogonal Distance Regression (ODRPACK) tests fail? ====================================================================== FAIL: test_explicit (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/net/opt_lnx/local_el5_64/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 50, in test_explicit -8.7849712165253724e-02]), File "/opt/local/lib/python2.5/site-packages/numpy/testing/utils.py", line 230, in assert_array_almost_equal header='Arrays are not almost equal') File "/opt/local/lib/python2.5/site-packages/numpy/testing/utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 1.26462971e+03, -5.42545890e+01, -8.64250389e-02]) y: array([ 1.26465481e+03, -5.40184100e+01, -8.78497122e-02]) ====================================================================== FAIL: test_multi (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/net/opt_lnx/local_el5_64/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 191, in test_multi 0.5101147161764654, 0.5173902330489161]), File "/opt/local/lib/python2.5/site-packages/numpy/testing/utils.py", line 230, in assert_array_almost_equal header='Arrays are not almost equal') File "/opt/local/lib/python2.5/site-packages/numpy/testing/utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 4.31272063, 2.44289312, 7.76215871, 0.55995622, 0.46423343]) y: array([ 4.37998803, 2.43330576, 8.00288459, 0.51011472, 0.51739023]) ---------------------------------------------------------------------- Ran 1716 tests in 3.270s FAILED (failures=2) David Cournapeau wrote:
Joseph VanAndel wrote:
I built ATLAS from source (using the ashigabou FC 7 SRPMS), using gfortran 4.1.2
If I remember well, I forced using gfortran for FC 7.
Is the ashigabou SRPM supposed to provide 'cblas'? Not really, because it is not needed. The problem is that ATLAS is basically impossible to build in a reproducible way, so I do not provide binary rpm. The idea was that you install RPM for scipy, and then build ATLAS from the SRPM on your machine, which can be used as a drop-in by scipy (ATLAS is picked up instead of BLAS/LAPACK at runtime).
Should I use http://math-atlas.sourceforge.net instead? It is your choice, but using the rpms is way easier. I have not tested on CENTOS, what is the difference between FC and CENTOS ? I built those rpms, but I do not use those distributions, so I do not necessarily know how to do thing the right way. How do I specify which fortran compiler is used to build scipy? This will force using gfortran:
python setup.py build --fcompiler=gnu95
I've attached the scipy log file. The log is incomplete: you should give us a complete log (that is, with
But this is taken care of by the scipy RPMS on ashigabou.... the build directory deleted first), because otherwise, most info are not there.
cheers,
David _______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
Joseph VanAndel wrote:
I rebuilt scipy, using g95 (thanks David!).
Any ideas on why these Orthogonal Distance Regression (ODRPACK) tests fail?
All these pass for me with Centos 5.1 test_explicit (test_odr.TestODR) ... ok test_implicit (test_odr.TestODR) ... ok test_lorentz (test_odr.TestODR) ... ok test_multi (test_odr.TestODR) ... ok test_pearson (test_odr.TestODR) ... ok with Python 2.5.1 (all code compiled from source) svn.version.version '0.7.0.dev3893' on x86_64 and Python 2.5.2 '0.7.0.dev4004' on i686
When I import scipy (or just scipy.io) on a CentOS 5 64 bit computer, 4 processor, 3.00 Ghz server, with Python 2.5.1, it takes ~10 seconds of elapsed time. When I'm developing and testing a Python script, I typically start the python interpreter dozens of times, so I concerned by how much time I spend waiting for the Python to startup. 1) Is there anything I can do to speed up the import of scipy? 2) What debugging techniques do you suggest that avoid restarting the interpreter? For example, do you routinely use ipython and reload(my_module)
On Tue, Mar 11, 2008 at 8:08 PM, Joseph VanAndel <vanandel@ucar.edu> wrote:
When I import scipy (or just scipy.io) on a CentOS 5 64 bit computer, 4 processor, 3.00 Ghz server, with Python 2.5.1, it takes ~10 seconds of elapsed time.
When I'm developing and testing a Python script, I typically start the python interpreter dozens of times, so I concerned by how much time I spend waiting for the Python to startup.
1) Is there anything I can do to speed up the import of scipy?
2) What debugging techniques do you suggest that avoid restarting the interpreter? For example, do you routinely use ipython and reload(my_module)
Which scipy version are you using? It takes 0.33s on my laptop and scipy in Debian: $ ipython Python 2.4.4 (#2, Mar 3 2008, 01:16:37) Type "copyright", "credits" or "license" for more information. IPython 0.8.2 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: time import scipy CPU times: user 0.24 s, sys: 0.07 s, total: 0.31 s Wall time: 0.33 s Ondrej
I'm using scipy 0.6.0 Ondrej Certik wrote:
On Tue, Mar 11, 2008 at 8:08 PM, Joseph VanAndel <vanandel@ucar.edu> wrote:
When I import scipy (or just scipy.io) on a CentOS 5 64 bit computer, 4 processor, 3.00 Ghz server, with Python 2.5.1, it takes ~10 seconds of elapsed time.
When I'm developing and testing a Python script, I typically start the python interpreter dozens of times, so I concerned by how much time I spend waiting for the Python to startup.
1) Is there anything I can do to speed up the import of scipy?
2) What debugging techniques do you suggest that avoid restarting the interpreter? For example, do you routinely use ipython and reload(my_module)
Which scipy version are you using? It takes 0.33s on my laptop and scipy in Debian:
$ ipython Python 2.4.4 (#2, Mar 3 2008, 01:16:37) Type "copyright", "credits" or "license" for more information.
IPython 0.8.2 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more.
In [1]: time import scipy CPU times: user 0.24 s, sys: 0.07 s, total: 0.31 s Wall time: 0.33 s
Ondrej _______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
Joseph VanAndel wrote:
When I import scipy (or just scipy.io) on a CentOS 5 64 bit computer, 4 processor, 3.00 Ghz server, with Python 2.5.1, it takes ~10 seconds of elapsed time.
When I'm developing and testing a Python script, I typically start the python interpreter dozens of times, so I concerned by how much time I spend waiting for the Python to startup.
1) Is there anything I can do to speed up the import of scipy?
Where is scipy (and its dependencies) installed ? Is it on NFS (or slow filesystem, usb, etc...) ? If so, putting it locally could be a huge win. 10 second for scipy the first time (cold start) is not surprising: scipy is a big package, and most time is spent on IO (reading files from the fs). But the 2d time, a lot of this is in memory (IO buffer), so it will be very fast. Numbers given by Ondrej suggest that it is a hot start in his case (or that he has an extremely powerful workstation:) ). In my case (and scipy is on NFS): (cold start) time python -c "import scipy" real 0m4.007s user 0m0.440s sys 0m0.236s (hot start) time python -c "import scipy" real 0m0.867s user 0m0.388s sys 0m0.212s
2) What debugging techniques do you suggest that avoid restarting the interpreter? For example, do you routinely use ipython and reload(my_module) It depends on the situation. If you are debugging one script, ipython has the %run method for that. But if you need to modify several modules which import each other, it becomes tricky.
cheers, David
On 11/03/2008, David Cournapeau <david@ar.media.kyoto-u.ac.jp> wrote:
1) Is there anything I can do to speed up the import of scipy?
Where is scipy (and its dependencies) installed ? Is it on NFS (or slow filesystem, usb, etc...) ? If so, putting it locally could be a huge win.
Linking time may be an issue as well. Do the "prelink" tools for C libraries help at all with scipy? Or, how much of the load time is loading compiled python code, and how much is loading shared libraries? For the OP: is python perhaps recompiling the .py files every time? Normally python produces a .pyc to accompany every .py file, but if the installation directory is not writeable, this may not be possible. Normally installation of python packages premakes all these files, but if you have installed it in some unusual fashion, they could be missing. Anne
On Wed, Mar 12, 2008 at 3:30 AM, David Cournapeau <david@ar.media.kyoto-u.ac.jp> wrote:
Joseph VanAndel wrote:
When I import scipy (or just scipy.io) on a CentOS 5 64 bit computer, 4 processor, 3.00 Ghz server, with Python 2.5.1, it takes ~10 seconds of elapsed time.
When I'm developing and testing a Python script, I typically start the python interpreter dozens of times, so I concerned by how much time I spend waiting for the Python to startup.
1) Is there anything I can do to speed up the import of scipy?
Where is scipy (and its dependencies) installed ? Is it on NFS (or slow filesystem, usb, etc...) ? If so, putting it locally could be a huge win.
10 second for scipy the first time (cold start) is not surprising: scipy is a big package, and most time is spent on IO (reading files from the fs). But the 2d time, a lot of this is in memory (IO buffer), so it will be very fast. Numbers given by Ondrej suggest that it is a hot start in his case (or that he has an extremely powerful workstation:) ).
In my case (and scipy is on NFS):
(cold start) time python -c "import scipy"
real 0m4.007s user 0m0.440s sys 0m0.236s
(hot start) time python -c "import scipy"
real 0m0.867s user 0m0.388s sys 0m0.212s
Yes, my numbers are for "hot start", because that is what is used when developing with scipy. Ondrej
Joseph VanAndel <vanandel <at> ucar.edu> writes:
However, scipy doesn't work:
import scipy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "scipy/__init__.py", line 54, in <module> from __config__ import show as show_config ImportError: No module named __config__
I'm having the same problem with my SuSE 10.1 box. I've had to install python 2.5 in /usr/local/; 2.4 is still in /usr/bin. This *shouldn't* be a problem, but I worry there might be some sort of conflict between the two. I hope there's not some compatibility problem between the latest python and scipy. Have you heard any solutions from others? Cheers, Mark Coletti mcoletti@gmail.com
Mark Coletti wrote:
I'm having the same problem with my SuSE 10.1 box. I've had to install python 2.5 in /usr/local/; 2.4 is still in /usr/bin. This *shouldn't* be a problem, but I worry there might be some sort of conflict between the two. I hope there's not some compatibility problem between the latest python and scipy.
This is because you are trying to import numpy while being in the numpy source tree, which does not work. The solution is to simply relaunch your python interpreter from another directory. The last svn has a better error message, because the above error is indeed quite obscure. Also, note that I put some CENTOS 5.0 RPM (well, RHEL 5, but they are supposed to be the same if I understand correctly) for scipy and numpy on ashigabou: http://download.opensuse.org/repositories/home:/ashigabou/ cheers, David
participants (7)
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Anne Archibald -
David Cournapeau -
Joseph VanAndel -
Mark Coletti -
Ondrej Certik -
Phil Austin -
Robert Kern