From: Benjamin Bouvier (benjamin.bouvier_at_ibcp.fr)
Date: Fri Jun 12 2009 - 11:33:47 CDT

> So, my opinion is that it looks to me like the new version of
> MacOS X has a buggy X11 server (or video driver), and that we will
> need to file a bug with Apple on this.

Thanks John. I suspected as much -- lots of complaints have popped up on
the web about things that this new X11 server has broken.
Hopefully an update from http://xquartz.macosforge.org/trac/wiki/Releases
will eventually fix the problem. Until then, I would advise people to
stick to 10.5.6, as there is no going back :-(
Cheers, B.

>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 12, 2009 at 05:45:37PM +0200, Benjamin Bouvier wrote:
>> John,
>>
>> Here is the log. It appears to be more related to the Linux machine
>> actually running VMD than to the Macbook doing the displaying, though...
>>
>> Info) VMD for LINUXAMD64, version 1.8.7beta5 (June 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, 4 CPUs detected.
>> Info) Free system memory: 7302MB (94%)
>> 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 X1600 OpenGL Engine
>> Info) Features: STENCIL STEREO MSAA(6) MDE MTX NPOT PP PS
>> Info) GLSL rendering mode is NOT available.
>> Info) Textures: 2-D (4096x4096), Multitexture (8)
>> vmd >
>>
>> On Fri, 12 Jun 2009 17:36:49 +0200, John Stone <johns_at_ks.uiuc.edu>
>> wrote:
>>
>> >
>> >Benjamin,
>> > If you run one of the recent VMD 1.8.7 beta versions, the console
>> >output will occur in whatever terminal you started VMD from. So this
>> >would be on your original ssh/xterm session, etc. Check there.
>> >
>> >Cheers,
>> > John
>> >
>> >On Fri, Jun 12, 2009 at 05:28:17PM +0200, Benjamin Bouvier wrote:
>> >>Hi John,
>> >>
>> >>When I tried to find the VMD console to check the startup log, I was
>> >>unable to find it, though it is listed as opened by the X11 server. It
>> >>seems that *somehow* the console opens inside the OpenGL window, hence
>> >>the
>> >>flashing -- what I had described as white frames in my previous posts
>> >>seem
>> >>in fact to contain garbled text (it varies upon dragging the window
>> >>around), which is reminiscent of the console window...
>> >>
>> >>Is there a startup switch to log the console output to some file? If
>> >>so, I
>> >>could retrieve the startup message there. I looked quickly in the
>> manual
>> >>but could not find one...
>> >>
>> >>Cheers,
>> >>Benjamin
>> >>
>> >>On Fri, 12 Jun 2009 17:02:33 +0200, John Stone <johns_at_ks.uiuc.edu>
>> >>wrote:
>> >>
>> >>>
>> >>>Benjamin,
>> >>> Can you send me the VMD startup messages you get when you
>> >>>display on the remote machine? The description you're giving
>> >>>sounds like they've somehow created a new bug/problem with
>> >>>OpenGL double buffering. I don't recall if glxgears is using
>> >>>double buffering or not, so the lack of trouble there may
>> >>>not be indicative of anything. If you send me the VMD startup
>> >>>messages, it will tell me more about what features their X11
>> >>>server implementation is advertising to the client Linux system,
>> >>>and with this we may be able to narrow down the source of the
>> problem.
>> >>>
>> >>>CHeers,
>> >>> John Stone
>> >>> vmd_at_ks.uiuc.edu
>> >>>
>> >>>On Fri, Jun 12, 2009 at 04:48:29PM +0200, Benjamin Bouvier wrote:
>> >>>>Hi all,
>> >>>>
>> >>>>I usually run VMD on a remote Linux machine (cluster frontend) and
>> use
>> >>>>MacOs's X11 implementation to forward the display to my MacBook Pro.
>> >>>>This
>> >>>>used to work fine.
>> >>>>
>> >>>>No so since I upgraded MacOS from 10.5.6 to the latest 10.5.7. The
>> >>>>contents of the VMD OpenGL window flash very quickly (one frame is
>> >>>>white,
>> >>>>the second one is the actual VMD rendering), making VMD unusable.
>> This
>> >>>>occurs with VMD 1.8.6 and 1.8.7, both 32 and 64 bits.
>> >>>>
>> >>>>I read that Apple had done modifications to X11 in 10.5.7. However,
>> >>the
>> >>>>problem seems limited to VMD : glxgears for instance is forwarded
>> OK,
>> >>as
>> >>>>are all non-openGL windows (including the VMD Main window).
>> >>>>
>> >>>>Are there any other users experiencing this ? Is there a simple
>> cure ?
>> >>>>
>> >>>>Thanks,
>> >>>>--
>> >>>>Benjamin Bouvier
>> >>>
>> >
>>
>>
>>