VMD-L Mailing List

From: Rich Cook (rcook_at_llnl.gov)
Date: Thu Dec 17 2009 - 12:52:54 CST

I definitely think it looks like a stereo issue, I agree! In
retrospect, it seems obvious. I tried your variable and it worked
like a charm for me.

On Dec 16, 2009, at 9:55 PM, John Stone wrote:

> Rich,
> From the startup messages you've provided below, it looks to
> me like this is being caused by another bug in the GLX implementation
> on the MacOS X11 server side. In particular, I see that the X11
> server is claiming that it has stereo, and so VMD went ahead and
> asked for a stereoscopic buffer. I seriously doubt however that
> the Mac in question actually has a stereo-capable GPU, so something
> is going amiss there. This would explain the flashing behavior,
> as more likely than not there's some bogus activity going on with
> buffer swaps if stereo is enabled but not actually supported by
> the hardware. Try having your colleague set the environment
> variable VMDDISABLESTEREO to 1 prior to running VMD, and see
> if that cures the flashing when you use the real OpenGL:
> /bin/bash:
> VMDDISABLESTEREO=1
> export VMDDISABLESTEREO
>
> /bin/csh
> setenv VMDDISABLESTEREO 1
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Dec 15, 2009 at 02:18:49PM -0800, Rich Cook wrote:
>> Sure here you go. To be honest, I suspect X11's involvement due to
>> some of the description from the end user, which I have not
>> duplicated. He claims that on his machine, the flickering occurs
>> where the VMD window used to be as well as where it is, which
>> definitely points at X11 involvement. However, since only VMD
>> displays this, I thought I'd try you first.
>>
>> There is this of note as well:
>> http://*xquartz.macosforge.org/trac/ticket/252
>>
>> VMDDISABLEATILINUXWORKAROUND does not do anything to help.
>>
>> rcook_at_yana2 (~): vmd
>> Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
>> 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, 8 CPUs detected.
>> Info) Free system memory: 10931MB (72%)
>> Info) No CUDA accelerator devices available.
>> Info) ATI Linux driver detected, limiting features to avoid driver
>> bugs.
>> Info) Set the environment variable VMDDISABLEATILINUXWORKAROUND
>> Info) to enable full functionality on a known-safe driver version.
>> Info) OpenGL renderer: ATI Radeon 9600 OpenGL Engine
>> Info) Features: STENCIL STEREO MDE MTX NPOT PP PS
>> Info) GLSL rendering mode is NOT available.
>> Info) Textures: 2-D (2048x2048), Multitexture (8)
>> vmd > Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
>> Info) Exiting normally.
>>
>>
>> On Dec 15, 2009, at 1:20 PM, John Stone wrote:
>>
>>>
>>> Rich,
>>> Can you send me the VMD startup messages that get printed on the
>>> text console when you're remote displaying on one of the machines
>>> that flickers? Whether you render with Mesa or some other OpenGL
>>> shouldn't have much effect since the rendering should be done on
>>> the local Mac display and not on the remote machine, and in
>>> particular
>>> since the glXSwapBuffers() call will be handled entirely on the Mac
>>> side and not by the remote machine. So the results you got with
>>> your
>>> Mesa test don't surprise me at present. The bugs in the ATI drivers
>>> have historically affected only the Linux platform, and not MacOS X
>>> or Windows, so I don't expect this has much to do with the graphics
>>> chipset if you only see this behavior when using a remote X11
>>> connection. If you saw the same flickering behavior on a locally
>>> displayed VMD session, then I would be more apt to question the
>>> ATI driver on the Mac. Send me those VMD startup messages on
>>> the afflicted machines, and I'll ponder what might be causing this
>>> other than some sort of bug on the MacOS X X11/GLX server side.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Tue, Dec 15, 2009 at 01:03:07PM -0800, Rich Cook wrote:
>>>> I'm wondering if folks here can help me troubleshoot this issue.
>>>>
>>>> We have VMD installed on our large computer clusters and users like
>>>> to
>>>> visualize their data and display back to their desktops. This is
>>>> more
>>>> convenient than moving the data.
>>>>
>>>> A few of my users are having flickering issues with VMD on their
>>>> Mac
>>>> laptops. The symptoms: VMD runs normally, but the screen flickers
>>>> between a garbage image, mostly white, and the correct display.
>>>> This
>>>> makes VMD unusable for them in the way they'd like to be using it.
>>>>
>>>> They are running Mac OS X 10.5.8, using Apple's X11 (X.org) version
>>>> 2.1.6 or the newer XQuartz 2.4.0 from
>>>> http://**xquartz.macosforge.org/trac/wiki and using ATI graphics
>>>> cards
>>>> (models 2600 and 4780). I have read "out there" that there are
>>>> ATI issues
>>>> with VMD. True?
>>>>
>>>> This problem exists on three different Mac laptops we've tested
>>>> here.
>>>> I don't have any problems displaying to my mac in my office, using
>>>> 10.5.8 and XQuarts 2.4.0 on an intel mac with nVidia GeForce 7300
>>>> card. They do not have any problem when running VMD on their
>>>> desktop,
>>>> only when displaying back. I suspected GLX at first, it looked
>>>> like
>>>> something was up with glSwapBuffers. To test this, I tried setting
>>>> LD_LIBRARY_PATH on the remote machine so that VMD loads OS Mesa and
>>>> thus does software rendering, but this surprisingly does not
>>>> eliminate
>>>> the flicker.
>>>>
>>>> How to proceed to get more information? I can run in debug mode,
>>>> but
>>>> don't know what to look for. I tried changing graphics settings in
>>>> the menu, but none made any difference.
>>>>
>>>> thanks!
>>>> /* A function that takes a single integer argument and returns
>>>> a pointer to a function that takes two integer arguments and
>>>> returns a floating-point number. */
>>>> float (*func2(int a))(int, int);
>>>> Rich Cook
>>>> rcook_at_llnl.gov
>>>>
>>>>
>>>>
>>>
>>> --
>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>> WWW: http://**www.**ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>>
>>
>>
>> /* A function that takes a single integer argument and returns
>> a pointer to a function that takes two integer arguments and
>> returns a floating-point number. */
>> float (*func2(int a))(int, int);
>> Rich Cook
>> rcook_at_llnl.gov
>>
>>
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://*www.*ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

/* A function that takes a single integer argument and returns
    a pointer to a function that takes two integer arguments and
    returns a floating-point number. */
float (*func2(int a))(int, int);
Rich Cook
rcook_at_llnl.gov