VMD-L Mailing List

From: theblueone_at_web.de
Date: Fri Feb 23 2018 - 07:23:58 CST

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@ks.uiuc.edu>
An: theblueone@web.de
Cc: vmd-l@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@ks.uiuc.edu

On Wed, Feb 21, 2018 at 09:27:47AM +0100, theblueone@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]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@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]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd@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" $*
> logout
> Saving session...
> ..copying shared history...
> ..saving history...truncating history files...
> ..completed.
> [Process completed]
>
> ines@xxx:~# /Applications/VMD\ 1.9.3.app/Contents/MacOS/startup.command ;
> exit;
> Info) VMD for MACOSXX86, version 1.9.3 (November 30, 2016)
> Info) [3]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd@ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) OpenGL renderer: Apple Software Renderer
> Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (16384x16384x16384), Multitexture
> (8)
> /Applications/VMD 1.9.3.app/Contents/MacOS/startup.command: line 7: 25128
> Bus error: 10 "$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. 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/

--
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/