[SciPy-Dev] scipy build error

Martin Hofsäß m.hofsaess@gmail....
Thu Mar 21 09:42:24 CDT 2013


Hi all,

I have a new fresh system with linux mint 14 (64bit) and had install
the intel compiler c and fortran successful.

Setting the path to the mkl destination in the site.cfg was no problem
and building numpy worked without error.

I build numpy and scipy with "python setup.py config
--compiler=intelem --fcompiler=intelem build_clib --compiler=intelem
--fcompiler=intelem build_ext --compiler=intelem --fcompiler=intelem
install --user"

But trying to build scipy-0.11 and scipy-0.12b I get the following error.


Thanks for your help.

Best regards Martin


Running from scipy source directory.
blas_opt_info:
blas_mkl_info:
  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/opt/intel/mkl/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/intel/mkl/include/']

  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/opt/intel/mkl/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/intel/mkl/include/']

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/opt/intel/mkl/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/intel/mkl/include/']

  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/opt/intel/mkl/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/intel/mkl/include/']

  FOUND:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/opt/intel/mkl/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/intel/mkl/include/']

umfpack_info:
amd_info:
  FOUND:
    libraries = ['amd']
    library_dirs = ['/usr/local/lib']
    swig_opts = ['-I/usr/local/include']
    define_macros = [('SCIPY_AMD_H', None)]
    include_dirs = ['/usr/local/include']

  FOUND:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/usr/local/lib']
    swig_opts = ['-I/usr/local/include', '-I/usr/local/include']
    define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
    include_dirs = ['/usr/local/include']

running config
running build_clib
running build_src
build_src
building py_modules sources
building library "dfftpack" sources
building library "fftpack" sources
building library "linpack_lite" sources
building library "mach" sources
building library "quadpack" sources
building library "odepack" sources
building library "dop" sources
building library "fitpack" sources
building library "odrpack" sources
building library "minpack" sources
building library "rootfind" sources
building library "superlu_src" sources
building library "arpack_scipy" sources
building library "qhull" sources
building library "sc_c_misc" sources
building library "sc_cephes" sources
building library "sc_mach" sources
building library "sc_toms" sources
building library "sc_amos" sources
building library "sc_cdf" sources
building library "sc_specfun" sources
building library "statlib" sources
building extension "scipy.cluster._vq" sources
building extension "scipy.cluster._hierarchy_wrap" sources
building extension "scipy.fftpack._fftpack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.integrate._quadpack" sources
building extension "scipy.integrate._odepack" sources
building extension "scipy.integrate.vode" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.integrate._dop" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.interpolate.interpnd" sources
building extension "scipy.interpolate._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/scipy/interpolate/src/dfitpack-f2pywrappers.f'
to sources.
building extension "scipy.interpolate._interpolate" sources
building extension "scipy.io.matlab.streams" sources
building extension "scipy.io.matlab.mio_utils" sources
building extension "scipy.io.matlab.mio5_utils" sources
building extension "scipy.lib.blas.fblas" sources
f2py options: ['skip:', ':']
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/lib/blas/fblas-f2pywrappers.f'
to sources.
building extension "scipy.lib.blas.cblas" sources
  adding 'build/src.linux-x86_64-2.7/scipy/lib/blas/cblas.pyf' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.lib.lapack.flapack" sources
f2py options: ['skip:', ':']
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.lib.lapack.clapack" sources
  adding 'build/src.linux-x86_64-2.7/scipy/lib/lapack/clapack.pyf' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.lib.lapack.calc_lwork" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.lib.lapack.atlas_version" sources
building extension "scipy.linalg.fblas" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/fblas-f2pywrappers.f'
to sources.
building extension "scipy.linalg.cblas" sources
  adding 'build/src.linux-x86_64-2.7/scipy/linalg/cblas.pyf' to sources.
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.linalg.flapack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/flapack-f2pywrappers.f'
to sources.
building extension "scipy.linalg.clapack" sources
  adding 'build/src.linux-x86_64-2.7/scipy/linalg/clapack.pyf' to sources.
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.linalg._flinalg" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.linalg.calc_lwork" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.linalg.atlas_version" sources
building extension "scipy.odr.__odrpack" sources
building extension "scipy.optimize._minpack" sources
building extension "scipy.optimize._zeros" sources
building extension "scipy.optimize._lbfgsb" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.optimize._slsqp" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.optimize._nnls" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal.spectral" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse.linalg.isolve._iterative" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.sparse.linalg.dsolve._superlu" sources
building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources
  adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources.
building extension "scipy.sparse.linalg.eigen.arpack._arpack" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/sparse/linalg/eigen/arpack/_arpack-f2pywrappers.f'
to sources.
building extension "scipy.sparse.sparsetools._csr" sources
building extension "scipy.sparse.sparsetools._csc" sources
building extension "scipy.sparse.sparsetools._coo" sources
building extension "scipy.sparse.sparsetools._bsr" sources
building extension "scipy.sparse.sparsetools._dia" sources
building extension "scipy.sparse.sparsetools._csgraph" sources
building extension "scipy.sparse.csgraph._shortest_path" sources
building extension "scipy.sparse.csgraph._traversal" sources
building extension "scipy.sparse.csgraph._min_spanning_tree" sources
building extension "scipy.sparse.csgraph._tools" sources
building extension "scipy.spatial.qhull" sources
building extension "scipy.spatial.ckdtree" sources
building extension "scipy.spatial._distance_wrap" sources
building extension "scipy.special._cephes" sources
building extension "scipy.special.specfun" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.special.orthogonal_eval" sources
building extension "scipy.special.lambertw" sources
building extension "scipy.special._logit" sources
building extension "scipy.stats.statlib" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.stats.vonmises_cython" sources
building extension "scipy.stats._rank" sources
building extension "scipy.stats.futil" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
building extension "scipy.stats.mvn" sources
f2py options: []
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/scipy/stats/mvn-f2pywrappers.f' to sources.
building extension "scipy.ndimage._nd_image" sources
building data_files sources
build_src: building npy-pkg config files
Found executable /opt/intel/composer_xe_2011_sp1.10.319/bin/intel64/icc
Could not locate executable ecc
customize IntelEM64TCCompiler
customize IntelEM64TCCompiler using build_clib
customize IntelEM64TFCompiler
Found executable /opt/intel/composer_xe_2011_sp1.10.319/bin/intel64/ifort
customize IntelEM64TFCompiler using build_clib
running build_ext
customize IntelEM64TCCompiler
customize IntelEM64TCCompiler using build_ext
extending extension 'scipy.sparse.linalg.dsolve._superlu'
defined_macros with [('USE_VENDOR_BLAS', 1)]
customize IntelEM64TCCompiler
customize IntelEM64TCCompiler using build_ext
customize IntelEM64TFCompiler
customize IntelEM64TFCompiler using build_ext
building 'scipy.interpolate._interpolate' extension
compiling C++ sources
C compiler: icc -m64 -O3 -g -fPIC -fp-model strict
-fomit-frame-pointer -openmp -xhost

compile options: '-Iscipy/interpolate/src
-I/home/likewise-open/hofsaess/.local/lib/python2.7/site-packages/numpy/core/include
-I/usr/include/python2.7 -c'
icc: scipy/interpolate/src/_interpolate.cpp
/usr/include/c++/4.7/ext/atomicity.h(48): error: identifier
"__ATOMIC_ACQ_REL" is undefined
    { return __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }
                                              ^

/usr/include/c++/4.7/ext/atomicity.h(48): error: identifier
"__atomic_fetch_add" is undefined
    { return __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }
             ^

/usr/include/c++/4.7/ext/atomicity.h(52): error: identifier
"__ATOMIC_ACQ_REL" is undefined
    { __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }
                                       ^

/usr/include/c++/4.7/ext/atomicity.h(52): error: identifier
"__atomic_fetch_add" is undefined
    { __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }
      ^

/home/likewise-open/hofsaess/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h(11):
warning #1224: #warning directive: "Using deprecated NumPy API,
disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
  #warning "Using deprecated NumPy API, disable it by #defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
   ^

compilation aborted for scipy/interpolate/src/_interpolate.cpp (code 2)
/usr/include/c++/4.7/ext/atomicity.h(48): error: identifier
"__ATOMIC_ACQ_REL" is undefined
    { return __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }
                                              ^

/usr/include/c++/4.7/ext/atomicity.h(48): error: identifier
"__atomic_fetch_add" is undefined
    { return __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }
             ^

/usr/include/c++/4.7/ext/atomicity.h(52): error: identifier
"__ATOMIC_ACQ_REL" is undefined
    { __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }
                                       ^

/usr/include/c++/4.7/ext/atomicity.h(52): error: identifier
"__atomic_fetch_add" is undefined
    { __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }
      ^

/home/likewise-open/hofsaess/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h(11):
warning #1224: #warning directive: "Using deprecated NumPy API,
disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
  #warning "Using deprecated NumPy API, disable it by #defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
   ^

compilation aborted for scipy/interpolate/src/_interpolate.cpp (code 2)
error: Command "icc -m64 -O3 -g -fPIC -fp-model strict
-fomit-frame-pointer -openmp -xhost -Iscipy/interpolate/src
-I/home/likewise-open/hofsaess/.local/lib/python2.7/site-packages/numpy/core/include
-I/usr/include/python2.7 -c scipy/interpolate/src/_interpolate.cpp -o
build/temp.linux-x86_64-2.7/scipy/interpolate/src/_interpolate.o"
failed with exit status 2


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