[Numpy-discussion] Numpy 1.6.1 installation problem

Tue Feb 14 10:40:59 EST 2012

Really not an expert here, but it looks like it's trying various
compilation options, some work and some don't, and for some reason it's
really unhappy about the one where it can't find Python.h.
Maybe add /usr/include/python2.6 to your CPATH, see if that helps (and make
sure permissions are correctly set on this directory)? However, it may very
well be something else....

-=- Olivier

Le 14 février 2012 03:44, Martin Raspaud <martin.raspaud at smhi.se> a écrit :

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi all,
>
> I am trying to compile numpy 1.6.1 from source on a Redhat Linux
> enterprise 6 machine, and I get a problem with Python.h : somehow it
> can't be located by numpy's install script:
> SystemError: Cannot compile 'Python.h'. Perhaps you need to install
> python-dev|python-devel.
>
> Now, the trick is that python-devel IS installed:
> bash-4.1$ rpm -qa | grep python-dev
> python-devel-2.6.6-29.el6.x86_64
>
> and Python.h is logically in /usr/include/python2.6
>
> Anyone got a clue ?
>
> The full log is included below.
>
> Best regards,
> Martin
>
>
> bash-4.1$ python setup.py build --fcompiler=gnu95
> 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/lib64
>  libraries mkl,vml,guide not found in /usr/local/lib
>  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
>  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
>  libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/atlas
>  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
>  libraries f77blas,cblas,atlas not found in /usr/local/lib
>  libraries f77blas,cblas,atlas not found in /usr/lib64/atlas
>  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
>
> /data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/system_info.py:1414:
> 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
>  libraries blas not found in /usr/local/lib
>  libraries blas not found in /usr/lib64
>  libraries blas not found in /usr/lib
>  NOT AVAILABLE
>
> /data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/system_info.py:1423:
> UserWarning:
>    Blas (http://www.netlib.org/blas/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [blas]) or by setting
>    the BLAS environment variable.
>  warnings.warn(BlasNotFoundError.__doc__)
> blas_src_info:
>  NOT AVAILABLE
>
> /data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/system_info.py:1426:
> UserWarning:
>    Blas (http://www.netlib.org/blas/) sources not found.
>    Directories to search for the sources can be specified in the
>    numpy/distutils/site.cfg file (section [blas_src]) or by setting
>    the BLAS_SRC environment variable.
>  warnings.warn(BlasSrcNotFoundError.__doc__)
>  NOT AVAILABLE
>
> lapack_opt_info:
> lapack_mkl_info:
> mkl_info:
>  libraries mkl,vml,guide not found in /usr/local/lib64
>  libraries mkl,vml,guide not found in /usr/local/lib
>  libraries mkl,vml,guide not found in /usr/lib64
>  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/lib64
>  libraries lapack_atlas not found in /usr/local/lib64
>  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/lib64/atlas
>  libraries lapack_atlas not found in /usr/lib64/atlas
>  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
>  libraries lapack_atlas not found in /usr/local/lib64
>  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/lib64/atlas
>  libraries lapack_atlas not found in /usr/lib64/atlas
>  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
>
> /data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/system_info.py:1330:
> 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
>  libraries lapack not found in /usr/local/lib
>  libraries lapack not found in /usr/lib64
>  libraries lapack not found in /usr/lib
>  NOT AVAILABLE
>
> /data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/system_info.py:1341:
> UserWarning:
>    Lapack (http://www.netlib.org/lapack/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [lapack]) or by setting
>    the LAPACK environment variable.
>  warnings.warn(LapackNotFoundError.__doc__)
> lapack_src_info:
>  NOT AVAILABLE
>
> /data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/system_info.py:1344:
> UserWarning:
>    Lapack (http://www.netlib.org/lapack/) sources not found.
>    Directories to search for the sources can be specified in the
>    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
>    the LAPACK_SRC environment variable.
>  warnings.warn(LapackSrcNotFoundError.__doc__)
>  NOT AVAILABLE
>
> 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
> build_src
> building py_modules sources
> building library "npymath" sources
> customize Gnu95FCompiler
> Found executable /usr/bin/gfortran
> customize Gnu95FCompiler using config
> C compiler: gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
> - -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> - --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
> - -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> - -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> - -D_GNU_SOURCE -fPIC -fwrapv -fPIC
>
> compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
> - -Inumpy/core/src/npymath -Inumpy/core/src/multiarray
> - -Inumpy/core/src/umath -Inumpy/core/include -c'
> gcc: _configtest.c
> gcc -pthread _configtest.o -o _configtest
> success!
> removing: _configtest.c _configtest.o _configtest
> C compiler: gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
> - -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> - --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
> - -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> - -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> - -D_GNU_SOURCE -fPIC -fwrapv -fPIC
>
> compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
> - -Inumpy/core/src/npymath -Inumpy/core/src/multiarray
> - -Inumpy/core/src/umath -Inumpy/core/include -c'
> gcc: _configtest.c
> _configtest.c:1: warning: conflicting types for built-in function 'exp'
> gcc -pthread _configtest.o -o _configtest
> _configtest.o: In function `main':
> /data/proj/safutv/src/numpy-1.6.1/_configtest.c:6: undefined reference
> to `exp'
> collect2: ld returned 1 exit status
> _configtest.o: In function `main':
> /data/proj/safutv/src/numpy-1.6.1/_configtest.c:6: undefined reference
> to `exp'
> collect2: ld returned 1 exit status
> failure.
> removing: _configtest.c _configtest.o
> C compiler: gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
> - -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> - --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
> - -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> - -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> - -D_GNU_SOURCE -fPIC -fwrapv -fPIC
>
> compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
> - -Inumpy/core/src/npymath -Inumpy/core/src/multiarray
> - -Inumpy/core/src/umath -Inumpy/core/include -c'
> gcc: _configtest.c
> _configtest.c:1: warning: conflicting types for built-in function 'exp'
> gcc -pthread _configtest.o -lm -o _configtest
> success!
> removing: _configtest.c _configtest.o _configtest
> building extension "numpy.core._sort" sources
> Generating build/src.linux-x86_64-2.6/numpy/core/include/numpy/config.h
> C compiler: gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
> - -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> - --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
> - -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> - -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> - -D_GNU_SOURCE -fPIC -fwrapv -fPIC
>
> compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
> - -Inumpy/core/src/npymath -Inumpy/core/src/multiarray
> - -Inumpy/core/src/umath -Inumpy/core/include -c'
> gcc: _configtest.c
> _configtest.c:1:20: error: Python.h: No such file or directory
> _configtest.c:1:20: error: Python.h: No such file or directory
> failure.
> removing: _configtest.c _configtest.o
> Traceback (most recent call last):
>  File "setup.py", line 196, in <module>
>    setup_package()
>  File "setup.py", line 189, in setup_package
>    configuration=configuration )
>  File "/data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/core.py",
> line 186, in setup
>    return old_setup(**new_attr)
>  File "/usr/lib64/python2.6/distutils/core.py", line 152, in setup
>    dist.run_commands()
>  File "/usr/lib64/python2.6/distutils/dist.py", line 975, in run_commands
>    self.run_command(cmd)
>  File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command
>    cmd_obj.run()
>  File
> "/data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/command/build.py",
> line 37, in run
>    old_build.run(self)
>  File "/usr/lib64/python2.6/distutils/command/build.py", line 134, in run
>    self.run_command(cmd_name)
>  File "/usr/lib64/python2.6/distutils/cmd.py", line 333, in run_command
>    self.distribution.run_command(command)
>  File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command
>    cmd_obj.run()
>  File
> "/data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/command/build_src.py",
> line 152, in run
>    self.build_sources()
>  File
> "/data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/command/build_src.py",
> line 169, in build_sources
>    self.build_extension_sources(ext)
>  File
> "/data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/command/build_src.py",
> line 328, in build_extension_sources
>    sources = self.generate_sources(sources, ext)
>  File
> "/data/proj6/safutv/src/numpy-1.6.1/numpy/distutils/command/build_src.py",
> line 385, in generate_sources
>    source = func(extension, build_dir)
>  File "numpy/core/setup.py", line 410, in generate_config_h
>    moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
>  File "numpy/core/setup.py", line 41, in check_types
>    out = check_types(*a, **kw)
>  File "numpy/core/setup.py", line 271, in check_types
>    "Cannot compile 'Python.h'. Perhaps you need to "\
> SystemError: Cannot compile 'Python.h'. Perhaps you need to install
> python-dev|python-devel.
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