Re: [cctbxbb] draw_symops <-- cctbx(/phenix) broken due to boost segfault handling ?

I tried the recommendation of setting the BOOST_ADAPTBX* env vars, but

Hi Cameron, There are quite a few 3rd party extensions causing floating-point exceptions (e.g. we have to turn off the floating-point traps when using wxPython). this doesn't remedy the problem. Did you get the same traceback? -- That would mean the env vars aren't defined in the right context. With the env vars defined, there shouldn't be any tracebacks anymore, just plain "Abort". You snipped out the most interesting part of the traceback. The first part is always the Python startup, and anything after boost::python::handle_exception is just the code producing the tracebacks. The important clues are somewhere in the middle. Ralf ________________________________ From: Cameron Mura To: [email protected]; Pymol-users Sent: Sunday, July 5, 2009 12:33:53 PM Subject: [cctbxbb] draw_symops <-- cctbx(/phenix) broken due to boost segfault handling ? Hi all, Apologies for the message to both mailing lists, but perhaps someone on either cctbxbb or pymol-users has had some recent experience with this... The subject line more-or-less says it all: I'm wondering if anyone has recently used Rob Campbell's draw_symops (or draw_symops_cctbx) Python modules with a relatively recent (within past year) version of the cctbx (particularly the Boost C++ parts) ? I succeeded in doing this a few years ago to generate images such as the ones near the top of http://muralab.org/~cmura/PyMOL/Sandbox/, but I can't get it to work on my present system (64-bit Fedora 10; Python 2.5.2 with Python 2.6 coexisting). Below is what happens when I... 1) Initiate a new PyMOL session (using a PyMOL v1.1 that I built in-place from source, so should be compatible with local python, system libs, etc) 2) load PDB files (tried with a few diff't files; verified that they contain proper CRYST specifications) 3) do the usual 'run draw_symops_cctbx.py' 4) call draw_symops() -- either implicitly, or by explicit specification of the u.c. params (i.e., using something like "draw_symops_param((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5,0.1)") ....which crashes the pymol session and yields the following trace: PyMOL>draw_symops_param((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5,0.1)

...

libc backtrace (48 frames, most recent call last): /usr/bin/python [0x400649] /lib64/libc.so.6(__libc_start_main+0xe6) [0x344081e576] /usr/lib64/libpython2.5.so.1.0(Py_Main+0xb11) [0x34584e7ef1] <snip> ... ... </snip> /usr/lib64/libpython2.5.so.1.0(PyObject_Call+0x13) [0x345843d493] /root/cctbx/working/v4/cctbx_build/lib/libboost_python.so [0x7ff19691db16]

/root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x9f) [0x7ff19692a2ef]

...

/root/cctbx/working/v4/cctbx_build/lib/libboost_python.so [0x7ff196920b08]

/root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0x125) [0x7ff196920635]

...

/root/cctbx/working/v4/cctbx_build/lib/cctbx_sgtbx_ext.so(boost::python::detail::caller_arity<2u>::impl >::operator()(_object*, _object*)+0x12a) [0x7ff18f820a3a]

...

/root/cctbx/working/v4/cctbx_build/lib/cctbx_sgtbx_ext.so [0x7ff18f8034cc]

/root/cctbx/working/v4/cctbx_build/lib/libboost_python.so(boost::python::throw_error_already_set()+0xe) [0x7ff196929dde]

...

/usr/lib64/libstdc++.so.6(__cxa_allocate_exception+0x2f) [0x3444cc2cdf] /lib64/libc.so.6 [0x3440832f90] Segmentation fault (libc call stack 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. PyMOL: abrupt program termination.

I tried the recommendation of setting the BOOST_ADAPTBX* env vars, but this doesn't remedy the problem. Also, I tried accomplishing this with many combinations of workflows: 1) old cctbx (e.g., 2005_04_29_1615), latest stable release of cctbx (2009_02_15_2320), bleeding-edge cctbx (2009_07_04_0143) 2) pre-built cctbx binaries versus building myself from src (for each of the above), insuring, again, optimal match between local system libs... 3) cctbx alone, cctbx in the context of Phenix, cctbx +/- its own bundled Python (2.5 and 2.6) Also, I tried this with different combinations of Rob's scripts -- e.g., the 'symop_axes.dat'-dependent "draw_symops.py", versus the 'all_axes_new.py'-dependent "draw_symops_cctbx.py". Interestingly, I found that get_all_axes() from 'all_axes_new.py' works fine for different PDB files. Investigating the above draw_symops stacktrace led me to this post from Ralf Grosse-Kunstleve to python-dev: http://mail.python.org/pipermail/python-dev/2008-September/082639.html It looks like exactly the same problem that's causing the pymol/draw_symops scripts to choke. Also, I can verify that issuing commands such as in Ralf's post (boost_adaptbx.segmentation_fault, boost_adaptbx.divide_by_zero) result in the same segfaults and errors as in his post, so... I believe this is the crux of it. Before delving into Boost codebase, cctbx's exception-handling in C++/Python Boost, etc., I'm wondering if anyone else has seen anything like this...? or has advice on how best to proceed? Any tips or suggestions would be most greatly appreciated. Thanks, Cam -- ------------------------------------------------------- Cameron Mura Assistant Professor University of Virginia Department of Chemistry McCormick Road, Box 400319 Charlottesville, VA 22904-4319 Email: [email protected] Web: http://muralab.org Tel: 434.924.7824 Fax: 434.924.3710 -------------------------------------------------------