[yt-users] yt on verne

Matthew Turk matthewturk at gmail.com
Fri May 1 13:37:19 PDT 2009


Hi Stephen,

It should not be resolving those symbols at all; Jeff Oishi and I
worked through this exact issue yesterday, and our solution was to add
the line:

linker_ext = /path/to/gfortran -g -Wall -shared

inside the [lapack_lite] section.  Be sure to wipe out the build and
dist directories inside the numpy directory.

-Matt

On Fri, May 1, 2009 at 12:41 PM, Stephen Skory <stephenskory at yahoo.com> wrote:
>
> Hi Matt,
>
> I now have these lines in site.cfg for numpy:
>
> [DEFAULT]
> library_dirs = /usr/lib64
> include_dirs = /nics/c/home/yt-verne/include/python2.6, numpy/core/include, numpy/core/src
>
> and it is no longer complaining about the libraries, however it appears that it isn't including the Python header files correctly? I've compared this part of the install log to an install on Ranger, and these lines seem to be functionally equivalent in terms of the libs and includes listed.
>
> Thanks!
>
> --------------
>
> building 'numpy.linalg.lapack_lite' extension
> compiling C sources
> C compiler: cc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
>
> creating build/temp.linux-x86_64-2.6/numpy/linalg
> compile options: '-DNO_ATLAS_INFO=1 -Inumpy/core/include -Ibuild/src.linux-x86_64-2.6/numpy/core/inclu
> de/numpy -Inumpy/core/src -Inumpy/core/include -I/nics/c/home/sskory/yt-verne/include/python2.6 -c'
> cc: numpy/linalg/python_xerbla.c
> cc: numpy/linalg/lapack_litemodule.c
> /usr/bin/gfortran -Wall -L/nics/c/home/sskory/yt-verne/lib/ -L/nics/c/home/sskory/yt-verne/lib64/ buil
> d/temp.linux-x86_64-2.6/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.6/numpy/linalg/pyth
> on_xerbla.o -L/usr/lib64 -llapack -lblas -lgfortran -o build/lib.linux-x86_64-2.6/numpy/linalg/lapack_
> lite.so
> build/temp.linux-x86_64-2.6/numpy/linalg/lapack_litemodule.o: In function `initlapack_lite':
> /nics/c/home/sskory/yt-verne/src/numpy-1.2.1/numpy/linalg/lapack_litemodule.c:827: undefined reference
>  to `Py_InitModule4_64'
> build/temp.linux-x86_64-2.6/numpy/linalg/lapack_litemodule.o: In function `_import_array':
> /nics/c/home/sskory/yt-verne/src/numpy-1.2.1/build/src.linux-x86_64-2.6/numpy/core/include/numpy/__mul
> tiarray_api.h:960: undefined reference to `PyImport_ImportModule'
> /nics/c/home/sskory/yt-verne/src/numpy-1.2.1/build/src.linux-x86_64-2.6/numpy/core/include/numpy/__mul
> tiarray_api.h:963: undefined reference to `PyObject_GetAttrString'
> /nics/c/home/sskory/yt-verne/src/numpy-1.2.1/build/src.linux-x86_64-2.6/numpy/core/include/numpy/__mul
> tiarray_api.h:965: undefined reference to `PyCObject_Type'
> /nics/c/home/sskory/yt-verne/src/numpy-1.2.1/build/src.linux-x86_64-2.6/numpy/core/include/numpy/__mul
> tiarray_api.h:973: undefined reference to `PyExc_RuntimeError'
> /nics/c/home/sskory/yt-verne/src/numpy-1.2.1/build/src.linux-x86_64-2.6/numpy/core/include/numpy/__mul
> tiarray_api.h:973: undefined reference to `PyErr_Format'
> build/temp.linux-x86_64-2.6/numpy/linalg/lapack_litemodule.o: In function `initlapack_lite':
> /nics/c/home/sskory/yt-verne/src/numpy-1.2.1/numpy/linalg/lapack_litemodule.c:830: undefined reference
>  to `PyErr_Print'
> (and so on...)
>
>  _______________________________________________________
> sskory at physics.ucsd.edu           o__  Stephen Skory
> http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
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