From: Mark Wistey (mwistey_at_nd.edu)
Date: Tue Jul 08 2014 - 19:05:07 CDT

On Jul 8, 2014, at 7:48 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> Have you tried launching VMD from a Launchpad? Does VMD start at all?

Yes, it starts, then crashes just after drawing the VMD Main and OpenGL Display windows.

> Also, in OS X 10.9 you should use lldb for debugging.

Thanks. Here’s the backtrace. Anything else I can do to help with diagnosis?

/Applications/Work/VMD-1.9.2a39/VMD 1.9.2.app/Contents/Resources/VMD.app/Contents/MacOS> lldb VMD
Current executable set to 'VMD' (x86_64).
(lldb) process launch
Process 18416 launched: '/Applications/Work/VMD-1.9.2a39-bad/VMD 1.9.2.app/Contents/Resources/VMD.app/Contents/MacOS/VMD' (x86_64)
Info) VMD for MACOSXX86_64, version 1.9.2a39 (March 21, 2014)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 2 CPUs detected.
Info) VMDNOCUDA environment variable is set, CUDA support disabled.
Info) No CUDA accelerator devices available.
Info) OpenCL Platform[0]: Apple, FULL_PROFILE Devices: 2
Info) [0] Intel(R) Core(TM)2 Duo CPU P8700 @ 2.53GHz 2 CU @ 2.53 GHz, 8.0GB RAM
Info) [1] GeForce 9400M 2 CU @ 1.10 GHz, 256MB RAM
Info) OpenGL renderer: NVIDIA GeForce 9400M OpenGL Engine
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (8)
2014-07-08 19:57:24.674 VMD[18416:303] CoreText performance note: Client called CTFontCreateWithName() using name "Arial" and got font with PostScript name "ArialMT". For best performance, only use PostScript names when calling this API.
2014-07-08 19:57:24.675 VMD[18416:303] CoreText performance note: Set a breakpoint on CTFontLogSuboptimalRequest to debug.
2014-07-08 19:57:24.705 VMD[18416:303] CoreText performance note: Client called CTFontCreateWithName() using name "Arial Italic" and got font with PostScript name "Arial-ItalicMT". For best performance, only use PostScript names when calling this API.
Info) Dynamically loaded 2 plugins in directory:
Info) /Applications/Work/VMD-1.9.2a39-bad/VMD 1.9.2.app/Contents/vmd/plugins/MACOSXX86_64/molfile
2014-07-08 19:57:26.047 VMD[18416:303] CoreText performance note: Client called CTFontCreateWithName() using name "Arial" and got font with PostScript name "ArialMT". For best performance, only use PostScript names when calling this API.
Process 18416 stopped
* thread #1: tid = 0x9d2f4, 0x0000000000000000, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
    frame #0: 0x0000000000000000
error: memory read failed for 0x0
(lldb) thread backtrace
* thread #1: tid = 0x9d2f4, 0x0000000000000000, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
  * frame #0: 0x0000000000000000
    frame #1: 0x0000000108d9ee1d Tcl`___lldb_unnamed_function817$$Tcl + 113
    frame #2: 0x0000000108d9ed8f Tcl`___lldb_unnamed_function816$$Tcl + 22
    frame #3: 0x0000000108d9e02f Tcl`Tcl_GetThreadData + 21
    frame #4: 0x0000000108d87cee Tcl`TclFreeObj + 259
    frame #5: 0x0000000108da8355 Tcl`Tcl_GetVar2Ex + 107
    frame #6: 0x0000000108da82cc Tcl`Tcl_GetVar2 + 9
    frame #7: 0x000000010a3130ce tcl_libbiokit.so`SWIG_InitializeModule + 119
    frame #8: 0x000000010a313616 tcl_libbiokit.so`Tcl_libbiokit_Init + 88
    frame #9: 0x0000000100bcd29f Tcl`___lldb_unnamed_function675$$Tcl + 2171
    frame #10: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #11: 0x0000000100b66a50 Tcl`___lldb_unnamed_function134$$Tcl + 2194
    frame #12: 0x0000000100b66e0c Tcl`Tcl_EvalEx + 29
    frame #13: 0x0000000100be0a69 Tcl`___lldb_unnamed_function773$$Tcl + 612
    frame #14: 0x0000000100be1004 Tcl`Tcl_PkgRequireProc + 17
    frame #15: 0x0000000100be1e39 Tcl`___lldb_unnamed_function775$$Tcl + 2223
    frame #16: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #17: 0x0000000100b66a50 Tcl`___lldb_unnamed_function134$$Tcl + 2194
    frame #18: 0x0000000100b66e0c Tcl`Tcl_EvalEx + 29
    frame #19: 0x0000000100bc7fdc Tcl`Tcl_FSEvalFileEx + 573
    frame #20: 0x0000000100b77b6e Tcl`___lldb_unnamed_function251$$Tcl + 162
    frame #21: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #22: 0x0000000100b66a50 Tcl`___lldb_unnamed_function134$$Tcl + 2194
    frame #23: 0x0000000100b66e0c Tcl`Tcl_EvalEx + 29
    frame #24: 0x0000000100be0a69 Tcl`___lldb_unnamed_function773$$Tcl + 612
    frame #25: 0x0000000100be1004 Tcl`Tcl_PkgRequireProc + 17
    frame #26: 0x0000000100be1e39 Tcl`___lldb_unnamed_function775$$Tcl + 2223
    frame #27: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #28: 0x0000000100b66a50 Tcl`___lldb_unnamed_function134$$Tcl + 2194
    frame #29: 0x0000000100b66e0c Tcl`Tcl_EvalEx + 29
    frame #30: 0x0000000100bc7fdc Tcl`Tcl_FSEvalFileEx + 573
    frame #31: 0x0000000100b77b6e Tcl`___lldb_unnamed_function251$$Tcl + 162
    frame #32: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #33: 0x0000000100b66a50 Tcl`___lldb_unnamed_function134$$Tcl + 2194
    frame #34: 0x0000000100b66e0c Tcl`Tcl_EvalEx + 29
    frame #35: 0x0000000100be0a69 Tcl`___lldb_unnamed_function773$$Tcl + 612
    frame #36: 0x0000000100be1004 Tcl`Tcl_PkgRequireProc + 17
    frame #37: 0x0000000100be1e39 Tcl`___lldb_unnamed_function775$$Tcl + 2223
    frame #38: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #39: 0x0000000100b66a50 Tcl`___lldb_unnamed_function134$$Tcl + 2194
    frame #40: 0x0000000100b66e0c Tcl`Tcl_EvalEx + 29
    frame #41: 0x0000000100bc7fdc Tcl`Tcl_FSEvalFileEx + 573
    frame #42: 0x0000000100b77b6e Tcl`___lldb_unnamed_function251$$Tcl + 162
    frame #43: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #44: 0x0000000100b66a50 Tcl`___lldb_unnamed_function134$$Tcl + 2194
    frame #45: 0x0000000100b66e0c Tcl`Tcl_EvalEx + 29
    frame #46: 0x0000000100be0a69 Tcl`___lldb_unnamed_function773$$Tcl + 612
    frame #47: 0x0000000100be1004 Tcl`Tcl_PkgRequireProc + 17
    frame #48: 0x0000000100be1e39 Tcl`___lldb_unnamed_function775$$Tcl + 2223
    frame #49: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #50: 0x0000000100ba4e4b Tcl`___lldb_unnamed_function463$$Tcl + 5157
    frame #51: 0x0000000100be53b6 Tcl`TclObjInterpProcCore + 1705
    frame #52: 0x0000000100be5a0b Tcl`TclObjInterpProc + 65
    frame #53: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #54: 0x0000000100ba4e4b Tcl`___lldb_unnamed_function463$$Tcl + 5157
    frame #55: 0x0000000100be53b6 Tcl`TclObjInterpProcCore + 1705
    frame #56: 0x0000000100be5a0b Tcl`TclObjInterpProc + 65
    frame #57: 0x0000000100b65cd3 Tcl`___lldb_unnamed_function133$$Tcl + 1428
    frame #58: 0x0000000100ba4e4b Tcl`___lldb_unnamed_function463$$Tcl + 5157
    frame #59: 0x0000000100bacc10 Tcl`___lldb_unnamed_function464$$Tcl + 490
    frame #60: 0x0000000100b6741b Tcl`TclEvalObjEx + 835
    frame #61: 0x0000000100b67508 Tcl`Tcl_EvalObjEx + 20
    frame #62: 0x0000000100bb27d3 Tcl`Tcl_RecordAndEvalObj + 385
    frame #63: 0x0000000100bb283b Tcl`Tcl_RecordAndEval + 87
    frame #64: 0x000000010010b59d VMD`NameList<int>::clear() + 2907
    frame #65: 0x00000001000cb89a VMD`UIObject::check_event() + 546
    frame #66: 0x0000000100033379 VMD`CmdRockOff::~CmdRockOff() + 107
    frame #67: 0x00000001000f1b7f VMD`Vrml2DisplayDevice::~Vrml2DisplayDevice() + 23493
    frame #68: 0x00000001000f1cfd VMD`Vrml2DisplayDevice::~Vrml2DisplayDevice() + 23875
    frame #69: 0x0000000100006064 VMD`Fl_Pixmap::Fl_Pixmap(char const* const*) + 708
(lldb)

On Jul 8, 2014, at 6:28 PM, Mark Wistey <mwistey_at_nd.edu> wrote:
> The 64 bit version of VMD 1.9.2a39 is crashing with a seg fault on startup, just after drawing the VMD Main and OpenGL Display windows. The 32 bit version seems to work fine. I can also start VMD with '-dispdev none’ without a display.