[cctbxbb] draw_symops <-- cctbx(/phenix) broken due to boost segfault handling ?
Cameron Mura
cmura at virginia.edu
Sun Jul 5 12:33:53 PDT 2009
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<cctbx::sgtbx::rt_mx
> (*)(cctbx::sgtbx::space_group const&, unsigned long),
> boost::python::default_call_policies,
> boost::mpl::vector3<cctbx::sgtbx::rt_mx, cctbx::sgtbx::space_group
> const&, unsigned long> >::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: cmura at virginia.edu
Web: http://muralab.org
Tel: 434.924.7824
Fax: 434.924.3710
-------------------------------------------------------
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