[Numpy-discussion] Numpy 1.6.1 installation problem

Bruce Southey bsouthey@gmail....
Tue Feb 14 09:48:22 CST 2012


On 02/14/2012 09:40 AM, Olivier Delalleau wrote:
> 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@smhi.se 
> <mailto:martin.raspaud@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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This there a reason why you are using the fcompiler option?
If not just try the basic approach:

$ python setup.py build

Bruce

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