From: Joshua A. Anderson (joaander_at_umich.edu)
Date: Wed Jan 25 2012 - 14:50:27 CST

macports has tcl 8.5.11

But nothing else in my macports tree is linked into tcl (at least that I'm using). So I should be able to setup a by hand build of 8.6.0b2 and test it out. I will let you know what I find.
--------
Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan

On Jan 25, 2012, at 10:59 AM, John Stone wrote:

>
> Joshua,
> Quick query regarding your macports source-code build:
> What version of Tcl/Tk is the macports build using? Do the macports
> guys have a beta build of Tcl/Tk 8.6.0 floating around yet? If so, it
> might be worth trying a build against the latest 8.6.0 beta to see if it
> has the Cocoa-based GUI code integrated, and whether it gets along with
> MacOS X 10.7.x better.
>
> Cheers,
> John
>
> On Thu, Jan 19, 2012 at 01:47:21PM -0500, Joshua A. Anderson 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?
>> --------
>> 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
>>>
>>>
>>
>
> --
> 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
>
>