VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 27 2015 - 12:36:31 CST

Nick,
  Thanks for sharing this information, I'm sure that other MacOS X Yosemite
users will be happy to hear about your results after to updating to 10.10.1.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 27, 2015 at 01:19:25PM -0500, Nick Fisher wrote:
> John,
> Updating to OS X 10.10.1 seems to have fixed the crashing I was observing
> with VMD 1.9.2. The program has been behaving normally since the update.
> (There's no mention of graphics driver updates in Apple's patch notes, but
> it seems fine).
> Regards,
> Nick
> ---------------------------------
> Nick Fisher, Ph.D.
> MSU-DOE Plant Research Laboratory
> Michigan State University
> Plant Biology Laboratories
> 612 Wilson Road, S-234
> East Lansing, MI 48824
> United States
>
> email: [1]nefisher_at_msu.edu
> tel: 517-432-0071 (lab)
>
> On 14 Nov 2014, at 16:48, John Stone <[2]johns_at_ks.uiuc.edu> wrote:
> Nick,
> The fact that VMD 1.9.0 works but 1.9.1 and 1.9.2 do not
> may help me narrow down the problem. I'm out of town for the
> next week at a conference, but when I return this issue will be
> high on my TODO list.
>
> Cheers,
> John
>
> On Fri, Nov 14, 2014 at 10:00:29AM -0500, Nick Fisher wrote:
>
> John,
> Thanks for your continued interest in this matter. Weirdly, VMD
> 1.9(.0)
> works fine, so I have been using that. 1.9.1/.2 are still
> problematic.
> Apple haven't issued a software update as far as I'm aware.
> Best,
> Nick
> ---------------------------------
> Nick Fisher, Ph.D.
> MSU-DOE Plant Research Laboratory
> Michigan State University
> Plant Biology Laboratories
> 612 Wilson Road, S-234
> East Lansing, MI 48824
> United States
>
> email: [1][3]nefisher_at_msu.edu
> tel: 517-432-0071 (lab)
>
> On 13 Nov 2014, at 23:49, John Stone <[2][4]johns_at_ks.uiuc.edu>
> wrote:
> Nick,
> I dug through that traceback and it definitely looks like there's
> some unusual issue with the GPU driver on your machine. It goes
> very deep into the OpenGL driver code, from what I saw in the
> trace you sent. I assume that you haven't found any workarounds
> yet
> and that Apple has not yet released any video driver updates for
> your
> system?
>
> Cheers,
> John Stone
> [3][5]vmd_at_ks.uiuc.edu
>
> On Fri, Oct 31, 2014 at 04:18:33PM -0400, Nick Fisher wrote:
>
> Great, thanks. Please find attached.
>
> ---------------------------------
> Nick Fisher, Ph.D.
> MSU-DOE Plant Research Laboratory
> Michigan State University
> Plant Biology Laboratories
> 612 Wilson Road, S-234
> East Lansing, MI 48824
> United States
>
> email: [4][6]nefisher_at_msu.edu
> tel: 517-432-0071 (lab)
>
> On 31 Oct 2014, at 16:10, John Stone <[5][7]johns_at_ks.uiuc.edu>
> wrote:
>
> Sure, send me what you have and I'll take a look.
>
> Cheers,
> John
>
> On Fri, Oct 31, 2014 at 04:02:17PM -0400, Nick Fisher wrote:
>
> Hi John
> I can send you the OS X console log files generated when
> the VMD
> problem
> occurs if that's helpful.
> Nick
>
> On 31 Oct 2014, at 12:22, John Stone
> <[1][6][8]johns_at_ks.uiuc.edu>
> wrote:
> Hi,
> This sounds like a new video driver bug of some kind,
> particularly since your problems started after you
> upgraded to
> Yosemite.
>
> What happens if you try resizing the display window, or
> you
> switch
> mouse focus to a different application and then switch
> back to
> VMD?
>
> Cheers,
> John Stone
> [2][7][9]vmd_at_ks.uiuc.edu
>
> On Fri, Oct 31, 2014 at 11:51:09AM -0400, Nick Fisher
> wrote:
>
> The OpenGL display window of VMD 1.9.1 (non-CUDA) is
> freezing
> immediately
> after loading a set of PDB coordinates in a fresh
> install
> of OS X
> 10.10
>
> Ia**m using a late-2012 Mac Mini (8 Gb RAM, 2.5 GHz
> i5,
> Intel HD
> 4000
> graphics). The spinning VMD logo freezes, and the
> molecule
> is not
> displayed. Herea**s the console log (note that the
> program
> does not
> crash,
> it is just unusable):
>
> Info) VMD for MACOSXX86, version 1.9.1 (February 4,
> 2012)
> Info)
> [1][3][8][10]http://www.ks.uiuc.edu/Research/vmd/
>
> Info) Email questions and bug reports to
> [2][4][9][11]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 HD Graphics 4000 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
> vmd > Info) Using plugin pdb for structure file
> /Applications/Bowman
> bc1
> /1SQP.pdb
> Info) Using plugin pdb for coordinates from file
> /Applications/Bowman bc1
> /1SQP.pdb
> Info) Determining bond structure from distance search
> ...
> Info) Analyzing structure ...
> Info) Atoms: 17274
> Info) Bonds: 17481
> Info) Angles: 0 Dihedrals: 0 Impropers: 0
> Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes:
> 0
> Impropertypes: 0
> Info) Residues: 2329
> Info) Waters: 215
> Warning) Unusual bond between residues: 83 (protein)
> and
> 382 (none)
> Warning) Unusual bond between residues: 37 (protein)
> and
> 243 (none)
> Info) Segments: 1
> Info) Fragments: 236 Protein: 11 Nucleic: 0
> Info) Finished with coordinate file
> /Applications/Bowman
> bc1
> /1SQP.pdb.
>
> References
>
> Visible links
> 1. [5][10][12]http://www.ks.uiuc.edu/Research/vmd/
> 2. [6][11][13]mailto:vmd_at_ks.uiuc.edu
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL
> 61801
> [7][12][14]http://www.ks.uiuc.edu/~johns/
> Phone:
> 217-244-3349
> [8][13][15]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. [14][16]mailto:johns_at_ks.uiuc.edu
> 2. [15][17]mailto:vmd_at_ks.uiuc.edu
> 3. [16][18]http://www.ks.uiuc.edu/Research/vmd/
> 4. [17][19]mailto:vmd_at_ks.uiuc.edu
> 5. [18][20]http://www.ks.uiuc.edu/Research/vmd/
> 6. [19][21]mailto:vmd_at_ks.uiuc.edu
> 7. [20][22]http://www.ks.uiuc.edu/~johns/
> 8. [21][23]http://www.ks.uiuc.edu/Research/vmd/
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [22][24]http://www.ks.uiuc.edu/~johns/ Phone:
> 217-244-3349
> [23][25]http://www.ks.uiuc.edu/Research/vmd/
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [24][26]http://www.ks.uiuc.edu/~johns/ Phone:
> 217-244-3349
> [25][27]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. [28]mailto:nefisher_at_msu.edu
> 2. [29]mailto:johns_at_ks.uiuc.edu
> 3. [30]mailto:vmd_at_ks.uiuc.edu
> 4. [31]mailto:nefisher_at_msu.edu
> 5. [32]mailto:johns_at_ks.uiuc.edu
> 6. [33]mailto:johns_at_ks.uiuc.edu
> 7. [34]mailto:vmd_at_ks.uiuc.edu
> 8. [35]http://www.ks.uiuc.edu/Research/vmd/
> 9. [36]mailto:vmd_at_ks.uiuc.edu
> 10. [37]http://www.ks.uiuc.edu/Research/vmd/
> 11. [38]mailto:vmd_at_ks.uiuc.edu
> 12. [39]http://www.ks.uiuc.edu/~johns/
> 13. [40]http://www.ks.uiuc.edu/Research/vmd/
> 14. [41]mailto:johns_at_ks.uiuc.edu
> 15. [42]mailto:vmd_at_ks.uiuc.edu
> 16. [43]http://www.ks.uiuc.edu/Research/vmd/
> 17. [44]mailto:vmd_at_ks.uiuc.edu
> 18. [45]http://www.ks.uiuc.edu/Research/vmd/
> 19. [46]mailto:vmd_at_ks.uiuc.edu
> 20. [47]http://www.ks.uiuc.edu/~johns/
> 21. [48]http://www.ks.uiuc.edu/Research/vmd/
> 22. [49]http://www.ks.uiuc.edu/~johns/
> 23. [50]http://www.ks.uiuc.edu/Research/vmd/
> 24. [51]http://www.ks.uiuc.edu/~johns/
> 25. [52]http://www.ks.uiuc.edu/Research/vmd/
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [53]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [54]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:nefisher_at_msu.edu
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:nefisher_at_msu.edu
> 4. mailto:johns_at_ks.uiuc.edu
> 5. mailto:vmd_at_ks.uiuc.edu
> 6. mailto:nefisher_at_msu.edu
> 7. mailto:johns_at_ks.uiuc.edu
> 8. mailto:johns_at_ks.uiuc.edu
> 9. mailto:vmd_at_ks.uiuc.edu
> 10. http://www.ks.uiuc.edu/Research/vmd/
> 11. mailto:vmd_at_ks.uiuc.edu
> 12. http://www.ks.uiuc.edu/Research/vmd/
> 13. mailto:vmd_at_ks.uiuc.edu
> 14. http://www.ks.uiuc.edu/~johns/
> 15. http://www.ks.uiuc.edu/Research/vmd/
> 16. mailto:johns_at_ks.uiuc.edu
> 17. mailto:vmd_at_ks.uiuc.edu
> 18. http://www.ks.uiuc.edu/Research/vmd/
> 19. mailto:vmd_at_ks.uiuc.edu
> 20. http://www.ks.uiuc.edu/Research/vmd/
> 21. mailto:vmd_at_ks.uiuc.edu
> 22. http://www.ks.uiuc.edu/~johns/
> 23. http://www.ks.uiuc.edu/Research/vmd/
> 24. http://www.ks.uiuc.edu/~johns/
> 25. http://www.ks.uiuc.edu/Research/vmd/
> 26. http://www.ks.uiuc.edu/~johns/
> 27. http://www.ks.uiuc.edu/Research/vmd/
> 28. mailto:nefisher_at_msu.edu
> 29. mailto:johns_at_ks.uiuc.edu
> 30. mailto:vmd_at_ks.uiuc.edu
> 31. mailto:nefisher_at_msu.edu
> 32. mailto:johns_at_ks.uiuc.edu
> 33. mailto:johns_at_ks.uiuc.edu
> 34. mailto:vmd_at_ks.uiuc.edu
> 35. http://www.ks.uiuc.edu/Research/vmd/
> 36. mailto:vmd_at_ks.uiuc.edu
> 37. http://www.ks.uiuc.edu/Research/vmd/
> 38. mailto:vmd_at_ks.uiuc.edu
> 39. http://www.ks.uiuc.edu/~johns/
> 40. http://www.ks.uiuc.edu/Research/vmd/
> 41. mailto:johns_at_ks.uiuc.edu
> 42. mailto:vmd_at_ks.uiuc.edu
> 43. http://www.ks.uiuc.edu/Research/vmd/
> 44. mailto:vmd_at_ks.uiuc.edu
> 45. http://www.ks.uiuc.edu/Research/vmd/
> 46. mailto:vmd_at_ks.uiuc.edu
> 47. http://www.ks.uiuc.edu/~johns/
> 48. http://www.ks.uiuc.edu/Research/vmd/
> 49. http://www.ks.uiuc.edu/~johns/
> 50. http://www.ks.uiuc.edu/Research/vmd/
> 51. http://www.ks.uiuc.edu/~johns/
> 52. http://www.ks.uiuc.edu/Research/vmd/
> 53. http://www.ks.uiuc.edu/~johns/
> 54. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/