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: cm...@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: cm...@virginia.edu
Web: http://muralab.org
Tel: 434.924.7824
Fax: 434.924.3710
-------------------------------------------------------
------------------------------------------------------------------------
_______________________________________________
cctbxbb mailing list
cctb...@phenix-online.org
http://www.phenix-online.org/mailman/listinfo/cctbxbb
------------------------------------------------------------------------------
Enter the BlackBerry Developer Challenge
This is your chance to win up to $100,000 in prizes! For a limited time,
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize
details at: http://p.sf.net/sfu/Challenge
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
