[chimera-dev] odd plugin crash
Mark Moll
mmoll at cs.rice.edu
Tue Dec 8 20:53:05 PST 2009
I have a plugin for Chimera that uses its own binary python module. The module is statically linked against the system python2.5 library on Snow Leopard. When I select my plugin, Chimera crashes. Attached is the crash report with Chimera 1.4 (it happens with build 28940 and probably other versions as well). However, if I open Chimera from the command line like so:
open /Users/mmoll/Downloads/Chimera.app
then there is no crash. The module is linked against the following libraries:
otool -L ~/labelhash/scripts/LabelHash/plat_darwin/_LabelHash.so
/Users/mmoll/labelhash/scripts/LabelHash/plat_darwin/_LabelHash.so:
/System/Library/Frameworks/Python.framework/Versions/2.5/Python (compatibility version 2.5.0, current version 2.5.1)
/usr//lib/libmpi_cxx.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr//lib/libmpi.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr//lib/libopen-rte.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr//lib/libopen-pal.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 242.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3)
/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.4.0)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4)
I can also use this module without problems if I import it in a script that uses /usr/bin/python2.5. Is there some environment variable that could explain the different behaviors?
--
Mark
Process: python2.5 [18782]
Path: /Users/mmoll/Downloads/Chimera.app/Contents/Resources/bin/python2.5
Identifier: edu.ucsf.cgl.chimera
Version: 1.4.0 (1.4.0.29530)
Code Type: X86 (Native)
Parent Process: launchd [99]
Date/Time: 2009-12-08 22:37:45.424 -0600
OS Version: Mac OS X 10.6.2 (10C540)
Report Version: 6
Interval Since Last Report: 134941 sec
Crashes Since Last Report: 5
Per-App Interval Since Last Report: 45 sec
Per-App Crashes Since Last Report: 2
Anonymous UUID: F46D9EAC-0238-44B8-87A2-7475B19DB90E
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Application Specific Information:
abort() called
Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 libSystem.B.dylib 0x90799732 __kill + 10
1 libSystem.B.dylib 0x90799724 kill$UNIX2003 + 32
2 libSystem.B.dylib 0x9082c98d raise + 26
3 libSystem.B.dylib 0x908429d9 __abort + 124
4 libSystem.B.dylib 0x90842a55 abort_report_np + 0
5 libstdc++.6.dylib 0x94c05fda __gnu_cxx::__verbose_terminate_handler() + 433
6 libstdc++.6.dylib 0x94c0417a __cxxabiv1::__terminate(void (*)()) + 10
7 libstdc++.6.dylib 0x94c041ba __cxxabiv1::__unexpected(void (*)()) + 0
8 libstdc++.6.dylib 0x94c042b8 __gxx_exception_cleanup(_Unwind_Reason_Code, _Unwind_Exception*) + 0
9 libstdc++.6.dylib 0x94bc0856 std::__throw_logic_error(char const*) + 158
10 libstdc++.6.dylib 0x94bebced char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag) + 57
11 libstdc++.6.dylib 0x94bec1fb std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) + 53
12 _LabelHash.so 0x1a00fae4 __static_initialization_and_destruction_0(int, int) + 180
13 dyld 0x8fe0ed6d ImageLoaderMachO::doModInitFunctions(ImageLoader::LinkContext const&) + 235
14 dyld 0x8fe0d31e ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int) + 246
15 dyld 0x8fe0d3d1 ImageLoader::runInitializers(ImageLoader::LinkContext const&) + 61
16 dyld 0x8fe0200b dyld::runInitializers(ImageLoader*) + 34
17 dyld 0x8fe0b299 dlopen + 558
18 libSystem.B.dylib 0x9073f048 dlopen + 66
19 org.python.python 0x000c6b7a _PyImport_GetDynLoadFunc + 283 (dynload_shlib.c:130)
20 org.python.python 0x000b4ed5 _PyImport_LoadDynamicModule + 107 (importdl.c:42)
21 org.python.python 0x000b2be5 load_module + 201 (import.c:1758)
22 org.python.python 0x000b30af import_submodule + 293 (import.c:2400)
23 org.python.python 0x000b32fd load_next + 195 (import.c:2220)
24 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001)
25 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072)
26 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49)
27 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861)
28 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442)
29 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067)
30 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
31 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500)
32 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675)
33 org.python.python 0x000b2428 load_source_module + 726 (import.c:959)
34 org.python.python 0x000b2f07 load_package + 427 (import.c:1015)
35 org.python.python 0x000b30af import_submodule + 293 (import.c:2400)
36 org.python.python 0x000b32fd load_next + 195 (import.c:2220)
37 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001)
38 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072)
39 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49)
40 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861)
41 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442)
42 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067)
43 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
44 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500)
45 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675)
46 org.python.python 0x000b2428 load_source_module + 726 (import.c:959)
47 org.python.python 0x000b2f07 load_package + 427 (import.c:1015)
48 org.python.python 0x000b30af import_submodule + 293 (import.c:2400)
49 org.python.python 0x000b32fd load_next + 195 (import.c:2220)
50 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001)
51 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072)
52 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49)
53 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861)
54 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442)
55 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067)
56 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
57 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500)
58 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675)
59 org.python.python 0x000b2428 load_source_module + 726 (import.c:959)
60 org.python.python 0x000b30af import_submodule + 293 (import.c:2400)
61 org.python.python 0x000b32fd load_next + 195 (import.c:2220)
62 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001)
63 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072)
64 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49)
65 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861)
66 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442)
67 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067)
68 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
69 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500)
70 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675)
71 org.python.python 0x000b2428 load_source_module + 726 (import.c:959)
72 org.python.python 0x000b30af import_submodule + 293 (import.c:2400)
73 org.python.python 0x000b32fd load_next + 195 (import.c:2220)
74 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001)
75 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072)
76 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49)
77 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861)
78 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442)
79 org.python.python 0x00096882 PyEval_EvalFrameEx + 8542 (ceval.c:2067)
80 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
81 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500)
82 org.python.python 0x000b1fd2 PyImport_ExecCodeModuleEx + 193 (import.c:675)
83 org.python.python 0x000b2428 load_source_module + 726 (import.c:959)
84 org.python.python 0x000b2f07 load_package + 427 (import.c:1015)
85 org.python.python 0x000b30af import_submodule + 293 (import.c:2400)
86 org.python.python 0x000b32fd load_next + 195 (import.c:2220)
87 org.python.python 0x000b37aa import_module_level + 142 (import.c:2001)
88 org.python.python 0x000b3ca1 PyImport_ImportModuleLevel + 45 (import.c:2072)
89 org.python.python 0x0008eab3 builtin___import__ + 156 (bltinmodule.c:49)
90 org.python.python 0x0009a72f PyEval_EvalFrameEx + 24587 (ceval.c:3573)
91 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
92 org.python.python 0x000987b4 PyEval_EvalFrameEx + 16528 (ceval.c:3669)
93 org.python.python 0x00099b6a PyEval_EvalFrameEx + 21574 (ceval.c:3659)
94 org.python.python 0x00099b6a PyEval_EvalFrameEx + 21574 (ceval.c:3659)
95 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
96 org.python.python 0x00030007 function_call + 320 (funcobject.c:517)
97 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861)
98 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442)
99 org.python.python 0x0008ed44 builtin_apply + 201 (bltinmodule.c:169)
100 org.python.python 0x0009a72f PyEval_EvalFrameEx + 24587 (ceval.c:3573)
101 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
102 org.python.python 0x00030007 function_call + 320 (funcobject.c:517)
103 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861)
104 org.python.python 0x00016946 instancemethod_call + 401 (classobject.c:2519)
105 org.python.python 0x0000ec98 PyObject_Call + 45 (abstract.c:1861)
106 org.python.python 0x0009389a PyEval_CallObjectWithKeywords + 112 (ceval.c:3442)
107 _tkinter.so 0x007dae57 PythonCmd + 220 (_tkinter.c:2014)
108 com.tcltk.tcllibrary 0x0185d0f7 TclInvokeStringCommand + 101
109 com.tcltk.tcllibrary 0x0185f67a Tcl_ListMathFuncs + 1281
110 com.tcltk.tcllibrary 0x0189c1e2 TclStackAlloc + 4767
111 com.tcltk.tcllibrary 0x018a4dc8 TclStackAlloc + 40581
112 com.tcltk.tcllibrary 0x018629df TclEvalObjEx + 788
113 com.tcltk.tcllibrary 0x01862ae1 Tcl_EvalObjEx + 47
114 com.tcltk.tklibrary 0x01961263 Tk_UndefineCursor + 234
115 com.tcltk.tklibrary 0x01962416 Tk_UndefineCursor + 4765
116 com.tcltk.tcllibrary 0x0185f67a Tcl_ListMathFuncs + 1281
117 com.tcltk.tcllibrary 0x0185fb77 Tcl_EvalObjv + 72
118 com.tcltk.tcllibrary 0x018627ce TclEvalObjEx + 259
119 com.tcltk.tcllibrary 0x018d9e62 TclObjGetFrame + 731
120 com.tcltk.tcllibrary 0x0185f67a Tcl_ListMathFuncs + 1281
121 com.tcltk.tcllibrary 0x0189c1e2 TclStackAlloc + 4767
122 com.tcltk.tcllibrary 0x018db5d3 TclObjInterpProcCore + 981
123 com.tcltk.tcllibrary 0x0185f67a Tcl_ListMathFuncs + 1281
124 com.tcltk.tcllibrary 0x01862102 Tcl_GetVersion + 6630
125 com.tcltk.tcllibrary 0x0186247a Tcl_EvalEx + 46
126 com.tcltk.tklibrary 0x01938e2a Tk_BindEvent + 4440
127 com.tcltk.tklibrary 0x0193da48 TkBindEventProc + 329
128 com.tcltk.tklibrary 0x01945969 Tk_HandleEvent + 1562
129 com.tcltk.tklibrary 0x01945a55 Tk_HandleEvent + 1798
130 com.tcltk.tcllibrary 0x018cc665 Tcl_ServiceEvent + 163
131 com.tcltk.tcllibrary 0x018cc977 Tcl_DoOneEvent + 365
132 _tkinter.so 0x007da74b Tkapp_MainLoop + 408 (_tkinter.c:2547)
133 org.python.python 0x0009a72f PyEval_EvalFrameEx + 24587 (ceval.c:3573)
134 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
135 org.python.python 0x000987b4 PyEval_EvalFrameEx + 16528 (ceval.c:3669)
136 org.python.python 0x00099b6a PyEval_EvalFrameEx + 21574 (ceval.c:3659)
137 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
138 org.python.python 0x000987b4 PyEval_EvalFrameEx + 16528 (ceval.c:3669)
139 org.python.python 0x0009afaa PyEval_EvalCodeEx + 1819 (ceval.c:2836)
140 org.python.python 0x0009b15e PyEval_EvalCode + 87 (ceval.c:500)
141 org.python.python 0x000be50c PyRun_FileExFlags + 260 (pythonrun.c:1273)
142 org.python.python 0x000be8a6 PyRun_SimpleFileExFlags + 640 (pythonrun.c:879)
143 org.python.python 0x000cbfce Py_Main + 3077 (main.c:523)
144 python2.5 0x000018ee _start + 216
145 python2.5 0x00001815 start + 41
Thread 1: Dispatch queue: com.apple.libdispatch-manager
0 libSystem.B.dylib 0x9075f0ea kevent + 10
1 libSystem.B.dylib 0x9075f804 _dispatch_mgr_invoke + 215
2 libSystem.B.dylib 0x9075ecc3 _dispatch_queue_invoke + 163
3 libSystem.B.dylib 0x9075ea68 _dispatch_worker_thread2 + 234
4 libSystem.B.dylib 0x9075e4f1 _pthread_wqthread + 390
5 libSystem.B.dylib 0x9075e336 start_wqthread + 30
Thread 2:
0 libSystem.B.dylib 0x9075e182 __workq_kernreturn + 10
1 libSystem.B.dylib 0x9075e718 _pthread_wqthread + 941
2 libSystem.B.dylib 0x9075e336 start_wqthread + 30
Thread 3:
0 libSystem.B.dylib 0x90774066 select$DARWIN_EXTSN$NOCANCEL + 10
1 libSystem.B.dylib 0x9080d11b select + 92
2 com.tcltk.tcllibrary 0x01900e76 TclUnixWaitForFile + 1347
3 libSystem.B.dylib 0x90765fbd _pthread_start + 345
4 libSystem.B.dylib 0x90765e42 thread_start + 34
Thread 4:
0 libSystem.B.dylib 0x907388da mach_msg_trap + 10
1 libSystem.B.dylib 0x90739047 mach_msg + 68
2 com.apple.opengl 0x912f2edb glcDebugListener + 426
3 libSystem.B.dylib 0x90765fbd _pthread_start + 345
4 libSystem.B.dylib 0x90765e42 thread_start + 34
Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00000000 ebx: 0x90842969 ecx: 0xbfff40bc edx: 0x90799732
edi: 0xa0045b10 esi: 0x01c97f7c ebp: 0xbfff40d8 esp: 0xbfff40bc
ss: 0x0000001f efl: 0x00000286 eip: 0x90799732 cs: 0x00000007
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
cr2: 0x42789000
Binary Images:
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0xffff0000 - 0xffff1fff libSystem.B.dylib ??? (???) <D45B91B2-2B4C-AAC0-8096-1FC48B7E9672> /usr/lib/libSystem.B.dylib
Model: MacBookPro2,2, BootROM MBP22.00A5.B07, 2 processors, Intel Core 2 Duo, 2.33 GHz, 3 GB, SMC 1.12f5
Graphics: ATI Radeon X1600, ATY,RadeonX1600, PCIe, 256 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x168C, 0x87), Atheros 5416: 2.0.19.4
Bluetooth: Version 2.2.4f3, 2 service, 1 devices, 1 incoming serial ports
Network Service: AirPort, AirPort, en1
Network Service: Rice, IPSec, utun0
Serial ATA Device: Hitachi HTS541616J9SA00, 149.05 GB
Parallel ATA Device: HL-DT-ST DVDRW GWA4080MA
USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8501, 0xfd400000
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x021a, 0x1d200000
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8205, 0x7d100000
USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8240, 0x5d200000
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