cython_numpy_stampede.txt

Processing dependencies for Cython==0.20.2
Finished processing dependencies for Cython==0.20.2
login3.stampede(22)$ cd ..
login3.stampede(23)$ cd numpy/
login3.stampede(24)$ python setup.py  install --user
Running from numpy source directory.
Cythonizing sources
numpy/random/mtrand/mtrand.pyx has not changed
/opt/apps/python/epd/7.3.2/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
non-existing path in 'numpy/distutils': 'site.cfg'
F2PY Version 2
numpy/core/setup_common.py:92: MismatchCAPIWarning: API mismatch detected, the C API version numbers have to be updated. Current C api version is 9, with checksum 9b8bce614655d3eb02acddcb508203cb, but recorded checksum for C API version 9 in codegen_dir/cversions.txt is 982c4ebb6e7e4c194bf46b1535b4ef1b. If functions were added in the C API, you have to update C_API_VERSION  in numpy/core/setup_common.pyc.
  MismatchCAPIWarning)
blas_opt_info:
blas_mkl_info:
/home1/02734/vivek91/adv/numpy/numpy/distutils/system_info.py:581: UserWarning: Specified path /opt/apps/intel/13/composer_xe_2013.2.146/mkl/lib/em64t is invalid.
  warnings.warn('Specified path %s is invalid.' % d)
  libraries mkl,vml,guide not found in []
  NOT AVAILABLE

openblas_info:
  libraries openblas not found in ['/opt/apps/python/epd/7.3.2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in ['/opt/apps/python/epd/7.3.2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in ['/opt/apps/python/epd/7.3.2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

/home1/02734/vivek91/adv/numpy/numpy/distutils/system_info.py:1530: 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 ['/opt/apps/python/epd/7.3.2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

/home1/02734/vivek91/adv/numpy/numpy/distutils/system_info.py:1539: 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

/home1/02734/vivek91/adv/numpy/numpy/distutils/system_info.py:1542: 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:
openblas_lapack_info:
  libraries openblas not found in ['/opt/apps/python/epd/7.3.2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in []
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /opt/apps/python/epd/7.3.2/lib
  libraries lapack_atlas not found in /opt/apps/python/epd/7.3.2/lib
  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
  libraries lapack_atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_threads_info'>
  NOT AVAILABLE

atlas_info:
  libraries f77blas,cblas,atlas not found in /opt/apps/python/epd/7.3.2/lib
  libraries lapack_atlas not found in /opt/apps/python/epd/7.3.2/lib
  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
  libraries lapack_atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_info'>
  NOT AVAILABLE

/home1/02734/vivek91/adv/numpy/numpy/distutils/system_info.py:1435: 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 ['/opt/apps/python/epd/7.3.2/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

/home1/02734/vivek91/adv/numpy/numpy/distutils/system_info.py:1446: 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

/home1/02734/vivek91/adv/numpy/numpy/distutils/system_info.py:1449: 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

/opt/apps/python/epd/7.3.2/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros'
  warnings.warn(msg)
running install
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
customize Gnu95FCompiler using config
C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -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/src/npysort -Inumpy/core/include -I/opt/apps/python/epd/7.3.2/include/python2.7 -c'
gcc: _configtest.c
gcc -pthread _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -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/src/npysort -Inumpy/core/include -I/opt/apps/python/epd/7.3.2/include/python2.7 -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':
/home1/02734/vivek91/adv/numpy/_configtest.c:6: undefined reference to `exp'
/usr/bin/ld: link errors found, deleting executable `_configtest'
collect2: ld returned 1 exit status
_configtest.o: In function `main':
/home1/02734/vivek91/adv/numpy/_configtest.c:6: undefined reference to `exp'
/usr/bin/ld: link errors found, deleting executable `_configtest'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -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/src/npysort -Inumpy/core/include -I/opt/apps/python/epd/7.3.2/include/python2.7 -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 library "npysort" sources
  adding 'build/src.linux-x86_64-2.7/numpy/core/src/private' to include_dirs.
None - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/src/private/npy_partition.h', 'build/src.linux-x86_64-2.7/numpy/core/src/private/npy_binsearch.h']
building extension "numpy.core._dummy" sources
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.
executing numpy/core/code_generators/generate_numpy_api.py
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.
numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h']
building extension "numpy.core.multiarray" sources
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.
executing numpy/core/code_generators/generate_numpy_api.py
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.
  adding 'build/src.linux-x86_64-2.7/numpy/core/src/multiarray' to include_dirs.
numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/src/multiarray/templ_common.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h']
building extension "numpy.core.umath" sources
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.
executing numpy/core/code_generators/generate_ufunc_api.py
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources.
  adding 'build/src.linux-x86_64-2.7/numpy/core/src/umath' to include_dirs.
numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/src/umath/funcs.inc', 'build/src.linux-x86_64-2.7/numpy/core/src/umath/simd.inc', 'build/src.linux-x86_64-2.7/numpy/core/src/umath/loops.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h']
building extension "numpy.core.scalarmath" sources
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.
executing numpy/core/code_generators/generate_numpy_api.py
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.
executing numpy/core/code_generators/generate_ufunc_api.py
  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources.
  adding 'build/src.linux-x86_64-2.7/numpy/core/src/private' to include_dirs.
numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/src/private/scalarmathmodule.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h']
building extension "numpy.core.umath_tests" sources
building extension "numpy.core.test_rational" sources
building extension "numpy.core.struct_ufunc_test" sources
building extension "numpy.core.multiarray_tests" sources
building extension "numpy.core.operand_flag_tests" sources
building extension "numpy.lib._compiled_base" sources
building extension "numpy.fft.fftpack_lite" sources
building extension "numpy.linalg.lapack_lite" sources
### Warning:  Using unoptimized lapack ###
  adding 'numpy/linalg/lapack_litemodule.c' to sources.
  adding 'numpy/linalg/lapack_lite/python_xerbla.c' to sources.
  adding 'numpy/linalg/lapack_lite/zlapack_lite.c' to sources.
  adding 'numpy/linalg/lapack_lite/dlapack_lite.c' to sources.
  adding 'numpy/linalg/lapack_lite/blas_lite.c' to sources.
  adding 'numpy/linalg/lapack_lite/dlamch.c' to sources.
  adding 'numpy/linalg/lapack_lite/f2c_lite.c' to sources.
building extension "numpy.linalg._umath_linalg" sources
### Warning:  Using unoptimized lapack ###
  adding 'numpy/linalg/umath_linalg.c.src' to sources.
  adding 'numpy/linalg/lapack_lite/python_xerbla.c' to sources.
  adding 'numpy/linalg/lapack_lite/zlapack_lite.c' to sources.
  adding 'numpy/linalg/lapack_lite/dlapack_lite.c' to sources.
  adding 'numpy/linalg/lapack_lite/blas_lite.c' to sources.
  adding 'numpy/linalg/lapack_lite/dlamch.c' to sources.
  adding 'numpy/linalg/lapack_lite/f2c_lite.c' to sources.
building extension "numpy.random.mtrand" sources
C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -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/src/npysort -Inumpy/core/include -I/opt/apps/python/epd/7.3.2/include/python2.7 -c'
gcc: _configtest.c
gcc -pthread _configtest.o -o _configtest
_configtest
failure.
removing: _configtest.c _configtest.o _configtest
building data_files sources
build_src: building npy-pkg config files
running build_py
copying numpy/version.py -> build/lib.linux-x86_64-2.7/numpy
copying build/src.linux-x86_64-2.7/numpy/__config__.py -> build/lib.linux-x86_64-2.7/numpy
copying build/src.linux-x86_64-2.7/numpy/distutils/__config__.py -> build/lib.linux-x86_64-2.7/numpy/distutils
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
running build_scripts
  adding 'build/scripts.linux-x86_64-2.7/f2py' to scripts
running install_lib
copying build/lib.linux-x86_64-2.7/numpy/__config__.py -> /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy
copying build/lib.linux-x86_64-2.7/numpy/version.py -> /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy
copying build/lib.linux-x86_64-2.7/numpy/distutils/__config__.py -> /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy/distutils
byte-compiling /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy/__config__.py to __config__.pyc
byte-compiling /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy/version.py to version.pyc
byte-compiling /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy/distutils/__config__.py to __config__.pyc
running install_scripts
changing mode of /home1/02734/vivek91/.local/bin/f2py to 755
running install_data
copying build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h -> /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy/core/include/numpy
copying build/src.linux-x86_64-2.7/numpy/core/include/numpy/ufunc_api.txt -> /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy/core/include/numpy
copying build/src.linux-x86_64-2.7/numpy/core/lib/npy-pkg-config/npymath.ini -> /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy/core/lib/npy-pkg-config
copying build/src.linux-x86_64-2.7/numpy/core/lib/npy-pkg-config/mlib.ini -> /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy/core/lib/npy-pkg-config
running install_egg_info
Removing /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy-1.10.0.dev_fa14ae0-py2.7.egg-info
Writing /home1/02734/vivek91/.local/lib/python2.7/site-packages/numpy-1.10.0.dev_fa14ae0-py2.7.egg-info
running install_clib
login3.stampede(25)$