VMD-L Mailing List

From: Davide Mercadante (dmer018_at_aucklanduni.ac.nz)
Date: Thu Sep 04 2014 - 17:32:21 CDT

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/