Hi, Can I just install numpy and scipy without ATLAS? And what does this means " gnu: no Fortran 90 compiler found"? Im installing on RHEL Thanks in advance! [root@giswk002 numpy-1.3.0]# python setup.py build Running from numpy source directory. non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/Python-2.6.2/lib libraries mkl,vml,guide not found in /usr/local/lib 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/Python-2.6.2/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib 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/Python-2.6.2/lib libraries f77blas,cblas,atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib/sse2 libraries f77blas,cblas,atlas not found in /usr/lib NOT AVAILABLE /usr/local/numpy-1.3.0/numpy/distutils/system_info.py:1383: 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/Python-2.6.2/lib libraries blas not found in /usr/local/lib FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /usr/local/Python-2.6.2/lib libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/Python-2.6.2/lib libraries lapack_atlas not found in /usr/local/Python-2.6.2/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib 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/Python-2.6.2/lib libraries lapack_atlas not found in /usr/local/Python-2.6.2/lib libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib 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 /usr/local/numpy-1.3.0/numpy/distutils/system_info.py:1290: 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/Python-2.6.2/lib libraries lapack not found in /usr/local/lib FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 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 "npymath" sources building extension "numpy.core._sort" sources adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h' to sources. numpy/core/code_generators/genapi.py:9: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 executing numpy/core/code_generators/generate_numpy_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h' to sources. numpy.core - nothing done with h_files = ['build/src.linux-i686-2.6/numpy/core/include/numpy/config.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h'] building extension "numpy.core.multiarray" sources adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h' to sources. executing numpy/core/code_generators/generate_numpy_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files = ['build/src.linux-i686-2.6/numpy/core/src/scalartypes.inc', 'build/src.linux-i686-2.6/numpy/core/src/arraytypes.inc', 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h'] building extension "numpy.core.umath" sources adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h' to sources. executing numpy/core/code_generators/generate_ufunc_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__ufunc_api.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files = ['build/src.linux-i686-2.6/numpy/core/src/scalartypes.inc', 'build/src.linux-i686-2.6/numpy/core/src/arraytypes.inc', 'build/src.linux-i686-2.6/numpy/core/src/umath_funcs.inc', 'build/src.linux-i686-2.6/numpy/core/src/umath_loops.inc', 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__ufunc_api.h'] building extension "numpy.core.scalarmath" sources adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h' to sources. executing numpy/core/code_generators/generate_numpy_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h' to sources. executing numpy/core/code_generators/generate_ufunc_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__ufunc_api.h' to sources. numpy.core - nothing done with h_files = ['build/src.linux-i686-2.6/numpy/core/include/numpy/config.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__ufunc_api.h'] building extension "numpy.core._dotblas" sources building extension "numpy.core.umath_tests" sources building extension "numpy.lib._compiled_base" sources building extension "numpy.numarray._capi" sources building extension "numpy.fft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources adding 'numpy/linalg/lapack_litemodule.c' to sources. adding 'numpy/linalg/python_xerbla.c' to sources. building extension "numpy.random.mtrand" sources /usr/local/numpy-1.3.0/numpy/distutils/command/config.py:39: DeprecationWarning: +++++++++++++++++++++++++++++++++++++++++++++++++ Usage of try_run is deprecated: please do not use it anymore, and avoid configuration checks involving running executable on the target machine. +++++++++++++++++++++++++++++++++++++++++++++++++ DeprecationWarning) customize GnuFCompiler Found executable /usr/bin/g77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/local/Python-2.6.2/include/python2.6 -c' gcc: _configtest.c gcc -pthread _configtest.o -o _configtest _configtest failure. removing: _configtest.c _configtest.o _configtest building data_files sources running build_py copying numpy/version.py -> build/lib.linux-i686-2.6/numpy copying build/src.linux-i686-2.6/numpy/__config__.py -> build/lib.linux-i686-2.6/numpy copying build/src.linux-i686-2.6/numpy/distutils/__config__.py -> build/lib.linux-i686-2.6/numpy/distutils running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using build_ext running scons running build_scripts adding 'build/scripts.linux-i686-2.6/f2py' to scripts ------ End of Forwarded Message
On Wed, May 26, 2010 at 11:25 AM, Padma TAN <tanwp@gis.a-star.edu.sg> wrote:
Hi,
Can I just install numpy and scipy without ATLAS? And what does this means " gnu: no Fortran 90 compiler found"?
Yes you can install without ATLAS. And BLAS and LAPACK were found so you should be fine. Did you have an actual problem or are you asking out of curiosity? Numpy does not contain any Fortran code, Scipy does. But that warning doesn't mean you have a problem - a number of compilers are checked and the first one that's found is used. Please also have a look at the RHEL section on http://www.scipy.org/Installing_SciPy/Linux. Cheers, Ralf
Im installing on RHEL
Thanks in advance!
[root@giswk002 numpy-1.3.0]# python setup.py build Running from numpy source directory. non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/Python-2.6.2/lib libraries mkl,vml,guide not found in /usr/local/lib 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/Python-2.6.2/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib 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/Python-2.6.2/lib libraries f77blas,cblas,atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib/sse2 libraries f77blas,cblas,atlas not found in /usr/lib NOT AVAILABLE
/usr/local/numpy-1.3.0/numpy/distutils/system_info.py:1383: 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/Python-2.6.2/lib libraries blas not found in /usr/local/lib FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77
FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77
lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /usr/local/Python-2.6.2/lib libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE
NOT AVAILABLE
atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/Python-2.6.2/lib libraries lapack_atlas not found in /usr/local/Python-2.6.2/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib 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/Python-2.6.2/lib libraries lapack_atlas not found in /usr/local/Python-2.6.2/lib libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib 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
/usr/local/numpy-1.3.0/numpy/distutils/system_info.py:1290: 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/Python-2.6.2/lib libraries lapack not found in /usr/local/lib FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77
FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77
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 "npymath" sources building extension "numpy.core._sort" sources adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h' to sources. numpy/core/code_generators/genapi.py:9: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 executing numpy/core/code_generators/generate_numpy_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h' to sources. numpy.core - nothing done with h_files = ['build/src.linux-i686-2.6/numpy/core/include/numpy/config.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h'] building extension "numpy.core.multiarray" sources adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h' to sources. executing numpy/core/code_generators/generate_numpy_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files = ['build/src.linux-i686-2.6/numpy/core/src/scalartypes.inc', 'build/src.linux-i686-2.6/numpy/core/src/arraytypes.inc', 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h'] building extension "numpy.core.umath" sources adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h' to sources. executing numpy/core/code_generators/generate_ufunc_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__ufunc_api.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files = ['build/src.linux-i686-2.6/numpy/core/src/scalartypes.inc', 'build/src.linux-i686-2.6/numpy/core/src/arraytypes.inc', 'build/src.linux-i686-2.6/numpy/core/src/umath_funcs.inc', 'build/src.linux-i686-2.6/numpy/core/src/umath_loops.inc', 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__ufunc_api.h'] building extension "numpy.core.scalarmath" sources adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h' to sources. executing numpy/core/code_generators/generate_numpy_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h' to sources. executing numpy/core/code_generators/generate_ufunc_api.py adding 'build/src.linux-i686-2.6/numpy/core/include/numpy/__ufunc_api.h' to sources. numpy.core - nothing done with h_files = ['build/src.linux-i686-2.6/numpy/core/include/numpy/config.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/numpyconfig.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__multiarray_api.h', 'build/src.linux-i686-2.6/numpy/core/include/numpy/__ufunc_api.h'] building extension "numpy.core._dotblas" sources building extension "numpy.core.umath_tests" sources building extension "numpy.lib._compiled_base" sources building extension "numpy.numarray._capi" sources building extension "numpy.fft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources adding 'numpy/linalg/lapack_litemodule.c' to sources. adding 'numpy/linalg/python_xerbla.c' to sources. building extension "numpy.random.mtrand" sources /usr/local/numpy-1.3.0/numpy/distutils/command/config.py:39: DeprecationWarning: +++++++++++++++++++++++++++++++++++++++++++++++++ Usage of try_run is deprecated: please do not use it anymore, and avoid configuration checks involving running executable on the target machine. +++++++++++++++++++++++++++++++++++++++++++++++++
DeprecationWarning) customize GnuFCompiler Found executable /usr/bin/g77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/local/Python-2.6.2/include/python2.6 -c' gcc: _configtest.c gcc -pthread _configtest.o -o _configtest _configtest failure. removing: _configtest.c _configtest.o _configtest building data_files sources running build_py copying numpy/version.py -> build/lib.linux-i686-2.6/numpy copying build/src.linux-i686-2.6/numpy/__config__.py -> build/lib.linux-i686-2.6/numpy copying build/src.linux-i686-2.6/numpy/distutils/__config__.py -> build/lib.linux-i686-2.6/numpy/distutils running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using build_ext running scons running build_scripts adding 'build/scripts.linux-i686-2.6/f2py' to scripts
------ End of Forwarded Message
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participants (2)
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Padma TAN -
Ralf Gommers