VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 05 2012 - 15:14:17 CST

Hi,
  I believe that this crashing issue is related to differences in the
shared libraries on the new MacOS X 10.7 (Lion) vs. the older revs.
I'm not sure which shared library might be causing the problem, so we'll try
a few simple experiments and narrow it down. It could also be something
else entirely, but these tests will help us figure it out.

Please try the following test for me on your machine, and let me know what happens:

Open a terminal shell and cd to the folder where you VMD 1.9.1 beta 1
version is installed. It will be named "VMD 1.9.1.app" (unless you renamed it).
>From there, cd to the "VMD 1.9.1.app/Contents/vmd" subdirectory.

Send me the output of this command (I assume "otool" is on your machine already):
  /usr/bin/otool -L vmd_MACOSXX86_64

Then, from your text command prompt, try running this command:
  ./vmd_MACOSXX86_64 -dispdev text

You should see output like this (this is the CUDA-enabled version):

Info) VMD for MACOSXX86_64, version 1.9.1beta1 (December 29, 2011)
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, 16 CPUs detected.
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] Quadro FX 4800 24 SM_1.3 @ 1.20 GHz, 1535MB RAM, KTO, OIO, ZCP
Info) OpenCL Platform[0]: Apple, FULL_PROFILE Devices: 2
Info) [0] Quadro FX 4800 24 CU @ 1.18 GHz, 1610MB RAM
Info) [1] Intel(R) Xeon(R) CPU E5620 @ 2.40GHz 16 CU @ 2.34 GHz, 19327MB RAM
Info) Dynamically loaded 2 plugins in directory:
Info) /Projects/vmd/vmd/macimages/x86_64/VMD-1.9.1/VMD 1.9.1.app/Contents/vmd/plugins/MACOSXX86_64/molfile
vmd >

If you get a crash at the same place as before, that is already very informative.

If you get a crash, try doing these steps:
  cd plugins/MACOSXX86_64/molfile
  mkdir bak
  mv hoomdplugin.so bak/
  mv dmsplugin.so bak/

Once those plugins are moved, then do:
  cd ../../..

and try running VMD again:
  ./vmd_MACOSXX86_64 -dispdev text

If VMD runs and does not crash, then try running it the normal way from
the GUI, and let me know what happens.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 30, 2011 at 08:30:45PM -0500, Joshua D. Moore wrote:
> Found this July 11 blog from Adobe and installed the developer drivers
>
> http://blogs.adobe.com/premiereprotraining/2011/06/quadro-4000-driver-and-cuda-driver-update-for-mac-osx-v10-6-8.html
>
> So now CUDA is detected on VMD startup, but I still get segmentation
> fault with 1.9.1beta. Version 1.9 is now detecting my CUDA though (it
> wasn't after my Lion upgrade) :). See below for output from
> 1.9.1.beta1.
>
> Thanks.
>
> Josh
>
> /Applications/VMD\ 1.9.1.app/Contents/MacOS/startup.command ; exit;
> Info) VMD for MACOSXX86_64, version 1.9.1beta1 (December 29, 2011)
> 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...
> 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 P7350 @ 2.00GHz 2 CU @ 1.95
> GHz, 4294MB RAM
> Info) [1] GeForce 9400M 2 CU @ 1.07 GHz, 268MB 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 (4096x4096), 3-D (256x256x256), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /Applications/VMD 1.9.1.app/Contents/vmd/plugins/MACOSXX86_64/molfile
> /Applications/VMD 1.9.1.app/Contents/MacOS/startup.command: line 7:
> 9915 Segmentation fault: 11
> "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> logout
>
>
>
>
>
> On Fri, Dec 30, 2011 at 8:07 PM, Joshua D. Moore <joshuadmoore_at_gmail.com> wrote:
> > Hi,
> >
> > As a follow-up to John's release of 1.9.1beta, I was wondering if
> > anyone else was having trouble finding the driver for OSX 10.7, Lion?
> >
> > NVIDIA has the driver for Snow-Leopard but I can't find one for Lion.
> >
> > Anyone else have this card?
> >
> > I get a Seg-Fault for both versions.  I'm not sure if I need to
> > install something special for OpenCL?
> >
> > See below for output if interested.
> >
> > Thanks.
> >
> > Josh
> >
> > OpenCL + CUDA:
> >
> > Info) No CUDA accelerator devices available.
> > Info) OpenCL Platform[0]: Apple, FULL_PROFILE  Devices: 2
> > Info)   [0] Intel(R) Core(TM)2 Duo CPU P7350 @ 2.00GHz  2 CU @ 1.95
> > GHz, 4294MB RAM
> > Info)   [1] GeForce 9400M                           2 CU @ 1.07 GHz,  268MB RAM
> > Info) OpenGL renderer: NVIDIA GeForce 9400M OpenGL Engine
> > Info)   Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> > Info)   Full GLSL rendering mode is available.
> > Info)   Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
> > Info) Dynamically loaded 2 plugins in directory:
> > Info) /Volumes/VMD-1.9.1/VMD 1.9.1.app/Contents/vmd/plugins/MACOSXX86_64/molfile
> > /Volumes/VMD-1.9.1/VMD 1.9.1.app/Contents/MacOS/startup.command: line
> > 7:  7535 Segmentation fault: 11
> > "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> > logout
> >
> > OpenCL:
> >
> > Info) OpenCL Platform[0]: Apple, FULL_PROFILE  Devices: 2
> > Info)   [0] Intel(R) Core(TM)2 Duo CPU P7350 @ 2.00GHz  2 CU @ 1.95
> > GHz, 4294MB RAM
> > Info)   [1] GeForce 9400M                           2 CU @ 1.07 GHz,  268MB RAM
> > Info) OpenGL renderer: NVIDIA GeForce 9400M OpenGL Engine
> > Info)   Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> > Info)   Full GLSL rendering mode is available.
> > Info)   Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
> > Info) Dynamically loaded 2 plugins in directory:
> > Info) /Volumes/VMD-1.9.1 1/VMD
> > 1.9.1.app/Contents/vmd/plugins/MACOSXX86_64/molfile
> > /Volumes/VMD-1.9.1 1/VMD 1.9.1.app/Contents/MacOS/startup.command:
> > line 7:  7915 Segmentation fault: 11
> > "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> > logout 

-- 
NIH Resource 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/       Fax: 217-244-6078