VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 25 2009 - 10:34:02 CDT

Hi,
  It's not a memory issue (we have it on our macs here too).
This is some kind of GUI event handling problem either in Tcl/Tk, or in FLTK.
I haven't tracked down which library is at fault yet, but my guess
is that is an FLTK problem. I will be upgrading the next version of
VMD to the latest FLTK, and hopefully this will cure the problem.
If not, then I'll have to dig into it further.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 25, 2009 at 05:49:10AM +0300, Joshua D. Moore wrote:
> VMD 1.8.7 also hangs for me sometimes on Mac OSX 10.5.8. I thought it
> might be a memory issue, even with my 4 GB of memory on 2.0 GHz Core 2
> Duo.
> Josh
> ------------------------------------------------
> Joshua D. Moore
> Graduate Student
> North Carolina State University
> Dept. of Chemical and Biomolecular Engineering
> Box 7905 Centennial Campus
> Engineering Building I
> 911 Partners Way
> Raleigh, NC 27695-7905
> Phone: (919) 513-2051
> Fax: (919) 513-2470
> Email: jdmoore_at_unity.ncsu.edu
> ------------------------------------------------
>
> On Tue, Aug 25, 2009 at 2:24 AM, Carolyn Phillips <phillicl_at_umich.edu>
> wrote:
>
> That works! I will alias to that in my bashrc file.
>
> Thanks for the help John.
> Carolyn
>
> On Aug 24, 2009, at 4:42 PM, John Stone wrote:
>
> Carolyn,
> Can you try running it like this and let me know if that works for
> you?:
> /Applications/VMD 1.8.7.app/Contents/MacOS/startup.command
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Aug 24, 2009 at 12:33:04PM -0400, Carolyn Phillips wrote:
>
> Hi John,
>
> To date it has happened every time.
>
> Here are some observations. The hanging occurs whether I load a
> molecule file or not. The hanging is associated with the GUI and
> not
> with the command line, which I can still use to exit out of the
> program.
>
> If I changed to the directory "/Applications/VMD\
> 1.8.7.app/Contents/
> vmd/" and then run it with "./vmd_MACOSXX86" I get precisely the
> same
> behavior.
>
> I can get VMD 1.8.7 to work successfully by using the Launcher
> instead, but then I have use the GUI browser to open my files, and
> can't just open them straight from the command line.
>
> -Carolyn
>
> On Aug 23, 2009, at 10:32 PM, John Stone wrote:
>
> Hi Carolyn,
> Does this occur repeatably, every single time, or is it
> intermittent?
> (I have no mac to test on at home)
>
> I didn't change anything Mac-specific in the VMD startup code for
> VMD 1.8.7, but there seem to be a few intermittent GUI event
> handling
> issues associated with Tcl/Tk 8.5.6 that have cropped up that
> affect
> VMD. I'm wondering if this is one of those, or if it's something
> entirely different.
>
> Do you get the same behavior if you change your working directory
> to "/Applications/VMD\ 1.8.7.app/Contents/vmd/" and then run it
> with
> ./vmd_MACOSXX86 or does it behave in the same way? (I'm wondering
> about shared library dependencies being an issue...)
>
> Run those tests and let me know what you find. Depending on the
> results, I may have ideas for workarounds for you.
>
> Cheers,
> John Stone
> johns_at_ks.uiuc.edu
>
> On Sun, Aug 23, 2009 at 04:13:40PM -0400, Carolyn Phillips wrote:
>
> Hello, I am using a Mac OSX 10.5.8 and just downloaded the
> newest
> version of VMD 1.8.7.
>
> With VMD 1.8.6, I could use vmd from my command line in terminal
> by
> simply typing
>
> /Applications/VMD\ 1.8.6.app/Contents/vmd/vmd_MACOSXX86
> MyFiles.mol2
>
> But the same line using VMD 1.8.7 (i.e.
>
> /Applications/VMD\ 1.8.7.app/Contents/vmd/vmd_MACOSXX86
> MyFiles.mol2
>
> )
>
> successfully opens the file but then VMD hangs... (i.e. mac's
> spinning
> pinwheel of death.)
>
> How can I recover command-line use of VMD 1.8.7 on a Mac?
>
> Thanks,
> Carolyn Phillips
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078