[Numpy-discussion] Numpy 1.6.1 installation problem

Martin Raspaud martin.raspaud at smhi.se
Tue Feb 14 03:44:53 EST 2012 

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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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