VMD-L Mailing List

From: Joshua A. Anderson (joaander_at_umich.edu)
Date: Thu Jan 19 2012 - 12:47:21 CST

How timely. I just updated my system to Lion. I use a 64-bit build of vmd not for memory usage, but to link against a 64-bit python installation connected to a whole bunch of libraries (in macports). I can confirm that I get the same problem on my system with a VMD _1.9_ compile.

When I disable TK, VMD loads without seg faulting. The extensions menu is gone, as you said it would be (which is fine by me).

The problem I am having is that the "pbc" command is also not working.
vmd > pbc box -color black -center origin
invalid command name "pbc"

Does the pbc command also use TK? Or is there some other reason it isn't loading?
--------
Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan

On Jan 13, 2012, at 3:52 PM, John Stone wrote:

> Hi,
> I just had one of my colleagues run more tests on MacOS X 10.7 and
> indeed the crashing appears to be caused by Tk. I have built a
> 64-bit test version of VMD that will run on MacOS X 10.7 by disabling
> the use of Tk, but this has the side effect of disabling everything in
> the VMD "Extensions" menu. This probably means that the 64-bit build
> of VMD for MacOS X is going to have to wait a bit longer until whatever
> is crashing Tk has been resolved. It could be a new conflict between
> Tk and FLTK, or it may just be a bug in the Cocoa-based Tk that only
> manifests itself on MacOS X 10.7. Given that the Cocoa-based version of Tk
> still isn't considered a "production" version, it's not entirely surprising
> that there are issues that are still cropping up. I will go ahead and
> make a 64-bit build of VMD for MacOS X for the 1.9.1 release, but I will
> put it on a separate download page and it will be considered an
> "unofficial" VMD build since we know it is not stable on MacOS X 10.7
> at present. I can make a version of it that has Tk disabled if that is
> of interest to VMD users that are running MacOS X 10.7, and they can
> live without the VMD "Extensions" menu for what they are doing.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Thu, Jan 12, 2012 at 10:48:06AM -0600, John Stone wrote:
>> Joshua,
>> Thanks for the feedback. It would appear that all of the people
>> I've had check this on MacOS X 10.7.x (Lion) are all experiencing
>> exactly the same issue. Since the problems only occur when running
>> VMD with the GUI enabled, this seems to point toward an issue with the
>> interaction between FLTK and Tk and the 64-bit MacOS X Cocoa APIs they use.
>>
>> The 64-bit MacOS X build of VMD is done in a very special way because
>> Apple doesn't support the older Carbon APIs for 64-bit mode. All of the
>> GUI toolkits that support MacOS X (FLTK, Tk, Qt, and many others) had to
>> be rewritten for Cocoa in order to work on 64-bit mode. On complication of
>> this is that Cocoa is an object-oriented API, and the way Apple designed the
>> Cocoa API, they want an application to instantiate a subclass of an application
>> object. The problem is that when a program like VMD incorporates multiple
>> libraries that create GUI windows (in this case both FLTK and Tk) they
>> _both_ try to create an application object, and this causes all kinds of
>> problems. In order to make it possible to build a 64-bit VMD on
>> MacOS X, I had to work closely with the developers of FLTK and Tk to
>> get them to change their code so that the application object that gets
>> created during initialization of both FLTK and TK wouldn't cause crashes.
>>
>> My guess is that something about the Cocoa application object initialization
>> behavior has changed for MacOS X 10.7, and there are new issues that will
>> have to be solved in order for FLTK and Tk to work together correctly in
>> 64-bit mode with Cocoa. If it turns out that this is indeed the cause,
>> then I will not be able to release a "production" 64-bit version of VMD
>> for MacOS X for a while longer. If this is the case, then I'm going to
>> have to skip releasing the 64-bit MacOS X builds this time, and save them
>> for a subsequent release or an interim update.
>>
>> I should know in the next day or two if the problems you are having are
>> indeed the result of a bad interaction between Tk/FLTK and the latest
>> Cocoa implementation on MacOS X 10.7.x. That's what it's looking like
>> currently, but I need to check a few more things to be sure.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>>
>> On Wed, Jan 11, 2012 at 08:09:50PM -0500, Joshua D. Moore wrote:
>>> 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
>>
>> --
>> 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
>
> --
> 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
>
>