VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon May 10 2021 - 08:14:12 CDT

Got it; thanks John for finding this and letting us know. I'll definitely
have a look at the diff, curious about the issue.

Patrick, if the problem persists after John posts the new build, please
notify us.
Thanks,
Peter

On Mon, May 10, 2021 at 2:01 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> FYI, I recently tracked down a memory corruption flaw in AutoPSF which
> is
> almost certainly the cause of the problem reported here.
>
> The flaw had been in the AutoPSF code since it was originally written,
> but it started creating the kind of hanging behavior reported here,
> and crashing in other cases, particularly with the new revs of MacOS
> and certin versions of Ubuntu Linux.
>
> I'm currently tracking down an unrelated but similar type of bug in the
> psfgen plugin, and after I've got that resolved, I plan
> to post new VMD builds for all platforms.
>
> Best,
> John
>
>
> On Sun, May 09, 2021 at 08:17:26PM -0400, Peter Freddolino wrote:
> > Hi Patrick, Could you please let us know what structure you were
> trying to
> > use autopsf on?
> > Thanks,
> > Peter
> > On Sun, May 9, 2021 at 4:39 PM Patrick Osmer <[1]posmer_at_gmail.com>
> wrote:
> >
> > Dear VMD support,
> >
> > IÂ have recently installed VMD 1.9.4a48-Catalina-Rev7 onto a
> MacBook Pro
> > 16-in running MacOS Catalina 10.15.7. It seemed to be running fine
> until
> > I tried to use the Automatic PSF Builder, which failed to complete
> the
> > â**Iâ**m feeling luckyâ** task and left VMD non-responsive. Is this
> a
> > known problem?
> >
> > The task has always worked fine for me with VMD 1.9.3, and it also
> > worked on a MacBook Air running VMD 1.9.4a51-arm64.Rev9 on macOS
> Big Sur
> > 11.2.3. Iâ**ll appreciate any help or suggestions for fixing the
> > problem.
> >
> > Â
> >
> > (By the way, pushing the â**full-screenâ** button for the OpenGL
> Display
> > crashes VMD 1.9.4, both on the MacBook Pro and MacBook Air.)
> >
> > Â
> >
> > Thanks,
> >
> > Â
> >
> > Patrick Osmer
> >
> > Professor Emeritus
> >
> > The Ohio State University
> >
> > [2]osmer.1_at_osu.edu
> >
> > References
> >
> > Visible links
> > 1. mailto:posmer_at_gmail.com
> > 2. mailto:osmer.1_at_osu.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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>