hainm/write_data_segmentation_fault.py

hainm · 2016-06-11T07:40:07Z

trace

Program received signal SIGSEGV, Segmentation fault.
0x00002aaaaeddeb2a in DataIO_CCP4::WriteSet3D(__gnu_cxx::__normal_iterator<DataSet* const*, std::vector<DataSet*, std::allocator<DataSet*> > > const&, CpptrajFile&) ()
   from /u1/haichit/pytraj_git/pytraj/cpptraj/lib/libcpptraj.so
(gdb) bt
#0  0x00002aaaaeddeb2a in DataIO_CCP4::WriteSet3D(__gnu_cxx::__normal_iterator<DataSet* const*, std::vector<DataSet*, std::allocator<DataSet*> > > const&, CpptrajFile&) ()
   from /u1/haichit/pytraj_git/pytraj/cpptraj/lib/libcpptraj.so
#1  0x00002aaaaeddf541 in DataIO_CCP4::WriteData(FileName const&, DataSetList const&) () from /u1/haichit/pytraj_git/pytraj/cpptraj/lib/libcpptraj.so
#2  0x00002aaaaedd8fe3 in DataFile::WriteDataOut() () from /u1/haichit/pytraj_git/pytraj/cpptraj/lib/libcpptraj.so
#3  0x00002aaaaee33ba8 in Exec_WriteDataFile::Execute(CpptrajState&, ArgList&) () from /u1/haichit/pytraj_git/pytraj/cpptraj/lib/libcpptraj.so
#4  0x00002aaaaeec0137 in Command::Dispatch(CpptrajState&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) () from /u1/haichit/pytraj_git/pytraj/cpptraj/lib/libcpptraj.so
#5  0x00002aaabdb1127f in __pyx_pf_6pytraj_4core_6c_core_7Command_12dispatch (__pyx_v_cls=0x2aaabdd56f40, __pyx_v_state=0x2aaaae9adbc8, __pyx_v_line=0x2aaabf7ce300) at pytraj/core/c_core.cpp:7999
#6  0x00002aaabdb10eb0 in __pyx_pw_6pytraj_4core_6c_core_7Command_13dispatch (__pyx_v_cls=0x2aaabdd56f40, __pyx_args=0x2aaaae9b26c8, __pyx_kwds=0x0) at pytraj/core/c_core.cpp:7950
#7  0x00002aaaaab6d1e1 in PyCFunction_Call (func=0x2aaabf7b6948, args=0x2aaaae9b26c8, kwds=<value optimized out>) at Objects/methodobject.c:98
#8  0x00002aaaaabf4482 in call_function (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:4655
#9  PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:3185
#10 0x00002aaaaabf5349 in _PyEval_EvalCodeWithName (_co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0,
    defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at Python/ceval.c:3966
#11 0x00002aaaaabf54d8 in PyEval_EvalCodeEx (_co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=<value optimized out>,
    kws=<value optimized out>, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0) at Python/ceval.c:3987
#12 0x00002aaaaabf551b in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>) at Python/ceval.c:777
#13 0x00002aaaaac1a750 in run_mod (fp=0x6dbf50, filename_str=<value optimized out>, start=<value optimized out>, globals=0x2aaaae648208, locals=0x2aaaae648208, closeit=<value optimized out>,
    flags=0x7fffffffe300) at Python/pythonrun.c:970
#14 PyRun_FileExFlags (fp=0x6dbf50, filename_str=<value optimized out>, start=<value optimized out>, globals=0x2aaaae648208, locals=0x2aaaae648208, closeit=<value optimized out>, flags=0x7fffffffe300)
    at Python/pythonrun.c:923
#15 0x00002aaaaac1bd23 in PyRun_SimpleFileExFlags (fp=0x6dbf50, filename=<value optimized out>, closeit=1, flags=0x7fffffffe300) at Python/pythonrun.c:396
#16 0x00002aaaaac36e97 in run_file (argc=<value optimized out>, argv=<value optimized out>) at Modules/main.c:318
#17 Py_Main (argc=<value optimized out>, argv=<value optimized out>) at Modules/main.c:769
#18 0x0000000000400add in main (argc=2, argv=0x7fffffffe478) at ./Programs/python.c:69

hainm · 2016-06-11T07:42:18Z

I do see the output test.ccp4 but it's empty.

	import pytraj as pt
	from pytraj.core.c_core import Command
	from pytraj import CpptrajState

	# data is DatasetGridFloat
	data = pt.io.read_data('fav8.guv.O.1.ccp4',
	options='name MyCcp4')[0]

	state = CpptrajState()

	# add DatasetGridFloat to CpptrajState's DataSetList
	state.data.add(dtype=data.dtype, name=data.key)

	# add data to DataSet
	state.data[0].data = data.values
	print(state)

	data = state.data[0]
	print(data.key, data.dtype, data.values[0])

	# create cpptraj command
	filename = 'test.ccp4'
	options = ''
	line = ' '.join(('writedata', filename, data.key, options))
	# line is: writedata test.ccp4 MyCcp4

	# dispatch
	pt._verbose()
	with Command() as cm:
	cm.dispatch(state, line)

hainm/write_data_segmentation_fault.py

hainm commented Jun 11, 2016

hainm commented Jun 11, 2016