Hi Ralf,
Thanks for your note...
> I tried the recommendation of setting the BOOST_ADAPTBX* env vars,
but 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".
Right -- This is what happened. I verified that the pymol context was
aware of these env vars:
PyMOL>import os
PyMOL>print os.environ.get('BOOST_ADAPTBX_FPE_DEFAULT')
1
PyMOL>print os.environ.get('BOOST_ADAPTBX_SIGNALS_DEFAULT')
1
So... with the vars set, no backtrace... just a simple crash:
<snip>....PyMOL session....</snip>
......
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
......
Symmetry: Found 12 symmetry operators.
CmdLoad: "1avv.pdb" loaded as "1avv".
PyMOL>run draw_symops_cctbx.py
Finished importing for draw_symops_cctbx.py
PyMOL>draw_symops 1avv
/usr/bin/pymol: line 4: 4756 Segmentation fault cctbx.python
/usr/lib64/python2.5/site-packages/pymol/__init__.py $*
$]
You snipped out the most interesting part of the traceback. The first
part is always the Python startup
right, the red part below(?) [up to frame 1/19]
and anything after boost::python::handle_exception is just the code
producing the tracebacks.
right, blue part below(?) [beyond libc's frame 13/19]
The important clues are somewhere in the middle.
Following is what happens in a simpler test run, outside of pymol, just
divide_by_zero.py from the command line (result is essentially identical
to your Sep-08 post to python-dev):
$] cctbx.python
/root/software/cctbx/2009_02_15_2320/working/cctbx_sources/boost_adaptbx/command_line/divide_by_zero.py
Now dividing by zero (in C++) ...
show_stack(1):
/root/software/cctbx/2009_02_15_2320/working/cctbx_sources/boost_adaptbx/command_line/divide_by_zero.py(11)
run
show_stack(2):
/root/software/cctbx/2009_02_15_2320/working/cctbx_sources/boost_adaptbx/command_line/divide_by_zero.py(26)
<module>
libc backtrace (19 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]
/usr/lib64/libpython2.5.so.1.0(PyRun_SimpleFileExFlags+0x1cd)
[0x34584ddfed]
/usr/lib64/libpython2.5.so.1.0(PyRun_FileExFlags+0x96) [0x34584dca06]
/usr/lib64/libpython2.5.so.1.0 [0x34584dc931]
/usr/lib64/libpython2.5.so.1.0(PyEval_EvalCode+0x32) [0x34584c0aa2]
/usr/lib64/libpython2.5.so.1.0(PyEval_EvalCodeEx+0x715) [0x34584c0865]
/usr/lib64/libpython2.5.so.1.0(PyEval_EvalFrameEx+0x658d) [0x34584bfe6d]
/usr/lib64/libpython2.5.so.1.0(PyEval_EvalFrameEx+0x36f3) [0x34584bcfd3]
/usr/lib64/libpython2.5.so.1.0(PyObject_Call+0x13) [0x345843d493]
/root/software/cctbx/2009_02_15_2320/working/cctbx_build/lib/libboost_python.so
[0x7f20bb3ba3b2]
/root/software/cctbx/2009_02_15_2320/working/cctbx_build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x85)
[0x7f20bb3c6625]
/root/software/cctbx/2009_02_15_2320/working/cctbx_build/lib/libboost_python.so(boost::function0<void>::operator()()
const+0x34) [0x7f20bb3c6f94]
/root/software/cctbx/2009_02_15_2320/working/cctbx_build/lib/libboost_python.so
[0x7f20bb3bd398]
/root/software/cctbx/2009_02_15_2320/working/cctbx_build/lib/libboost_python.so(boost::python::objects::function::call(_object*,
_object*) const+0x125) [0x7f20bb3bcec5]
/root/software/cctbx/2009_02_15_2320/working/cctbx_build/lib/boost_python_meta_ext.so(boost::python::objects::caller_py_function_impl<boost::python::detail::caller<double
(*)(double const&, double const&),
boost::python::default_call_policies, boost::mpl::vector3<double,
double const&, double const&> > >::operator()(_object*,
_object*)+0xf3) [0x7f20bb5f5333]
/root/software/cctbx/2009_02_15_2320/working/cctbx_build/lib/boost_python_meta_ext.so
[0x7f20bb5f0a54]
/lib64/libc.so.6 [0x3440832f90]
Floating-point error (Python and libc call stacks 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.
$]
I'm still at somewhat of a loss (mainly due to ignorance about
boost/python interactions), but will let you know if I solve it.
thanks,
cam
=== Ralf W. Grosse-Kunstleve wrote (on 07/05/2009 11:38 PM): ===
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).
> I tried the recommendation of setting the BOOST_ADAPTBX* env vars,
but 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 <cm...@virginia.edu>
*To:* cctb...@phenix-online.org; Pymol-users
<pymol-users@lists.sourceforge.net>
*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<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
------------------------------------------------------------------------------
_______________________________________________
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
