[Paraview-developers] error building numpy in superbuild

[Joshua Murphy]

Hello,

I am trying to build the superbuild on Linux, and NUMPY is erroring out with the following:

compile options: '-DNO_ATLAS_INFO=1 -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/include -I/home/jomu9721/Developer/ParaView/build/install/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'
gcc: numpy/linalg/lapack_litemodule.c
gcc: numpy/linalg/python_xerbla.c
/usr/bin/gfortran -Wall -L/home/jomu9721/Developer/ParaView/build/install/lib build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/home/jomu9721/Developer/ParaView/build/install/lib -L/home/jomu9721/Developer/ParaView/build/install/lib -Lbuild/temp.linux-x86_64-2.7 -llapack -lblas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 0 has invalid symbol index 10
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 1 has invalid symbol index 11
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 2 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 3 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 4 has invalid symbol index 10
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 5 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 6 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 7 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 8 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 9 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 10 has invalid symbol index 11
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 11 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 12 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 13 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 14 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 15 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 16 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 17 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 18 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 19 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 20 has invalid symbol index 19
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -L/home/jomu9721/Developer/ParaView/build/install/lib build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/home/jomu9721/Developer/ParaView/build/install/lib -L/home/jomu9721/Developer/ParaView/build/install/lib -Lbuild/temp.linux-x86_64-2.7 -llapack -lblas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 0 has invalid symbol index 10
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 1 has invalid symbol index 11
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 2 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 3 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 4 has invalid symbol index 10
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 5 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 6 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 7 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 8 has invalid symbol
index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 9 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 10 has invalid symbol index 11
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 11 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 12 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 13 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 14 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 15 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 16 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 17 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 18 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 19 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 20 has invalid symbol index 19
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
CMake Error at /home/jomu9721/Developer/ParaView/build/pv-numpy-build.cmake:26 (message):
  Failed!!!


make[2]: *** [numpy/src/numpy-stamp/numpy-build] Error 1
make[1]: *** [CMakeFiles/numpy.dir/all] Error 2
make: *** [all] Error 2
jomu9721 at ubuntu:~/Developer/ParaView/build$ ^C


I know there has been some chat about failures on the mailing list, but cannot seem to find the answer on how to fix this… it occurs on every configuration of linux I can get my hands on…

Coincidentally, Numpy will build/install use fine on my system if installing I it to my system python setup…

If someone can point me to the answer, I would be grateful! I am supposed to get a binary version of plugin to my boss today, if possible…

Thanks,

Josh

[cid:36C40BBD-89F3-442B-B973-AA2CD67CA0B2]
Joshua J. Murphy
Computer Scientist
Laboratory for Atmospheric and Space Physics
University of Colorado, Boulder


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