From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 10 2021 - 10:49:16 CDT

Peter,
  The bug was nothing too exciting.
This bug was just one of the million C string handling bugs that can crop up.
As I recall, it was writing a NUL '\0' character past the end of a fixed
size buffer in a safety check that was intended to handle overly-long
strings. The original code was almost right... :-)

Best,
  John

On Mon, May 10, 2021 at 09:14:12AM -0400, Peter Freddolino wrote:
> 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 <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â FYI, I recently tracked down a memory corruption flaw in AutoPSF
> which is
> almost certainly the cause of the problem reported here.Â
>
> 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.Â
>
> 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,
> Â John
>
> On Sun, May 09, 2021 at 08:17:26PM -0400, Peter Freddolino wrote:
> >Â Â Hi Patrick, Could you please let us know what structure you were
> trying to
> >Â Â use autopsf on?
> >Â Â Thanks,
> >Â Â Peter
> >Â Â On Sun, May 9, 2021 at 4:39 PM Patrick Osmer
> <[1][2]posmer_at_gmail.com> wrote:
> >
> >Â Â Â Dear VMD support,
> >
> >Â Â Â IÃ* have recently installed VMD 1.9.4a48-Catalina-Rev7 onto a
> MacBook Pro
> >Â Â Â 16-in running MacOS Catalina 10.15.7. It seemed to be running
> fine until
> >Â Â Â 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
> >Â Â Â known problem?
> >
> >Â Â Â The task has always worked fine for me with VMD 1.9.3, and it
> also
> >Â Â Â 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
> >Â Â Â problem.
> >
> >Â Â Â Ã*
> >
> >   (By the way, pushing the â**full-screenâ** button for the
> OpenGL Display
> >Â Â Â crashes VMD 1.9.4, both on the MacBook Pro and MacBook Air.)
> >
> >Â Â Â Ã*
> >
> >Â Â Â Thanks,
> >
> >Â Â Â Ã*
> >
> >Â Â Â Patrick Osmer
> >
> >Â Â Â Professor Emeritus
> >
> >Â Â Â The Ohio State University
> >
> >Â Â Â [2][3]osmer.1_at_osu.edu
> >
> > References
> >
> >Â Â Visible links
> >Â Â 1. mailto:[4]posmer_at_gmail.com
> >Â Â 2. mailto:[5]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
> [6]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [7]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:posmer_at_gmail.com
> 3. mailto:osmer.1_at_osu.edu
> 4. mailto:posmer_at_gmail.com
> 5. mailto:osmer.1_at_osu.edu
> 6. http://www.ks.uiuc.edu/~johns/
> 7. 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/