[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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