<div dir="ltr">Graeme,<div><br></div><div style>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.</div>
<div style><br></div><div style>Nick</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Oct 15, 2013 at 8:25 AM, <span dir="ltr"><<a href="mailto:Graeme.Winter@diamond.ac.uk" target="_blank">Graeme.Winter@diamond.ac.uk</a>></span> wrote:<br>
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<p class="MsoNormal">Hi Folks,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Just trying to use something here which depends on scipy but it seems scipy is not playing nice with flex:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">from scitbx.array_family import flex<u></u><u></u></p>
<p class="MsoNormal">import scipy.linalg<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">A tiny and inoffensive script however…<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">cctbx.python boom.py<u></u><u></u></p>
<p class="MsoNormal">show_stack(1): /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/scipy/linalg/blas.py(113) <module><u></u><u></u></p>
<p class="MsoNormal">show_stack(2): /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/scipy/linalg/misc.py(5) <module><u></u><u></u></p>
<p class="MsoNormal">show_stack(3): /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/scipy/linalg/__init__.py(147) <module><u></u><u></u></p>
<p class="MsoNormal">show_stack(4): /scratch/gw56/2013/OCT/15/multi-lattice/boom/boom.py(2) <module><u></u><u></u></p>
<p class="MsoNormal">libc backtrace (2 frames, most recent call last):<u></u><u></u></p>
<p class="MsoNormal"> /home/gw56/svn/cctbx_base_15oct13/cctbx_plus_build/base/lib/python2.7/site-packages/numpy/core/multiarray.so(PyArray_API+0) [0x7fb2064c9940]<u></u><u></u></p>
<p class="MsoNormal"> /lib64/libc.so.6() [0x37b3232920]<u></u><u></u></p>
<p class="MsoNormal">Segmentation fault (Python and libc call stacks above)<u></u><u></u></p>
<p class="MsoNormal"> This crash may be due to a problem in any imported<u></u><u></u></p>
<p class="MsoNormal"> Python module, including modules which are not part<u></u><u></u></p>
<p class="MsoNormal"> of the cctbx project. To disable the traps leading<u></u><u></u></p>
<p class="MsoNormal"> to this message, define these environment variables<u></u><u></u></p>
<p class="MsoNormal"> (e.g. assign the value 1):<u></u><u></u></p>
<p class="MsoNormal"> BOOST_ADAPTBX_FPE_DEFAULT<u></u><u></u></p>
<p class="MsoNormal"> BOOST_ADAPTBX_SIGNALS_DEFAULT<u></u><u></u></p>
<p class="MsoNormal"> This will NOT solve the problem, just mask it, but<u></u><u></u></p>
<p class="MsoNormal"> may allow you to proceed in case it is not critical.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I did a fresh nightly build install just to be sure :o(<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">if I export those naughty env vars I get a core dump:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">cctbx.python boom.py<u></u><u></u></p>
<p class="MsoNormal">Segmentation fault (core dumped)<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">RHEL6.4 / scipy 0.12.0 and 0.12.1<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">any ideas?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks, Graeme<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Dr. Graeme Winter</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Senior Software Scientist</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Diamond Light Source</span><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif""><a href="tel:%2B44%201235%20778091" value="+441235778091" target="_blank">+44 1235 778091</a> (work)</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif""><a href="tel:%2B44%207786%20662784" value="+447786662784" target="_blank">+44 7786 662784</a> (work mobile)</span><span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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