I get a segmentation fault when I issue:
from rosetta import *
in function PyInt_FromLong. But I am not sure what is wrong, since PyRosetta compilation worked fine.
The binary distribution PyRosetta.MacOSX.SnowLeopard-r48781.64Bit works on my computer with the system python 2.6.1, but I would like to compile a version for the EPDPython 2.7, which I normally use. Also, I thought of this as training for a compilation on an older Centos system, for which there is no binary distribution.
-Mac OS X 10.6.8 32bit
-Python 2.7.1 |EPD 7.0-2 (64-bit)|
-PyRosetta from src/python/bindings of rosetta3.4
I installed gccxml and boost 1.49 using homebrew. Then I installed pygccxml, pyplusplus using pip.
Then I ran:
./BuildBindings.py -I/Library/Frameworks/EPD64.framework/Versions/Current/include/python2.7 -L/Library/Frameworks/EPD64.framework/Versions/Current/lib --boost_lib boost_python-mt
This didn't compile, because of missing files. I updated two extensions from .inc to .ipp in
Next, there was another problem in directory src/python/bindings/rosetta/core/scoring/ when building __scoring_all_at_once_.so
"core::scoring::compute_jump_rmsd(core::pose::Pose const&, core::pose::Pose const&, boost::unordered::unordered_map, std::equal_to, std::allocator > >*)", referenced from:
__scoring_all_at_once__partial_1() in __scoring_all_at_once_.1.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
The problem is that "...boost::unordered::unordered_map..." is not defined but libmini contains boost::unordered_map
After looking around online, I guessed that boost 1.49 changed behavior of unordered_map.
I rolled boost back to 1.46.1 and then PyRosetta compiled fine.
However, when I issue:
from rosetta import *
I get a segmentation fault.
The backtrace from gdb tells me the seg fault is at:
#0 0x00000001006d7932 in PyInt_FromLong ()
#1 0x00000001093cf64b in boost::python::detail::keywords<1ul>::operator= ()
#2 0x00000001093a4047 in init_module___scoring_all_at_once_ ()
#3 0x0000000106ff5431 in boost::python::handle_exception_impl ()
#4 0x0000000106ff6596 in boost::python::handle_exception ()
#5 0x0000000106ff621b in boost::python::detail::init_module ()
#6 0x00000001000e6792 in _PyImport_LoadDynamicModule ()
Do you have any idea what is wrong or any advice what to change?