[Numpy-discussion] Building problem on CentOS 5.3

Patrik Jonsson code@familjenjonsson....
Mon Sep 21 13:05:40 CDT 2009


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
-------------- next part --------------
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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