VMD-L Mailing List

From: Joshua D. Moore (joshuadmoore_at_gmail.com)
Date: Wed Jan 11 2012 - 19:09:50 CST

Dear John,

Sorry for my delay in replying. I didn't get a crash running,
./vmd_MACOSXX86_64 -dispdev text. However, I still get the seg fault
running the GUI, even after moving the molfile plugins that you
mentioned.

/usr/bin/otool -L vmd_MACOSXX86_64 output:

vmd_MACOSXX86_64:
        /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 315.0.0)
        /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
(compatibility version 1.0.0, current version 1.0.0)
        /System/Library/Frameworks/AGL.framework/Versions/A/AGL
(compatibility version 1.0.0, current version 1.0.0)
        @executable_path/libcudart.dylib (compatibility version 1.1.0,
current version 4.0.0)
        /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
(compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 125.2.1)
        @executable_path/../Frameworks/Tk.framework/Versions/8.5/Tk
(compatibility version 8.5.0, current version 8.5.9)
        @executable_path/../Frameworks/Tcl.framework/Versions/8.5/Tcl
(compatibility version 8.5.0, current version 8.5.9)
        /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
(compatibility version 1.0.0, current version 15.0.0)
        /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.9.0)
        /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 227.0.0)
        /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
(compatibility version 1.0.0, current version 44.0.0)
        /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
(compatibility version 150.0.0, current version 550.42.0)
        /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
(compatibility version 1.0.0, current version 38.0.0)
        /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
(compatibility version 300.0.0, current version 751.42.0)
        /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
(compatibility version 45.0.0, current version 1038.35.0)

On Thu, Jan 5, 2012 at 4:14 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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