VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 21 2017 - 14:38:48 CDT

Ram,
  I am very suspicious about the "Apple Software Renderer" mentioned during
the VMD startup messages you included. Have you run any other OpenGL
apps on this Mac? Do they work properly? I will probably have to ask you
to run a bunch of subsequent tests to help narrow down the problem, but
I'm out of time presently, so I'll have to get back to you with further
questions.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 21, 2017 at 03:32:10PM -0400, Janakiraman Balachandran wrote:
> Sorry,
>
> Just tested it but even 1.9.3 is not working and I get the following
> segmentation error
>
> Info) Multithreading available, 4 CPUs detected.
> Info) OpenGL renderer: Apple Software Renderer
> Info)Â Â Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
> Info)Â Â Full GLSL rendering mode is available.
> Info)Â Â Textures: 2-D (16384x16384), 3-D (16384x16384x16384),
> Multitexture (8)
> /Applications/VMD 1.9.3.app/Contents/MacOS/startup.command: line 7: 12381
> Segmentation fault: 11Â "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> logout
> Saving session...
> ...copying shared history...
> ...saving history...truncating history files...
> ...completed.
>
> Best Regards
> Ram Balachandran
> [1][IMG]Â [2][IMG]
> On Fri, Jul 21, 2017 at 3:20 PM, John Stone <[3]johns_at_ks.uiuc.edu> wrote:
>
> Were you able to run VMD 1.9.3 without trouble on that same machine?
>
> Cheers,
> Â John Stone
> On Fri, Jul 21, 2017 at 03:17:35PM -0400, Janakiraman Balachandran
> wrote:
> >Â Â The graphics card in my machine is Intel HD Graphics 5000 1536
> MB. I'm
> >Â Â trying to install and use it locally,
> >Â Â Best Regards
> >Â Â Ram Balachandran
> >Â Â [1][IMG]Ã* [2][IMG]
> >Â Â On Fri, Jul 21, 2017 at 3:11 PM, John Stone
> <[3][4]johns_at_ks.uiuc.edu> wrote:
> >
> >Â Â Â Thanks, that is very helpful.Ã*Â Next question:Ã*Â What kind
> of graphics
> >Â Â Â hardware
> >Â Â Â is in your Mac?Ã*Â Is it AMD or Intel hardware?Ã*Â I ask
> because I notice
> >Â Â Â that
> >Â Â Â you're getting a very strange "Apple Software Renderer" shown
> as the
> >Â Â Â OpenGL
> >Â Â Â Renderer when you're running VMD.Ã*Â Are you running VMD
> locally, or via
> >Â Â Â some
> >Â Â Â sort of remote desktop?
> >
> >Â Â Â Cheers,
> >Â Â Â Ã*Â John Stone
> >Â Â Â Ã*Â [4][5]vmd_at_ks.uiuc.edu
> >Â Â Â On Fri, Jul 21, 2017 at 03:06:02PM -0400, Janakiraman
> Balachandran
> >Â Â Â wrote:
> >Â Â Â >Ã*Â Ã*Â Hi John,
> >Â Â Â >
> >Â Â Â >Ã*Â Ã*Â I removed the experimental plugin, but I still get
> an error
> >Â Â Â except that
> >Â Â Â >Ã*Â Ã*Â this time it describes 2 Dynamically loaded plugins
> in directory.
> >Â Â Â The full
> >Â Â Â >Ã*Â Ã*Â error message is below
> >Â Â Â >Ã*Â Ã*Â ```
> >Â Â Â >Ã*Â Ã*Â Info) Multithreading available, 4 CPUs detected.
> >Â Â Â >Ã*Â Ã*Â Info) OpenGL renderer: Apple Software Renderer
> >Â Â Â >Ã*Â Ã*Â Info)Ã** Ã**Ã*Â Features: STENCIL MDE MTX NPOT PP
> PS GLSL(OVF)
> >Â Â Â >Ã*Â Ã*Â Info)Ã** Ã**Ã*Â Full GLSL rendering mode is
> available.
> >Â Â Â >Ã*Â Ã*Â Info)Ã** Ã**Ã*Â Textures: 2-D (16384x16384), 3-D
> >Â Â Â (16384x16384x16384),
> >Â Â Â >Ã*Â Ã*Â Multitexture (8)
> >Â Â Â >Ã*Â Ã*Â Info) Dynamically loaded 2 plugins in directory:
> >Â Â Â >Ã*Â Ã*Â Info) /Applications/VMD
> >Â Â Â 1.9.4.app/Contents/vmd/plugins/MACOSXX86/molfile
> >Â Â Â >Ã*Â Ã*Â VMD(11830,0xa2fe3000) malloc: *** error for object
> 0x78e769d4:
> >Â Â Â incorrect
> >Â Â Â >Ã*Â Ã*Â checksum for freed object - object was probably
> modified after
> >Â Â Â being
> >Â Â Â >Ã*Â Ã*Â freed.
> >Â Â Â >Ã*Â Ã*Â *** set a breakpoint in malloc_error_break to debug
> >Â Â Â >Ã*Â Ã*Â /Applications/VMD
> 1.9.4.app/Contents/MacOS/startup.command: line
> >Â Â Â 7: 11830
> >Â Â Â >Ã*Â Ã*Â Abort trap: 6Ã** Ã** Ã** Ã** Ã** Ã** Ã** Ã** Ã**
> Ã**
> >Â Â Â >Ã*Â Ã*Â "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> >Â Â Â >Ã*Â Ã*Â logout
> >Â Â Â >Ã*Â Ã*Â Saving session...
> >Â Â Â >Ã*Â Ã*Â ...copying shared history...
> >Â Â Â >Ã*Â Ã*Â ...saving history...truncating history files...
> >Â Â Â >Ã*Â Ã*Â ...completed.
> >Â Â Â >Ã*Â Ã*Â ```
> >Â Â Â >Ã*Â Ã*Â Best Regards
> >Â Â Â >Ã*Â Ã*Â Ram Balachandran
> >Â Â Â >Ã*Â Ã*Â [1][IMG]Ã** [2][IMG]
> >Â Â Â >Ã*Â Ã*Â On Fri, Jul 21, 2017 at 2:58 PM, John Stone
> >Â Â Â <[3][5][6]johns_at_ks.uiuc.edu> wrote:
> >Â Â Â >
> >Â Â Â >Ã*Â Ã*Â Ã*Â Hi,
> >Â Â Â >Ã*Â Ã*Â Ã*Â Ã**Ã*Â Thanks for your note.Ã**Ã*Â I am
> wondering if this is
> >Â Â Â caused
> >Â Â Â >Ã*Â Ã*Â Ã*Â by an experimental plugin that we added to the
> VMD 1.9.4a7
> >Â Â Â test build.
> >Â Â Â >Ã*Â Ã*Â Ã*Â Try removing this experimental plugin and see
> if the problem
> >Â Â Â goes away
> >Â Â Â >Ã*Â Ã*Â Ã*Â Using a terminal shell, cd to the directory
> that contains your
> >Â Â Â VMD .app
> >Â Â Â >Ã*Â Ã*Â Ã*Â bundle,
> >Â Â Â >Ã*Â Ã*Â Ã*Â and then run this command:
> >Â Â Â >Ã*Â Ã*Â Ã*Â Ã**Ã*Â mv VMD\
> >Â Â Â >Ã*Â Ã*Â Ã*Â
> 1.9.4.app/Contents/vmd/plugins/MACOSXX86/molfile/orcaplugin.so
> >Â Â Â /tmp
> >Â Â Â >
> >Â Â Â >Ã*Â Ã*Â Ã*Â Once you've done that, try restarting VMD and
> let me know if
> >Â Â Â you still
> >Â Â Â >Ã*Â Ã*Â Ã*Â have
> >Â Â Â >Ã*Â Ã*Â Ã*Â the same problem or not.
> >Â Â Â >
> >Â Â Â >Ã*Â Ã*Â Ã*Â Best regards,
> >Â Â Â >Ã*Â Ã*Â Ã*Â Ã**Ã*Â John Stone
> >Â Â Â >Ã*Â Ã*Â Ã*Â Ã**Ã*Â [4][6][7]vmd_at_ks.uiuc.edu
> >Â Â Â >
> >Â Â Â >Ã*Â Ã*Â Ã*Â On Fri, Jul 21, 2017 at 02:14:22PM -0400,
> Janakiraman
> >Â Â Â Balachandran
> >Â Â Â >Ã*Â Ã*Â Ã*Â wrote:
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Hi,
> >Â Â Â >Ã*Â Ã*Â Ã*Â >
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â I installed VMD 1.9.4 in Mac
> OSX (10.11.6). BUt
> >Â Â Â when I try to
> >Â Â Â >Ã*Â Ã*Â Ã*Â open, the
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â application fails to open
> with the following error
> >Â Â Â >Ã*Â Ã*Â Ã*Â >
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Info) Multithreading
> available, 4 CPUs detected.
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Info) OpenGL renderer: Apple
> Software Renderer
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Info)Ã*** Ã***Ã**Ã*Â
> Features: STENCIL MDE MTX NPOT PP
> >Â Â Â PS GLSL(OVF)
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Info)Ã*** Ã***Ã**Ã*Â Full
> GLSL rendering mode is
> >Â Â Â available.
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Info)Ã*** Ã***Ã**Ã*Â
> Textures: 2-D (16384x16384), 3-D
> >Â Â Â >Ã*Â Ã*Â Ã*Â (16384x16384x16384),
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Multitexture (8)
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Info) Dynamically loaded 3
> plugins in directory:
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Info) /Applications/VMD
> >Â Â Â >Ã*Â Ã*Â Ã*Â
> 1.9.4.app/Contents/vmd/plugins/MACOSXX86/molfile
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â VMD(10946,0xa2fe3000) malloc:
> *** error for object
> >Â Â Â 0x7d0263a4:
> >Â Â Â >Ã*Â Ã*Â Ã*Â incorrect
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â checksum for freed object -
> object was probably
> >Â Â Â modified after
> >Â Â Â >Ã*Â Ã*Â Ã*Â being
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â freed.
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â *** set a breakpoint in
> malloc_error_break to debug
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â /Applications/VMD
> >Â Â Â 1.9.4.app/Contents/MacOS/startup.command: line
> >Â Â Â >Ã*Â Ã*Â Ã*Â 7: 10946
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Abort trap: 6Ã*** Ã*** Ã***
> Ã*** Ã*** Ã*** Ã*** Ã*** Ã***
> >Â Â Â Ã***
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â
> "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â logout
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Saving session...
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â ...copying shared history...
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â ...saving
> history...truncating history files...
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â ...completed.
> >Â Â Â >Ã*Â Ã*Â Ã*Â >
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Best Regards
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Ram Balachandran
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â [1][IMG]Ã*** [2][IMG]
> >Â Â Â >Ã*Â Ã*Â Ã*Â >
> >Â Â Â >Ã*Â Ã*Â Ã*Â > References
> >Â Â Â >Ã*Â Ã*Â Ã*Â >
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â Visible links
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â 1.
> [5][7][8]http://www.linkedin.com/in/rambalachandran
> >Â Â Â >Ã*Â Ã*Â Ã*Â >Ã**Ã*Â Ã**Ã*Â 2.
> [6][8][9]https://twitter.com/RamBalachandran
> >Â Â Â >Ã*Â Ã*Â Ã*Â --
> >Â Â Â >Ã*Â Ã*Â Ã*Â NIH Center for Macromolecular Modeling and
> Bioinformatics
> >Â Â Â >Ã*Â Ã*Â Ã*Â Beckman Institute for Advanced Science and
> Technology
> >Â Â Â >Ã*Â Ã*Â Ã*Â University of Illinois, 405 N. Mathews Ave,
> Urbana, IL 61801
> >Â Â Â >Ã*Â Ã*Â Ã*Â
> [7][9][10]http://www.ks.uiuc.edu/~johns/Ã**Ã*Â Ã**Ã*Â Ã**Ã*Â Ã**Ã*Â
> Ã**Ã*
> >Â Â Â Ã** Phone: [8]217-244-3349
> >Â Â Â >Ã*Â Ã*Â Ã*Â
> [9][10][11]http://www.ks.uiuc.edu/Research/vmd/
> >Â Â Â >
> >Â Â Â > References
> >Â Â Â >
> >Â Â Â >Ã*Â Ã*Â Visible links
> >Â Â Â >Ã*Â Ã*Â 1.
> [11][12]http://www.linkedin.com/in/rambalachandran
> >Â Â Â >Ã*Â Ã*Â 2. [12][13]https://twitter.com/RamBalachandran
> >Â Â Â >Ã*Â Ã*Â 3. mailto:[13][14]johns_at_ks.uiuc.edu
> >Â Â Â >Ã*Â Ã*Â 4. mailto:[14][15]vmd_at_ks.uiuc.edu
> >Â Â Â >Ã*Â Ã*Â 5.
> [15][16]http://www.linkedin.com/in/rambalachandran
> >Â Â Â >Ã*Â Ã*Â 6. [16][17]https://twitter.com/RamBalachandran
> >Â Â Â >Ã*Â Ã*Â 7. [17][18]http://www.ks.uiuc.edu/~johns/
> >Â Â Â >Ã*Â Ã*Â 8. file:///tmp/tel:[18]217-244-3349
> >Â Â Â >Ã*Â Ã*Â 9. [19][19]http://www.ks.uiuc.edu/Research/vmd/
> >Â Â Â --
> >Â Â Â NIH Center for Macromolecular Modeling and Bioinformatics
> >Â Â Â Beckman Institute for Advanced Science and Technology
> >Â Â Â University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Â Â Â [20][20]http://www.ks.uiuc.edu/~johns/Ã*Â Ã*Â Ã*Â Ã*Â Ã*Â
> Ã* Phone:
> >Â Â Â [21]217-244-3349
> >Â Â Â [22][21]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> >Â Â Visible links
> >Â Â 1. [22]http://www.linkedin.com/in/rambalachandran
> >Â Â 2. [23]https://twitter.com/RamBalachandran
> >Â Â 3. mailto:[24]johns_at_ks.uiuc.edu
> >Â Â 4. mailto:[25]vmd_at_ks.uiuc.edu
> >Â Â 5. mailto:[26]johns_at_ks.uiuc.edu
> >Â Â 6. mailto:[27]vmd_at_ks.uiuc.edu
> >Â Â 7. [28]http://www.linkedin.com/in/rambalachandran
> >Â Â 8. [29]https://twitter.com/RamBalachandran
> >Â Â 9. [30]http://www.ks.uiuc.edu/~johns/%C3%82
> >Â Â 10. [31]http://www.ks.uiuc.edu/Research/vmd/
> >Â Â 11. [32]http://www.linkedin.com/in/rambalachandran
> >Â Â 12. [33]https://twitter.com/RamBalachandran
> >Â Â 13. mailto:[34]johns_at_ks.uiuc.edu
> >Â Â 14. mailto:[35]vmd_at_ks.uiuc.edu
> >Â Â 15. [36]http://www.linkedin.com/in/rambalachandran
> >Â Â 16. [37]https://twitter.com/RamBalachandran
> >Â Â 17. [38]http://www.ks.uiuc.edu/~johns/
> >Â Â 18. file:///tmp/tel:[39]217-244-3349
> >Â Â 19. [40]http://www.ks.uiuc.edu/Research/vmd/
> >Â Â 20. [41]http://www.ks.uiuc.edu/~johns/
> >Â Â 21. file:///tmp/tel:[42]217-244-3349
> >Â Â 22. [43]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
> [44]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone:
> [45]217-244-3349
> [46]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://www.linkedin.com/in/rambalachandran
> 2. https://twitter.com/RamBalachandran
> 3. mailto:johns_at_ks.uiuc.edu
> 4. mailto:johns_at_ks.uiuc.edu
> 5. mailto:vmd_at_ks.uiuc.edu
> 6. mailto:johns_at_ks.uiuc.edu
> 7. mailto:vmd_at_ks.uiuc.edu
> 8. http://www.linkedin.com/in/rambalachandran
> 9. https://twitter.com/RamBalachandran
> 10. http://www.ks.uiuc.edu/~johns/%C3%83*%C3%82
> 11. http://www.ks.uiuc.edu/Research/vmd/
> 12. http://www.linkedin.com/in/rambalachandran
> 13. https://twitter.com/RamBalachandran
> 14. mailto:johns_at_ks.uiuc.edu
> 15. mailto:vmd_at_ks.uiuc.edu
> 16. http://www.linkedin.com/in/rambalachandran
> 17. https://twitter.com/RamBalachandran
> 18. http://www.ks.uiuc.edu/~johns/
> 19. http://www.ks.uiuc.edu/Research/vmd/
> 20. http://www.ks.uiuc.edu/~johns/%C3%82
> 21. http://www.ks.uiuc.edu/Research/vmd/
> 22. http://www.linkedin.com/in/rambalachandran
> 23. https://twitter.com/RamBalachandran
> 24. mailto:johns_at_ks.uiuc.edu
> 25. mailto:vmd_at_ks.uiuc.edu
> 26. mailto:johns_at_ks.uiuc.edu
> 27. mailto:vmd_at_ks.uiuc.edu
> 28. http://www.linkedin.com/in/rambalachandran
> 29. https://twitter.com/RamBalachandran
> 30. http://www.ks.uiuc.edu/~johns/%C3%82
> 31. http://www.ks.uiuc.edu/Research/vmd/
> 32. http://www.linkedin.com/in/rambalachandran
> 33. https://twitter.com/RamBalachandran
> 34. mailto:johns_at_ks.uiuc.edu
> 35. mailto:vmd_at_ks.uiuc.edu
> 36. http://www.linkedin.com/in/rambalachandran
> 37. https://twitter.com/RamBalachandran
> 38. http://www.ks.uiuc.edu/~johns/
> 39. file:///tmp/tel:217-244-3349
> 40. http://www.ks.uiuc.edu/Research/vmd/
> 41. http://www.ks.uiuc.edu/~johns/
> 42. file:///tmp/tel:217-244-3349
> 43. http://www.ks.uiuc.edu/Research/vmd/
> 44. http://www.ks.uiuc.edu/~johns/
> 45. file:///tmp/tel:217-244-3349
> 46. 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/