[Numpy-discussion] Instaling numpy without root access

Lahiru Samarakoon lahiruts at gmail.com
Fri Oct 10 12:51:19 EDT 2014


Dear all,

I am trying to install numpy without root access. So I am building from the
source.  I have installed atlas which also has lapack with it.  I changed
the site.cfg file as given below

[DEFAULT]
library_dirs = /home/svu/a0095654/ATLAS/build/lib
include_dirs = /home/svu/a0095654/ATLAS/build/include


However, I am getting a segmentation fault when importing numpy.

Please advise. I also put the build log file at the end of the email if
necessary.

Thank you,
Best Regards,
Lahiru

Log starts below.

* python2.7 setup.py build  --fcompiler=gnu95*
Running from numpy source directory.
/home/svu/a0095654/lib/python2.7/distutils/dist.py:267: UserWarning:
Unknown distribution option: 'test_suite'
  warnings.warn(msg)
non-existing path in 'numpy/f2py': 'docs'
non-existing path in 'numpy/f2py': 'f2py.1'
F2PY Version 2
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in
['/home/svu/a0095654/ATLAS/build/lib']
  NOT AVAILABLE

openblas_info:
  libraries openblas not found in ['/home/svu/a0095654/ATLAS/build/lib']
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}

C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv
-O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/home/svu/a0095654/ATLAS/build/install/lib
-lptf77blas -lptcblas -latlas -o _configtest
_configtest.o: In function `main':
/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:5: undefined reference
to `ATL_buildinfo'
collect2: ld returned 1 exit status
_configtest.o: In function `main':
/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:5: undefined reference
to `ATL_buildinfo'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255
Output: compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}

C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv
-O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/home/svu/a0095654/ATLAS/build/install/lib
-lptf77blas -lptcblas -latlas -o _configtest
_configtest.o: In function `main':
/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:5: undefined reference
to `ATL_buildinfo'
collect2: ld returned 1 exit status

Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"None\\""')]

  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"None\\""')]

non-existing path in 'numpy/lib': 'benchmarks'
lapack_opt_info:
openblas_lapack_info:
  libraries openblas not found in ['/home/svu/a0095654/ATLAS/build/lib']
  NOT AVAILABLE

lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in
['/home/svu/a0095654/ATLAS/build/lib']
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas not found in
/home/svu/a0095654/ATLAS/build/install/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
/hpctmp/a0095654/Software/numpy-1.9.0/numpy/distutils/system_info.py:1095:
UserWarning:
*********************************************************************
    Lapack library (from ATLAS) is probably incomplete:
      size of /home/svu/a0095654/ATLAS/build/install/lib/liblapack.so is
5.0673828125k (expected >4000k)

    Follow the instructions in the KNOWN PROBLEMS section of the file
    numpy/INSTALL.txt.
*********************************************************************

  warnings.warn(message)
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"None\\""')]

  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"None\\""')]

/home/svu/a0095654/lib/python2.7/distutils/dist.py:267: UserWarning:
Unknown distribution option: 'define_macros'
  warnings.warn(msg)
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
customize Gnu95FCompiler using config
C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv
-O3 -Wall -Wstrict-prototypes -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/home/svu/a0095654/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 -g -fwrapv
-O3 -Wall -Wstrict-prototypes -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/home/svu/a0095654/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':
/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:6: undefined reference
to `exp'
collect2: ld returned 1 exit status
_configtest.o: In function `main':
/hpctmp/a0095654/Software/numpy-1.9.0/_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 -g -O2 -DNDEBUG -g -fwrapv
-O3 -Wall -Wstrict-prototypes -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/home/svu/a0095654/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.
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.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._dotblas" sources
  adding 'numpy/core/blasdot/_dotblas.c' to sources.
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
  adding 'numpy/linalg/lapack_litemodule.c' to sources.
  adding 'numpy/linalg/lapack_lite/python_xerbla.c' to sources.
building extension "numpy.linalg._umath_linalg" sources
  adding 'numpy/linalg/umath_linalg.c.src' to sources.
  adding 'numpy/linalg/lapack_lite/python_xerbla.c' to sources.
building extension "numpy.random.mtrand" sources
C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv
-O3 -Wall -Wstrict-prototypes -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/home/svu/a0095654/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
building 'npymath' library
compiling C sources
C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv
-O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/build
creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy
creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core
creating
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src
creating
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/npymath
creating build/temp.linux-x86_64-2.7/numpy
creating build/temp.linux-x86_64-2.7/numpy/core
creating build/temp.linux-x86_64-2.7/numpy/core/src
creating build/temp.linux-x86_64-2.7/numpy/core/src/npymath
compile options: '-Inumpy/core/include
-Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy
-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/home/svu/a0095654/include/python2.7
-Ibuild/src.linux-x86_64-2.7/numpy/core/src/private
-Ibuild/src.linux-x86_64-2.7/numpy/core/src/private
-Ibuild/src.linux-x86_64-2.7/numpy/core/src/private
-Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -c'
gcc: numpy/core/src/npymath/halffloat.c
gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c
gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math.c
gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math_complex.c
ar: adding 4 object files to build/temp.linux-x86_64-2.7/libnpymath.a
building 'npysort' library
compiling C sources
C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv
-O3 -Wall -Wstrict-prototypes -fPIC

creating
build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/npysort
compile options: '-Ibuild/src.linux-x86_64-2.7/numpy/core/src/private
-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy
-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/home/svu/a0095654/include/python2.7
-Ibuild/src.linux-x86_64-2.7/numpy/core/src/private
-Ibuild/src.linux-x86_64-2.7/numpy/core/src/private
-Ibuild/src.linux-x86_64-2.7/numpy/core/src/private
-Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -c'
gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/selection.c
gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/quicksort.c
gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/mergesort.c
gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/binsearch.c
gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/heapsort.c
ar: adding 5 object files to build/temp.linux-x86_64-2.7/libnpysort.a
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
running build_scripts
  adding 'build/scripts.linux-x86_64-2.7/f2py2.7' to scripts
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