[cctbxbb] Using iotbx.pdb as C++ only dynamic (shared) library

[Ralf Grosse-Kunstleve]

Hi Jeff,

Did you copy all the -DXXX that you see on the compilation line for the
iotbx/pb files? In particular, the -DBOOST_DISABLE_THREADS is probably
critical, but highly I recommend you copy all -DXXX. Otherwise you'll most
likely violate the C++ One Definition Rule (ODR) which could explain your
crash.

Did you try to link against lib/libiotbx_pdb.a instead of the .o files? (On
the Mac I couldn't figure out how to link dynamically loaded Python
extensions against shared libraries, but it is probably 7+ years ago that I
tried the last time.)

Ralf

On Thu, Dec 8, 2011 at 10:36 AM, <vanv0059 at umn.edu> wrote:

> 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
>
>
>
>
>
>
>
>
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