Hi all,

In case anyone else runs into it, just wanted to let you know that I've solved the (possibly Fedora 10-specific) segfault-induced crashing described in the email below.  In a nutshell, it required editing the module in question (in this case, line 153 of "all_axes_new.py") so that it loops over the space group matrices of an sgtbx-returned object ('mysg') by calling all_ops() to explicitly render the object iterable; i.e., loop over mysg.all_ops() rather than plain mysg.  In this case, change this:
  for smx in space_group_info.group():
to this:
  for smx in space_group_info.group().all_ops():

With best regards,
Cam
-- 
-------------------------------------------------------
 Cameron Mura
 Assistant Professor
 University of Virginia
 Department of Chemistry
 McCormick Road, Box 400319
 Charlottesville, VA 22904-4319
 Email: cmura@virginia.edu
 Web: http://muralab.org
 Tel: 434.924.7824
 Fax: 434.924.3710
-------------------------------------------------------

=== Cameron Mura wrote (on 07/05/2009 03:33 PM): ===
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@virginia.edu
 Web: http://muralab.org
 Tel: 434.924.7824
 Fax: 434.924.3710
-------------------------------------------------------
  

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