[Paraview-developers] error building numpy in superbuild

[Joshua Murphy]

I don't know if this is the correct solution, but according to this python mailing list, the error occurs when setting the $CFLAGS and $LDFLAGS (http://thread.gmane.org/gmane.comp.python.scientific.user/10391), as it overwrites required flags.

This is, of course, done in the pv-numpy-build.cmake file.

I removed the setting of the $CFLAGS and $LDFLAGS (and $CXX_Flags, etc) and it builds just fine.

My question is, will this change what it is linking against?  It still seems to be linking against the super build libraries, but I am not familiar enough with the inner workings of the build system to know for sure…

Thanks,
Josh

From: Joshua Murphy <Joshua.Murphy at lasp.colorado.edu<mailto:Joshua.Murphy at lasp.colorado.edu>>
Date: Thursday, July 11, 2013 10:13 AM
To: "paraview-developers at paraview.org<mailto:paraview-developers at paraview.org>" <paraview-developers at paraview.org<mailto:paraview-developers at paraview.org>>
Subject: [Paraview-developers] error building numpy in superbuild

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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