[Numpy-discussion] Numpy 1.6.1 installation problem
Martin Raspaud
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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Olivier Delalleau
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
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Bruce Southey
If not just try the basic approach:
$ python setup.py build
Bruce
Martin Raspaud
Hash: SHA1
On 14/02/12 16:48, Bruce Southey wrote:
> 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....
> This there a reason why you are using the fcompiler option?
> If not just try the basic approach:
> $ python setup.py build
Hi guys,
Thanks for the help. I'm getting past this error thanks to the CPATH
environment variable.
Unfortunately I get another error later on that the compiler can't find
some C files...
I attach the error.
Best regards,
Martin
[...]
creating build/temp.linux-x86_64-2.6/numpy/core/src/multiarray
compile options: '-Inumpy/core/include
- -Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy
- -I/usr/lib64/python2.6/site-packages/numpy/core/include
- -I/usr/include/python2.6 -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: numpy/core/src/multiarray/multiarraymodule_onefile.c
numpy/core/src/multiarray/multiarraymodule_onefile.c:10:25: error:
scalartypes.c: No such file or directory
numpy/core/src/multiarray/multiarraymodule_onefile.c:14:24: error:
arraytypes.c: No such file or directory
In file included from
numpy/core/src/multiarray/multiarraymodule_onefile.c:35:
numpy/core/src/multiarray/conversion_utils.c: In function
'PyArray_PyIntAsInt':
numpy/core/src/multiarray/conversion_utils.c:378: error: 'INT_Descr'
undeclared (first use in this function)
numpy/core/src/multiarray/conversion_utils.c:378: error: (Each
undeclared identifier is reported only once
numpy/core/src/multiarray/conversion_utils.c:378: error: for each
function it appears in.)
numpy/core/src/multiarray/conversion_utils.c: In function
'PyArray_PyIntAsIntp':
numpy/core/src/multiarray/conversion_utils.c:467: error: 'LONG_Descr'
undeclared (first use in this function)
numpy/core/src/multiarray/multiarraymodule_onefile.c:38:20: error:
nditer.c: No such file or directory
numpy/core/src/multiarray/multiarraymodule_onefile.c:40:36: error:
lowlevel_strided_loops.c: No such file or directory
numpy/core/src/multiarray/multiarraymodule_onefile.c:42:20: error:
einsum.c: No such file or directory
numpy/core/src/multiarray/multiarraymodule_onefile.c:10:25: error:
scalartypes.c: No such file or directory
numpy/core/src/multiarray/multiarraymodule_onefile.c:14:24: error:
arraytypes.c: No such file or directory
In file included from
numpy/core/src/multiarray/multiarraymodule_onefile.c:35:
numpy/core/src/multiarray/conversion_utils.c: In function
'PyArray_PyIntAsInt':
numpy/core/src/multiarray/conversion_utils.c:378: error: 'INT_Descr'
undeclared (first use in this function)
numpy/core/src/multiarray/conversion_utils.c:378: error: (Each
undeclared identifier is reported only once
numpy/core/src/multiarray/conversion_utils.c:378: error: for each
function it appears in.)
numpy/core/src/multiarray/conversion_utils.c: In function
'PyArray_PyIntAsIntp':
numpy/core/src/multiarray/conversion_utils.c:467: error: 'LONG_Descr'
undeclared (first use in this function)
numpy/core/src/multiarray/multiarraymodule_onefile.c:38:20: error:
nditer.c: No such file or directory
numpy/core/src/multiarray/multiarraymodule_onefile.c:40:36: error:
lowlevel_strided_loops.c: No such file or directory
numpy/core/src/multiarray/multiarraymodule_onefile.c:42:20: error:
einsum.c: No such file or directory
error: Command "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 -Inumpy/core/include
- -Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy
- -I/usr/lib64/python2.6/site-packages/numpy/core/include
- -I/usr/include/python2.6 -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
numpy/core/src/multiarray/multiarraymodule_onefile.c -o
build/temp.linux-x86_64-2.6/numpy/core/src/multiarray/multiarraymodule_onefile.o"
failed with exit status 1
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Olivier Delalleau
It looks suspicious though that you're having so much trouble... Have you tried without the fcompiler option like Bruce suggested?
-=- Olivier