VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 28 2014 - 13:06:53 CDT

John,
  Just as a quick sanity check, are you able to run your VMD compile
in text mode without encountering the segfaul? If so, that would basically
prove that the issue is indeed GUI-related, as I suggested in my previous
reply. If the problem turns out to NOT to be GUI, then we can take that
up, otherwise it's likely the Tk/FLTK vs. Cocoa thing I already mentioned.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 27, 2014 at 07:10:15PM +0000, John Grime wrote:
> Hi John,
>
> I have no idea what?s going on with these emails I?m trying to send to the VMD mailing list, they keep being truncated for some reason. They?re fine in the copies I have in my outbox, for some reason.
>
> The oringal mail should have read:
>
> I?m trying to use the 64-bit VMD with Mac OS 10.9.4, and I?m getting immediate crashes on VMD startup (I downloaded the VMD binary rather than building it from source).
>
> As this has been mentioned previously on the mailing list, I tried to make sure that:
>
> 1. I installed VMD into the Applications directory, rather than trying to run it from the disk image.
> 2. I tried running VMD through Launchpad, running by double-clicking on the VMD icon in Application, and running through the terminal.
>
> I have pasted some example output from the terminal at the end of the email.
>
> This looks to be related to the issue Carolyn Phillips was having (CUDA drivers), so I tried to install updated drivers from the NVIDIA website for 10.9.4 (13E28), which is what the Mac OS system information claims I have. The driver installation says ?This computer is not compatible with the NVIDIA Web Driver? (it?s an "iMac 27-inch, Late 2013?, according to the system information).
>
> Next, I tried installing the CUDA drivers through this page:
>
> http://www.nvidia.com/object/macosx-cuda-6.0.51-driver.html
>
> ? which worked, and added a preference pane in System Preferences. This pane notified me that there was a CUDA driver update available, but trying to install it via the ?Install CUDA Update? button in the pane just gave me a ?CUDA update failed? message.
>
> Apparently, my CUDA driver version is 6.0.51 after installing the driver from NVIDIA. At this point, when I run VMD it?s picking up the presence of a CUDA-accelerated device (which it did not previously, see output at end of email) but I still get segmentation faults:
>
>
> jgrime$ /Applications/VMD\ 1.9.1.app/Contents/MacOS/startup.command
> ? preamble ...
> Info) Creating CUDA device pool and initializing hardware...
> CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
> Info) Detected 1 available CUDA accelerator:
> Info) [0] GeForce GTX 780M 8 SM_3.0 @ 0.78 GHz, 4.0GB RAM, KTO, OIO, ZCP
> Info) OpenCL Platform[0]: Apple, FULL_PROFILE Devices: 2
> Info) [0] Intel(R) Core(TM) i7-4771 CPU @ 3.50GHz 8 CU @ 3.50 GHz, 16GB RAM
> Info) [1] GeForce GTX 780M 8 CU @ 0.78 GHz, 4.0GB RAM
> Info) OpenGL renderer: NVIDIA GeForce GTX 780M OpenGL Engine
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (8)
> 2014-08-27 10:54:41.040 VMD[1231:507] 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.
> 2014-08-27 10:54:41.041 VMD[1231:507] CoreText performance note: Set a breakpoint on CTFontLogSuboptimalRequest to debug.
> 2014-08-27 10:54:41.042 VMD[1231:507] 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/VMD 1.9.1.app/Contents/vmd/plugins/MACOSXX86_64/molfile
> 2014-08-27 10:54:41.214 VMD[1231:507] 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/VMD 1.9.1.app/Contents/MacOS/startup.command: line 7: 1231 Segmentation fault: 11 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
>
>
> I?m not familiar with CUDA in general - can anyone suggest where I?m going wrong here?
>
> Cheers,
>
> J.
>
> jgrime$ /Volumes/Macintosh\ HD/Applications/VMD\ 1.9.1.app/Contents/MacOS/startup.command
> Info) VMD for MACOSXX86_64, version 1.9.1 (February 1, 2012)
> 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, 8 CPUs detected.
> Warning) Detected a mismatch between CUDA runtime and GPU driver
> Warning) Check to make sure that GPU drivers are up to date.
> Info) No CUDA accelerator devices available.
> Info) OpenCL Platform[0]: Apple, FULL_PROFILE Devices: 2
> Info) [0] Intel(R) Core(TM) i7-4771 CPU @ 3.50GHz 8 CU @ 3.50 GHz, 16GB RAM
> Info) [1] GeForce GTX 780M 8 CU @ 0.78 GHz, 4.0GB RAM
> Info) OpenGL renderer: NVIDIA GeForce GTX 780M OpenGL Engine
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (8)
> 2014-08-27 10:18:13.270 VMD[816:507] 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.
> 2014-08-27 10:18:13.271 VMD[816:507] CoreText performance note: Set a breakpoint on CTFontLogSuboptimalRequest to debug.
> 2014-08-27 10:18:13.271 VMD[816:507] 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) /Volumes/Macintosh HD/Applications/VMD 1.9.1.app/Contents/vmd/plugins/MACOSXX86_64/molfile
> 2014-08-27 10:18:13.449 VMD[816:507] 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.
> /Volumes/Macintosh HD/Applications/VMD 1.9.1.app/Contents/MacOS/startup.command: line 7: 816 Segmentation fault: 11 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
>
>
> jgrime$ /Volumes/Macintosh\ HD/Applications/VMD\ 1.9.1.app/Contents/Resources/VMD.app/Contents/MacOS/VMD
> Info) VMD for MACOSXX86_64, version 1.9.1 (February 1, 2012)
> 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, 8 CPUs detected.
> Warning) Detected a mismatch between CUDA runtime and GPU driver
> Warning) Check to make sure that GPU drivers are up to date.
> Info) No CUDA accelerator devices available.
> Info) OpenCL Platform[0]: Apple, FULL_PROFILE Devices: 2
> Info) [0] Intel(R) Core(TM) i7-4771 CPU @ 3.50GHz 8 CU @ 3.50 GHz, 16GB RAM
> Info) [1] GeForce GTX 780M 8 CU @ 0.78 GHz, 4.0GB RAM
> Info) OpenGL renderer: NVIDIA GeForce GTX 780M OpenGL Engine
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (8)
> 2014-08-27 10:22:19.915 VMD[848:507] 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.
> 2014-08-27 10:22:19.916 VMD[848:507] CoreText performance note: Set a breakpoint on CTFontLogSuboptimalRequest to debug.
> 2014-08-27 10:22:19.916 VMD[848:507] 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) /Volumes/Macintosh HD/Applications/VMD 1.9.1.app/Contents/vmd/plugins/MACOSXX86_64/molfile
> 2014-08-27 10:22:20.105 VMD[848:507] 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.
> Segmentation fault: 11 

-- 
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/