VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 05 2014 - 10:05:28 CDT

Davide,
  It's almost certain that things in the display system have changed
from Mavericks to Yosemite. In particular, Apple itself has indicated
that the main user interfaces have all been redesigned, and they have
added translucency to all of the toolbars, etc, all of which requires
accelerated rendering support from the underlying video drivers.

Apple provides the beta versions of Yosemite knowing full well that
users are going to encounter problems, it is implicitly
understood that it is not a finished product yet...

I note that others have experienced a variety of issues with Yosemite
beta versions, so it should be no surprise that you're seeing them too:
  http://www.cultofmac.com/282560/os-x-yosemite-nightmare/
  http://www.macworld.com/article/2456613/os-x-yosemite-public-beta-what-you-need-to-know.html

I think that the best thing that can be done is to report the problems
that you observe to Apple so they are in Apple's bug tracking system
and they get fixed before Yosemite is finalized.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 05, 2014 at 12:32:21AM +0200, Davide Mercadante wrote:
> Dear John and Axel,
>
> many thanks for your replies. I have filed a bug report to Apple to let
> them know. I am not sure what or when they are going to reply but I will
> keep the vmd-list informed.
>
> John, as far as I understand, nothing in the OpenGL drivers changed in
> the latest OS release. Maybe something else is screwing up visualization
> when VMD access the Finder window. I hope that the problem will be
> solved soon, otherwise there is no other options than switching back to
> the older OS or changing visualization software.
>
> Interestingly, VMD seems to be working totally fine and there is no
> warning/error message in the terminal. This is an example of when I load
> a molecule and the OpenGL window freezes.
>
> ######
>
> Info) VMD for MACOSXX86, version 1.9.1 (February 4, 2012)
> 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) OpenGL renderer: Intel Iris OpenGL Engine
> Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /Applications/VMD 1.9.1.app/Contents/vmd/plugins/MACOSXX86/molfile
> Info) File loading in progress, please wait.
> Info) Using plugin pdb for structure file XXX.pdb
> Info) Using plugin pdb for coordinates from file XXX.pdb
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file XXX.pdb.
> Info) Analyzing structure ...
> Info) Atoms: 2384
> Info) Bonds: 2441
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 307
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1 Protein: 1 Nucleic: 0
>
>
> #####
>
> I am not sure this is of great help. My hardware information are:
> MacBook Retina late 2013 - Graphics: Intel Iris 1536 Mb. OS: Yosemite
> 10.10 - 2nd beta release.
>
> If there is any updates on your side about this please let me know.
>
> Thank you in advance.
>
> Cheers,
> Davide
>
>
> On 4/09/14 4:53 pm, John Stone wrote:
> >Davide,
> > As Axel has mentioned, this your systems seem to indicate a problem with
> >the new MacOS X Yosemite OpenGL implementation, as compared with prior
> >versions of MacOS X. Apple has a history of having OpenGL bugs in new
> >OS releases, and I imagine this is similar to past instances. Can you
> >copy the VMD startup text messages into an email and send them? While
> >we probably can't do anything about the OpenGL driver issues it sounds
> >like you're encountering, it would be useful to know which graphics
> >chipset or GPU you're using, in case other people run into the same
> >problem.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Thu, Sep 04, 2014 at 02:08:57PM +0200, Davide Mercadante wrote:
> >> Hello everyone,
> >>
> >> as an update of my latest report (see forwarded) I was not able to
> >> solve
> >> it by uninstalling quicklook. It's not that the problem that must come
> >> from either OpenGL or VMD on the latest MacOS.
> >>
> >> After running several tests I noticed that the OpenGL window freezes
> >> when
> >> VMD opens a window from the OS. For example, it freezes when I open
> >> windows that would browse through my files (Finder window). For
> >> example:
> >>
> >> * Load new molecule or add data into a molecule
> >> * Load visualization state
> >> * Save file/image/state etc...
> >>
> >> As soon as the Finder window is open, the OpenGL display freezes.
> >> Is there any possibility to look into this issue as soon as possible?
> >> I
> >> cannot work on VMD anymore...
> >>
> >> Thank you.
> >>
> >> Cheers,
> >> Davide
> >>
> >> On 3/09/14 9:37 pm, Davide Mercadante wrote:
> >>
> >> Hello,
> >>
> >> I am encountering the following issue using VMD after updating my OS
> >> with a (beta) version of Yosemite, the newest OS of Mac. The OpenGL
> >> windows randomly freezes and I get this messages in the terminal:
> >>
> >> vmd[5984:194283] [QL]
> >> [1]file://localhost/Library/QuickLook/GBQLGenerator.qlgenerator/
> >> has no
> >> identifier: ignoring
> >> vmd[5984:194283] [QL]
> >> [2]file://localhost/Library/QuickLook/SogouSkinPreviewer.qlgenerator/
> >> has no identifier: ignoring
> >>
> >> After this happens there is no other way of using it than killing
> >> it and
> >> start again. This happens randomly, sometimes just opening another
> >> window from the VMD menu, or loading another molecule, etc... All
> >> the
> >> windows still work, open and close, but the molecule in the OpenGL
> >> windows just doesn't move, cannot be rotated or translated. I am not
> >> sure if this is related to the newest OS, however, this wasn't
> >> happening
> >> before.
> >>
> >> I would be grateful if you would give me hints on how to solve this.
> >>
> >> Thank you.
> >>
> >> Cheers,
> >> Davide
> >>
> >>References
> >>
> >> Visible links
> >> 1. file://localhost/Library/QuickLook/GBQLGenerator.qlgenerator/
> >> 2. file://localhost/Library/QuickLook/SogouSkinPreviewer.qlgenerator/ 

-- 
NIH Center 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/