VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 19 2012 - 13:55:04 CST

On Thu, Jan 19, 2012 at 1:47 PM, Joshua A. Anderson <joaander_at_umich.edu> wrote:
> 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?

no it doesn't. but since it is in a separate package,
it has to be "required" before use.

since you don't have the Tk based extensions loaded,
a lot of the packages that those extensions "require"
are no longer loaded by default.

try:

package require pbctools

and see what it says and if that returns
the pbctools version number, you should
be able to use pbctools and the pbc command.

cheers,
    axel.

> --------
> 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
>>
>>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.