VMD-L Mailing List

From: Mark Wistey (mwistey_at_nd.edu)
Date: Tue Jul 08 2014 - 18:28:09 CDT

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.
Hardware: 1999 MacBookPro5,4, 2.53 GHz Core 2 Duo, 8 GB RAM, MacOS 10.9.4.
DYLD_LIBRARY_PATH and LD_LIBRARY_PATH are unset.
No debugger installed.
I’m running 1.9.2a38 & a38 binaries from biocore. These ran okay several months ago.
Version 1.9.1 (no CUDA) also runs fine but has a bug in non-orthonormal unit cells.

Here's the crash log for 1.9.2a38 (64 bit) without CUDA installed:

/Applications/Work/VMD-1.9.2a38/VMD 1.9.2.app/Contents/MacOS> ../Resources/VMD.app/Contents/MacOS/VMD -debug 5
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 18:36:12.273 VMD[16884:303] 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 18:36:12.273 VMD[16884:303] CoreText performance note: Set a breakpoint on CTFontLogSuboptimalRequest to debug.
2014-07-08 18:36:12.314 VMD[16884:303] 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-1.9.2a38/VMD 1.9.2.app/Contents/vmd/plugins/MACOSXX86_64/molfile
Info) File loading in progress, please wait.
ERROR) Cannot read file of type debug
ERROR) Loading of startup molecule files aborted.
2014-07-08 18:36:13.008 VMD[16884:303] 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.
Segmentation fault

And here's the crash log with 1.9.2a39 (64 bit) after installing CUDA (CUDA out of memory error):

grunibeard:~% /Applications/Work/VMD-1.9.2a39/VMD\ 1.9.2.app/Contents/MacOS/startup.command ; exit;
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) Creating CUDA device pool and initializing hardware...
Warning) thread[0] can't init GPU[0] found by device query
Warning) CUDA error: out of memory
CUDA error: out of memory, CUDAClearDevice.cu line 62
Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce 9400M 2 SM_1.1 @ 1.10 GHz, 253MB RAM, KTO, ZCP
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 19:09:42.271 VMD[17797:507] 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 19:09:42.272 VMD[17797:507] CoreText performance note: Set a breakpoint on CTFontLogSuboptimalRequest to debug.
2014-07-08 19:09:42.323 VMD[17797:507] 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/VMD 1.9.2.app/Contents/vmd/plugins/MACOSXX86_64/molfile
2014-07-08 19:09:42.939 VMD[17797:507] 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.
/Applications/Work/VMD-1.9.2a39/VMD 1.9.2.app/Contents/MacOS/startup.command: line 7: 17797 Segmentation fault: 11 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*

Setting VMDNOCUDA still crashes...

/Applications/Work/VMD-1.9.2a39/VMD 1.9.2.app/Contents/Resources/VMD.app/Contents/MacOS> ./VMD
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 19:16:09.737 VMD[17837:303] 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 19:16:09.737 VMD[17837:303] CoreText performance note: Set a breakpoint on CTFontLogSuboptimalRequest to debug.
2014-07-08 19:16:09.762 VMD[17837:303] 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/VMD 1.9.2.app/Contents/vmd/plugins/MACOSXX86_64/molfile
2014-07-08 19:16:10.113 VMD[17837:303] 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.
Segmentation fault