Hi,
The iotbx.pdb Python module is very useful and fast.
I am trying to use the C++ library and have gotten an example program to
run correctly when compiling in the object files in cctbx_build/iotbx/pdb:
atom_selection.o construct_hierarchy.o hierarchy.o hierarchy_atoms.o
hierarchy_select.o hierarchy_write.o hybrid_36_c.o hybrid_36_cpp.o input.o
input_write.o overall_counts.o utils.o write_utils.o
However, I would like to have a shared library that wraps all of the
objects into shared library (or dynamic on Mac OSX). I have created such a
library on my Mac using the command:
g++ -dynamiclib -fPIC -O3 --fast-math -o libiotbx_pdb.dylib
atom_selection.o construct_hierarchy.o hierarchy.o hierarchy_atoms.o
hierarchy_select.o hierarchy_write.o hybrid_36_c.o hybrid_36_cpp.o input.o
input_write.o overall_counts.o utils.o write_utils.o -install_name
/Users/jvanvoorst/Python_VEs/Lore30/lib/libiotbx_pdb.dylib
-Wl,-single_module
When I link my program to that library I always get a segment fault in the
deconstructor of the last instance of iotbx::pdb::hierarchy::root::~root().
gdb traceback is:
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x000000000000001a
0x00000001000030e6 in std::vector<iotbx::pdb::hierarchy::model,
std::allocator<iotbx::pdb::hierarchy::model> >::~vector ()
(gdb) where
#0 0x00000001000030e6 in std::vector<iotbx::pdb::hierarchy::model,
std::allocator<iotbx::pdb::hierarchy::model> >::~vector ()
#1 0x00000001000035fe in iotbx::pdb::hierarchy::root_data::~root_data ()
#2 0x0000000100003662 in
boost::checked_delete<iotbx::pdb::hierarchy::root_data> ()
#3 0x0000000100003687 in
boost::detail::sp_counted_impl_p<iotbx::pdb::hierarchy::root_data>::dispose
()
#4 0x0000000100001342 in boost::detail::sp_counted_base::release ()
#5 0x0000000100001372 in boost::detail::shared_count::~shared_count ()
#6 0x000000010000149b in
boost::shared_ptr<iotbx::pdb::hierarchy::root_data>::~shared_ptr ()
#7 0x00000001000014e9 in iotbx::pdb::hierarchy::root::~root ()
#8 0x00000001000053c9 in FooBar::~FooBar ()
#9 0x0000000100001150 in main ()
I can send you my program but I have pruned FooBar down to only two class
variables (one for a root object and the other for the input). All the
class does is read the input from a file and construct the hierarchy. The
seg fault only happens on the cleanup of the last object. That is if I vary
the number of FooBar instances, the program faults on the cleanup of the
last root object.
I tried numerous combinations of flags to the linker (g++), but (as
expected) the result is always the same. I am using "g++ -I{include for
sources} -I{include for build} test.C libiotbx_pdb.dylib" to compile the
program.
I am likely overlooking something. Also, I am not proficient in debugging
dynamic libraries via gdb. Therefore, any tips or pointers would be much
appreciated.
If there is an edit I can make to my Sconscript to automagically generate
the shared library I could use that as well. The libtbx/configure.py output
looks right (Static libraries: False). However, when running scons using -Q
the source files are getting compiled with -fPIC (good), but the libraries
are getting created using ar (implies static libraries) -- unless I am
looking in the wrong directory for the shared libraries (cctbx_build/lib).
Thanks,
Jeff Van Voorst
