<div dir="ltr"><div><div><div><div><div><div>Dear all,<br><br></div>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<br><br>[DEFAULT]<br>library_dirs = /home/svu/a0095654/ATLAS/build/lib<br>include_dirs = /home/svu/a0095654/ATLAS/build/include<br><br><br></div>However, I am getting a segmentation fault when importing numpy. <br><br></div>Please advise. I also put the build log file at the end of the email if necessary.<br><br></div>Thank you,<br>Best Regards,<br></div>Lahiru<br><br></div>Log starts below.<br><div><div><div><br><b> python2.7 setup.py build  --fcompiler=gnu95</b><br>Running from numpy source directory.<br>/home/svu/a0095654/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_suite'<br>  warnings.warn(msg)<br>non-existing path in 'numpy/f2py': 'docs'<br>non-existing path in 'numpy/f2py': 'f2py.1'<br>F2PY Version 2<br>blas_opt_info:<br>blas_mkl_info:<br>  libraries mkl,vml,guide not found in ['/home/svu/a0095654/ATLAS/build/lib']<br>  NOT AVAILABLE<br><br>openblas_info:<br>  libraries openblas not found in ['/home/svu/a0095654/ATLAS/build/lib']<br>  NOT AVAILABLE<br><br>atlas_blas_threads_info:<br>Setting PTATLAS=ATLAS<br>Setting PTATLAS=ATLAS<br>customize Gnu95FCompiler<br>Found executable /usr/bin/gfortran<br>customize Gnu95FCompiler<br>customize Gnu95FCompiler using config<br>compiling '_configtest.c':<br><br>/* This file is generated from numpy/distutils/system_info.py */<br>void ATL_buildinfo(void);<br>int main(void) {<br>  ATL_buildinfo();<br>  return 0;<br>}<br><br>C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC<br><br>compile options: '-c'<br>gcc: _configtest.c<br>gcc -pthread _configtest.o -L/home/svu/a0095654/ATLAS/build/install/lib -lptf77blas -lptcblas -latlas -o _configtest<br>_configtest.o: In function `main':<br>/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:5: undefined reference to `ATL_buildinfo'<br>collect2: ld returned 1 exit status<br>_configtest.o: In function `main':<br>/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:5: undefined reference to `ATL_buildinfo'<br>collect2: ld returned 1 exit status<br>failure.<br>removing: _configtest.c _configtest.o<br>Status: 255<br>Output: compiling '_configtest.c':<br><br>/* This file is generated from numpy/distutils/system_info.py */<br>void ATL_buildinfo(void);<br>int main(void) {<br>  ATL_buildinfo();<br>  return 0;<br>}<br><br>C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC<br><br>compile options: '-c'<br>gcc: _configtest.c<br>gcc -pthread _configtest.o -L/home/svu/a0095654/ATLAS/build/install/lib -lptf77blas -lptcblas -latlas -o _configtest<br>_configtest.o: In function `main':<br>/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:5: undefined reference to `ATL_buildinfo'<br>collect2: ld returned 1 exit status<br><br>Setting PTATLAS=ATLAS<br>  FOUND:<br>    libraries = ['ptf77blas', 'ptcblas', 'atlas']<br>    library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']<br>    language = c<br>    define_macros = [('ATLAS_INFO', '"\\"None\\""')]<br><br>  FOUND:<br>    libraries = ['ptf77blas', 'ptcblas', 'atlas']<br>    library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']<br>    language = c<br>    define_macros = [('ATLAS_INFO', '"\\"None\\""')]<br><br>non-existing path in 'numpy/lib': 'benchmarks'<br>lapack_opt_info:<br>openblas_lapack_info:<br>  libraries openblas not found in ['/home/svu/a0095654/ATLAS/build/lib']<br>  NOT AVAILABLE<br><br>lapack_mkl_info:<br>mkl_info:<br>  libraries mkl,vml,guide not found in ['/home/svu/a0095654/ATLAS/build/lib']<br>  NOT AVAILABLE<br><br>  NOT AVAILABLE<br><br>atlas_threads_info:<br>Setting PTATLAS=ATLAS<br>  libraries lapack_atlas not found in /home/svu/a0095654/ATLAS/build/install/lib<br>numpy.distutils.system_info.atlas_threads_info<br>Setting PTATLAS=ATLAS<br>/hpctmp/a0095654/Software/numpy-1.9.0/numpy/distutils/system_info.py:1095: UserWarning: <br>*********************************************************************<br>    Lapack library (from ATLAS) is probably incomplete:<br>      size of /home/svu/a0095654/ATLAS/build/install/lib/liblapack.so is 5.0673828125k (expected >4000k)<br><br>    Follow the instructions in the KNOWN PROBLEMS section of the file<br>    numpy/INSTALL.txt.<br>*********************************************************************<br><br>  warnings.warn(message)<br>Setting PTATLAS=ATLAS<br>  FOUND:<br>    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']<br>    library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']<br>    language = c<br>    define_macros = [('ATLAS_INFO', '"\\"None\\""')]<br><br>  FOUND:<br>    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']<br>    library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']<br>    language = c<br>    define_macros = [('ATLAS_INFO', '"\\"None\\""')]<br><br>/home/svu/a0095654/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros'<br>  warnings.warn(msg)<br>running build<br>running config_cc<br>unifing config_cc, config, build_clib, build_ext, build commands --compiler options<br>running config_fc<br>unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options<br>running build_src<br>build_src<br>building py_modules sources<br>building library "npymath" sources<br>customize Gnu95FCompiler<br>customize Gnu95FCompiler using config<br>C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC<br><br>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'<br>gcc: _configtest.c<br>gcc -pthread _configtest.o -o _configtest<br>success!<br>removing: _configtest.c _configtest.o _configtest<br>C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC<br><br>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'<br>gcc: _configtest.c<br>_configtest.c:1: warning: conflicting types for built-in function ‘exp’<br>gcc -pthread _configtest.o -o _configtest<br>_configtest.o: In function `main':<br>/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:6: undefined reference to `exp'<br>collect2: ld returned 1 exit status<br>_configtest.o: In function `main':<br>/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:6: undefined reference to `exp'<br>collect2: ld returned 1 exit status<br>failure.<br>removing: _configtest.c _configtest.o<br>C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC<br><br>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'<br>gcc: _configtest.c<br>_configtest.c:1: warning: conflicting types for built-in function ‘exp’<br>gcc -pthread _configtest.o -lm -o _configtest<br>success!<br>removing: _configtest.c _configtest.o _configtest<br>building library "npysort" sources<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/src/private' to include_dirs.<br>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']<br>building extension "numpy.core._dummy" sources<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.<br>executing numpy/core/code_generators/generate_numpy_api.py<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.<br>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']<br>building extension "numpy.core.multiarray" sources<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.<br>executing numpy/core/code_generators/generate_numpy_api.py<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.<br>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']<br>building extension "numpy.core.umath" sources<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.<br>executing numpy/core/code_generators/generate_ufunc_api.py<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources.<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/src/umath' to include_dirs.<br>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']<br>building extension "numpy.core.scalarmath" sources<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.<br>executing numpy/core/code_generators/generate_numpy_api.py<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.<br>executing numpy/core/code_generators/generate_ufunc_api.py<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources.<br>  adding 'build/src.linux-x86_64-2.7/numpy/core/src/private' to include_dirs.<br>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']<br>building extension "numpy.core._dotblas" sources<br>  adding 'numpy/core/blasdot/_dotblas.c' to sources.<br>building extension "numpy.core.umath_tests" sources<br>building extension "numpy.core.test_rational" sources<br>building extension "numpy.core.struct_ufunc_test" sources<br>building extension "numpy.core.multiarray_tests" sources<br>building extension "numpy.core.operand_flag_tests" sources<br>building extension "numpy.lib._compiled_base" sources<br>building extension "numpy.fft.fftpack_lite" sources<br>building extension "numpy.linalg.lapack_lite" sources<br>  adding 'numpy/linalg/lapack_litemodule.c' to sources.<br>  adding 'numpy/linalg/lapack_lite/python_xerbla.c' to sources.<br>building extension "numpy.linalg._umath_linalg" sources<br>  adding 'numpy/linalg/umath_linalg.c.src' to sources.<br>  adding 'numpy/linalg/lapack_lite/python_xerbla.c' to sources.<br>building extension "numpy.random.mtrand" sources<br>C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC<br><br>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'<br>gcc: _configtest.c<br>gcc -pthread _configtest.o -o _configtest<br>_configtest<br>failure.<br>removing: _configtest.c _configtest.o _configtest<br>building data_files sources<br>build_src: building npy-pkg config files<br>running build_py<br>copying numpy/version.py -> build/lib.linux-x86_64-2.7/numpy<br>copying build/src.linux-x86_64-2.7/numpy/__config__.py -> build/lib.linux-x86_64-2.7/numpy<br>copying build/src.linux-x86_64-2.7/numpy/distutils/__config__.py -> build/lib.linux-x86_64-2.7/numpy/distutils<br>running build_clib<br>customize UnixCCompiler<br>customize UnixCCompiler using build_clib<br>building 'npymath' library<br>compiling C sources<br>C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC<br><br>creating build/temp.linux-x86_64-2.7<br>creating build/temp.linux-x86_64-2.7/build<br>creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7<br>creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy<br>creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core<br>creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src<br>creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/npymath<br>creating build/temp.linux-x86_64-2.7/numpy<br>creating build/temp.linux-x86_64-2.7/numpy/core<br>creating build/temp.linux-x86_64-2.7/numpy/core/src<br>creating build/temp.linux-x86_64-2.7/numpy/core/src/npymath<br>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'<br>gcc: numpy/core/src/npymath/halffloat.c<br>gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c<br>gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math.c<br>gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math_complex.c<br>ar: adding 4 object files to build/temp.linux-x86_64-2.7/libnpymath.a<br>building 'npysort' library<br>compiling C sources<br>C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC<br><br>creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/npysort<br>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'<br>gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/selection.c<br>gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/quicksort.c<br>gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/mergesort.c<br>gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/binsearch.c<br>gcc: build/src.linux-x86_64-2.7/numpy/core/src/npysort/heapsort.c<br>ar: adding 5 object files to build/temp.linux-x86_64-2.7/libnpysort.a<br>running build_ext<br>customize UnixCCompiler<br>customize UnixCCompiler using build_ext<br>running build_scripts<br>  adding 'build/scripts.linux-x86_64-2.7/f2py2.7' to scripts<br><br></div></div></div></div>