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