Hi all,
I've installed python 2.5 on my centos 5.3 x86_64 machine (system
standard is 2.4), and now I want to install numpy for it. However, the
build fails. The final message is:
"EnvironmentError: math library missing; rerun setup.py after setting
the MATHLIB env variable"
However, from looking earlier in the output, it seems it's looking for
a library called libcpml. I'm not sure what this library is (there is
no yum package for it), and since numpy works for python 2.4 it seems
all libraries should be installed. Any help would be most appreciated.
The full build output is attached.
Thanks,
/Patrik Jonsson
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/lib
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/lib
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/lib
libraries f77blas,cblas,atlas not found in /usr/lib/sse2
libraries f77blas,cblas,atlas not found in /usr/lib
NOT AVAILABLE
/home/patrik/system-stuff/numpy-1.3.0/numpy/distutils/system_info.py:1383:
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/lib
FOUND:
libraries = ['blas']
library_dirs = ['/usr/lib']
language = f77
FOUND:
libraries = ['blas']
library_dirs = ['/usr/lib']
define_macros = [('NO_ATLAS_INFO', 1)]
language = f77
lapack_opt_info:
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in /usr/local/lib
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/lib
libraries lapack_atlas not found in /usr/local/lib
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/lib
libraries lapack_atlas not found in /usr/local/lib
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
/home/patrik/system-stuff/numpy-1.3.0/numpy/distutils/system_info.py:1290:
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/lib
FOUND:
libraries = ['lapack']
library_dirs = ['/usr/lib']
language = f77
FOUND:
libraries = ['lapack', 'blas']
library_dirs = ['/usr/lib']
define_macros = [('NO_ATLAS_INFO', 1)]
language = f77
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
building py_modules sources
building library "npymath" sources
building extension "numpy.core._sort" sources
Generating build/src.linux-x86_64-2.5/numpy/core/include/numpy/config.h
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler using config
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
success!
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c: In function 'main':
_configtest.c:5: error: size of array 'test_array' is negative
_configtest.c: In function 'main':
_configtest.c:5: error: size of array 'test_array' is negative
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
_configtest.c: In function 'main':
_configtest.c:5: error: size of array 'test_array' is negative
_configtest.c: In function 'main':
_configtest.c:5: error: size of array 'test_array' is negative
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
success!
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
success!
removing: _configtest.c _configtest.o
/home/patrik/system-stuff/numpy-1.3.0/numpy/distutils/command/config.py:39:
DeprecationWarning:
+++++++++++++++++++++++++++++++++++++++++++++++++
Usage of try_run is deprecated: please do not
use it anymore, and avoid configuration checks
involving running executable on the target machine.
+++++++++++++++++++++++++++++++++++++++++++++++++
DeprecationWarning)
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
gcc -pthread _configtest.o -o _configtest
/usr/bin/ld: warning: i386 architecture of input file `_configtest.o' is
incompatible with i386:x86-64 output
_configtest.o: In function `main':
/home/patrik/system-stuff/numpy-1.3.0/_configtest.c:5: undefined reference to
`exp'
collect2: ld returned 1 exit status
/usr/bin/ld: warning: i386 architecture of input file `_configtest.o' is
incompatible with i386:x86-64 output
_configtest.o: In function `main':
/home/patrik/system-stuff/numpy-1.3.0/_configtest.c:5: undefined reference to
`exp'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
gcc -pthread _configtest.o -lm -o _configtest
/usr/bin/ld: warning: i386 architecture of input file `_configtest.o' is
incompatible with i386:x86-64 output
_configtest
failure.
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/usr/include/python2.5 -c'
gcc: _configtest.c
gcc -pthread _configtest.o -lcpml -o _configtest
/usr/bin/ld: cannot find -lcpml
collect2: ld returned 1 exit status
/usr/bin/ld: cannot find -lcpml
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
File "setup.py", line 172, in <module>
setup_package()
File "setup.py", line 165, in setup_package
configuration=configuration )
File "/home/patrik/system-stuff/numpy-1.3.0/numpy/distutils/core.py", line
184, in setup
return old_setup(**new_attr)
File "/usr/lib/python2.5/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/lib/python2.5/distutils/dist.py", line 974, in run_commands
self.run_command(cmd)
File "/usr/lib/python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File
"/home/patrik/system-stuff/numpy-1.3.0/numpy/distutils/command/build.py", line
37, in run
old_build.run(self)
File "/usr/lib/python2.5/distutils/command/build.py", line 112, in run
self.run_command(cmd_name)
File "/usr/lib/python2.5/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File
"/home/patrik/system-stuff/numpy-1.3.0/numpy/distutils/command/build_src.py",
line 130, in run
self.build_sources()
File
"/home/patrik/system-stuff/numpy-1.3.0/numpy/distutils/command/build_src.py",
line 147, in build_sources
self.build_extension_sources(ext)
File
"/home/patrik/system-stuff/numpy-1.3.0/numpy/distutils/command/build_src.py",
line 250, in build_extension_sources
sources = self.generate_sources(sources, ext)
File
"/home/patrik/system-stuff/numpy-1.3.0/numpy/distutils/command/build_src.py",
line 307, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 289, in generate_config_h
mathlibs = check_mathlib(config_cmd)
File "numpy/core/setup.py", line 253, in check_mathlib
raise EnvironmentError("math library missing; rerun "
EnvironmentError: math library missing; rerun setup.py after setting the
MATHLIB env variable
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