[cctbxbb] Scipy / cctbx core dump

[Nicholas Sauter]

Graeme,

Try reversing the import order please.  I've always had to import linalg
first before any scitbx modules, to avoid the core dump.  Best practice in
the long run is to remove the linalg dependency.

Nick


On Tue, Oct 15, 2013 at 8:25 AM, <Graeme.Winter at diamond.ac.uk> wrote:

>  Hi Folks,****
>
> ** **
>
> Just trying to use something here which depends on scipy but it seems
> scipy is not playing nice with flex:****
>
> ** **
>
> from scitbx.array_family import flex****
>
> import scipy.linalg****
>
> ** **
>
> A tiny and inoffensive script however…****
>
> ** **
>
> cctbx.python boom.py****
>
> show_stack(1):
> /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/scipy/linalg/blas.py(113)
> <module>****
>
> show_stack(2):
> /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/scipy/linalg/misc.py(5)
> <module>****
>
> show_stack(3):
> /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/scipy/linalg/__init__.py(147)
> <module>****
>
> show_stack(4): /scratch/gw56/2013/OCT/15/multi-lattice/boom/boom.py(2)
> <module>****
>
> libc backtrace (2 frames, most recent call last):****
>
>
> /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/numpy/core/multiarray.so(PyArray_API+0)
> [0x7fb2064c9940]****
>
>   /lib64/libc.so.6() [0x37b3232920]****
>
> Segmentation fault (Python and libc call stacks above)****
>
>                 This crash may be due to a problem in any imported****
>
>                 Python module, including modules which are not part****
>
>                 of the cctbx project. To disable the traps leading****
>
>                 to this message, define these environment variables****
>
>                 (e.g. assign the value 1):****
>
>                     BOOST_ADAPTBX_FPE_DEFAULT****
>
>                     BOOST_ADAPTBX_SIGNALS_DEFAULT****
>
>                 This will NOT solve the problem, just mask it, but****
>
>                 may allow you to proceed in case it is not critical.****
>
> ** **
>
> I did a fresh nightly build install just to be sure :o(****
>
> ** **
>
> if I export those naughty env vars I get a core dump:****
>
> ** **
>
> cctbx.python boom.py****
>
> Segmentation fault (core dumped)****
>
> ** **
>
> RHEL6.4  / scipy 0.12.0 and 0.12.1****
>
> ** **
>
> any ideas?****
>
> ** **
>
> Thanks, Graeme****
>
> ** **
>
> Dr. Graeme Winter****
>
> Senior Software Scientist****
>
> Diamond Light Source****
>
>  ****
>
> +44 1235 778091 (work)****
>
> +44 7786 662784 (work mobile)****
>
>  ****
>
> ** **
>
>
>
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-- 
Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Physical Biosciences Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 64R0121
Berkeley, CA 94720-8118
(510) 486-5713
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