VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 23 2018 - 10:07:37 CST

At present I don't have a specific suggestion for you, but having additional
information is helpful. If someone else encounters the same type
of problem we may glean for facts and end up coming up with a solution or
workaround as more people update their older Macs to El Capitan.

Best,
  John

On Fri, Feb 23, 2018 at 02:23:58PM +0100, theblueone_at_web.de wrote:
> Hi John,
>
> thanks for your fast reply! Unfortunately, I do not remember if and under
> which conditions VMD was running
> on this particular macbook. I was in parallel working on a linux system
> and it could be that I used VMD only
> there. The problem is that I had a break of a couple of months working on
> my dissertation...
> It could also be that VMD was running on my macbook when I still had
> Yosemite installed. But
> downgrading is not an option for me due to other dependencies.
>
> Do you have any other suggestion or specific information that I could
> provide?
>
> Best,
> Ines
>
> Gesendet: Freitag, 23. Februar 2018 um 00:16 Uhr
> Von: "John Stone" <johns_at_ks.uiuc.edu>
> An: theblueone_at_web.de
> Cc: vmd-l_at_ks.uiuc.edu
> Betreff: Re: vmd-l: VMD crashes on Macbook with Intel Graphics
> Hi,
> I assume that this machine worked with VMD previously at some point right?
> My read on the symptoms you describe is that it's a video driver issue,
> since there are others running the same versions of both MacOS and
> the VMD software that haven't reported this problem yet. That being said,
> let me know if you have any other insights or information to add about
> the history of how well this machine worked with VMD, etc.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Feb 21, 2018 at 09:27:47AM +0100, theblueone_at_web.de wrote:
> > Dear all,
> >
> > I have trouble to run VMD on my Macbook Pro Retina 13 from late 2013.
> When
> > I start VMD it immediately crashes with the error messages below (tested
> > VMD 1.9.4 and VMD 1.9.3).
> >
> > My hardware is:
> > MacBook Pro (Retina, 13-inch, Late 2013) with Intel Iris 1536 MB
> Graphics
> > running OS X El Capitan Version 10.11.6.
> >
> > I tried different VMD versions but without success. I also search the
> > mailing list for crashes on Macs and tried all suggestions without luck.
> > In one thread, John Stone wondered about the detected Apple Software
> > Renderer
> >
> ([1][1]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28740.html).
> >
> > I would greatly appreciate any help in order to get VMD running on my
> > machine because I am in the final phase of my dissertation and need VMD
> to
> > render some molecule images.
> >
> > Thanks a lot in advance!
> >
> > Best,
> > Ines
> >
> > ines_at_xxx:~# /Applications/VMD\ 1.9.4.app/Contents/MacOS/startup.command
> ;
> > exit;
> > Info) VMD for MACOSXX86, version 1.9.4a12 (December 21, 2017)
> > Info) [2][2]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: Apple Software Renderer
> > Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
> > Info) Full GLSL rendering mode is available.
> > Info) Textures: 2-D (16384x16384), 3-D (16384x16384x16384), Multitexture
> > (8)
> > VMD(23594,0xa38ba000) malloc: *** error for object 0x7af7caa4: incorrect
> > checksum for freed object - object was probably modified after being
> > freed.
> > *** set a breakpoint in malloc_error_break to debug
> > /Applications/VMD 1.9.4.app/Contents/MacOS/startup.command: line 7:
> 23594
> > Abort trap: 6 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> > logout
> > Saving session...
> > ..copying shared history...
> > ..saving history...truncating history files...
> > ..completed.
> > [Process completed]
> >
> > ines_at_xxx:~# /Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command
> ;
> > exit;
> > Info) VMD for MACOSXX86, version 1.9.3 (November 30, 2016)
> > Info) [3][3]http://www.ks.uiuc.edu/Research/vmd/
> > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > Info) Please include this reference in published work using VMD:
> > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > Info) -------------------------------------------------------------
> > Info) Multithreading available, 4 CPUs detected.
> > Info) OpenGL renderer: Apple Software Renderer
> > Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
> > Info) Full GLSL rendering mode is available.
> > Info) Textures: 2-D (16384x16384), 3-D (16384x16384x16384), Multitexture
> > (8)
> > /Applications/VMD 1.9.3.app/Contents/MacOS/startup.command: line 7:
> 25128
> > Bus error: 10 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> > logout
> > Saving session...
> > ..copying shared history...
> > ..saving history...truncating history files...
> > ..completed.
> > [Process completed]
> >
> > References
> >
> > Visible links
> > 1. [4]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28740.html
> > 2. [5]http://www.ks.uiuc.edu/Research/vmd/
> > 3. [6]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
> [7]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [8]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28740.html
> 2. http://www.ks.uiuc.edu/Research/vmd/
> 3. http://www.ks.uiuc.edu/Research/vmd/
> 4. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28740.html
> 5. http://www.ks.uiuc.edu/Research/vmd/
> 6. http://www.ks.uiuc.edu/Research/vmd/
> 7. http://www.ks.uiuc.edu/~johns/
> 8. 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/