VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 09 2014 - 15:50:21 CDT

Hi,
  The 64-bit MacOS X builds are not stable due to issues with the
Cocoa versions of the Tk/FLTK GUI toolkits that VMD uses. The 64-bit
VMD build is compiled against experimental Cocoa branches of Tk/FLTK,
but those expermintal builds are now stale vs. the latest revs of
MacOS X. For now, please just continue using the 32-bit MacOS X build.
I am hoping that newer revs of the Cocoa-based Tk/FLTK toolkits will
solve this problem, but I won't have a chance to dig into this until
I return from travel next week.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 08, 2014 at 07:28:09PM -0400, Mark Wistey 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.
> 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
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/