[cctbxbb] Scipy / cctbx core dump

[Graeme.Winter at diamond.ac.uk]

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)





-- 

This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.

Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. 

Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.

Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

 







-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20131015/14ac8a30/attachment.htm>