id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2937	Segmentation fault in Point_List::bounding_box() for large models (?)	Tristan Croll	Tom Goddard	"I've been seeing a quite intermittent segmentation fault lately when associating a model with a cryo-EM map in Clipper, but every time I attempted to capture it with `gdb` it would stubbornly refuse to manifest (until now). I suspect it's more common for larger models, but I've seen it happen once during ISOLDE's flexible-fitting tutorial with 6mhz (910 residues). Anyway, I was finally able to reproduce it (at least, I ''assume'' it's the same crash) with:

{{{
isolde start
open 6q3g
open 4459 from emdb
clipper assoc #2 to #1
}}}

Note that this is a staggeringly large model/map (1 billion voxels) so be patient.

Stack trace:

{{{
Program received signal SIGSEGV, Segmentation fault.
0x00007fffec58aaca in Point_List::bounding_box() const [clone .part.9] () from /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/geometry/_geometry.so
Missing separate debuginfos, use: debuginfo-install ucsf-chimerax-0.92-1.el7.x86_64
(gdb) bt
#0  0x00007fffec58aaca in Point_List::bounding_box() const [clone .part.9] () at /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/geometry/_geometry.so
#1  0x00007fffec58c9c6 in find_close_points_boxes(Point_List const&, Point_List const&, float, Index_Set&, Index_Set&, Nearest_Points*) ()
    at /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/geometry/_geometry.so
#2  0x00007fffec58d3af in find_close_points_boxes(Point_List const&, Point_List const&, float, Index_Set&, Index_Set&, Nearest_Points*) ()
    at /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/geometry/_geometry.so
#3  0x00007fffec58fd98 in find_close_points(Close_Points_Method, float const*, int, float const*, int, float, float*, std::vector<int, std::allocator<int> >*, std::vector<int, std::allocator<int> >*, std::vector<int, std::allocator<int> >*) () at /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/geometry/_geometry.so
#4  0x00007fffec592cd7 in find_close_points () at /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/geometry/_geometry.so
#5  0x00007ffff7906223 in _PyMethodDef_RawFastCallKeywords (method=0x7fffec5aa960 <Geometry_Cpp::geometry_cpp_methods+224>, self=<optimized out>, args=0x7ffe640c4318, nargs=3, kwnames=<optimized out>)
    at Objects/call.c:694
#6  0x00007ffff79062a5 in _PyCFunction_FastCallKeywords (func=0x7fffe56dfc30, args=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:734
#7  0x00007ffff78df9ca in _PyEval_EvalFrameDefault (kwnames=0x0, oparg=3, pp_stack=<synthetic pointer>) at Python/ceval.c:4568
#8  0x00007ffff78df9ca in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3124
#9  0x00007ffff79f1f7e in _PyEval_EvalCodeWithName (_co=0x7fff94b4ced0, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=1, kwnames=0x7fff94b41468, kwargs=0x7ffe6b746bf0, kwcount=1, kwstep=1, defs=0x7fff94b456a8, defcount=3, kwdefs=0x0, closure=0x0, name=0x7fff94b41470, qualname=0x7fff94b3fb20) at Python/ceval.c:3930
#10 0x00007ffff7905d05 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:433
#11 0x00007ffff78dfda1 in _PyEval_EvalFrameDefault (kwnames=0x7fff94b41450, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616
#12 0x00007ffff78dfda1 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3139
#13 0x00007ffff79f1f7e in _PyEval_EvalCodeWithName (_co=_co@entry=0x7fff94b4cc00, globals=globals@entry=0x7fff3b491f50, locals=locals@entry=0x0, args=args@entry=0x7fffffff93b0, argcount=argcount@entry=3, kwnames=kwnames@entry=0x0, kwargs=0x0, kwcount=0, kwstep=2, defs=0x7fff94b45658, defcount=3, kwdefs=0x0, closure=0x7fffac127610, name=0x7ffff7f944f0, qualname=0x7fff94b3fa30) at Python/ceval.c:3930
#14 0x00007ffff7905aa5 in _PyFunction_FastCallDict (func=0x7fffac12ccb0, args=0x7fffffff93b0, nargs=3, kwargs=0x0) at Objects/call.c:376
#15 0x00007ffff7906e22 in _PyObject_Call_Prepend (callable=callable@entry=0x7fffac12ccb0, obj=obj@entry=0x7ffd40ef0050, args=args@entry=0x7ffe5d5cd2d0, kwargs=kwargs@entry=0x0) at Objects/call.c:908
#16 0x00007ffff796acd5 in slot_tp_init (self=0x7ffd40ef0050, args=0x7ffe5d5cd2d0, kwds=0x0) at Objects/typeobject.c:6636
...
}}}"	defect	closed	major		Core		fixed						all	ChimeraX