VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon May 10 2021 - 11:03:17 CDT

Hah oops -- cool, thanks!

On Mon, May 10, 2021 at 11:49 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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,
> > ย FYI, I recently tracked down a memory corruption flaw in AutoPSF
> > which is
> > almost certainly the cause of the problem reported here.ย
> >
> > 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.ย
> >
> > 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,
> > ย John
> >
> > On Sun, May 09, 2021 at 08:17:26PM -0400, Peter Freddolino wrote:
> > >ย ย Hi Patrick, Could you please let us know what structure you
> were
> > trying to
> > >ย ย use autopsf on?
> > >ย ย Thanks,
> > >ย ย Peter
> > >ย ย On Sun, May 9, 2021 at 4:39 PM Patrick Osmer
> > <[1][2]posmer_at_gmail.com> wrote:
> > >
> > >ย ย ย Dear VMD support,
> > >
> > >ย ย ย Iร* have recently installed VMD 1.9.4a48-Catalina-Rev7
> onto a
> > MacBook Pro
> > >ย ย ย 16-in running MacOS Catalina 10.15.7. It seemed to be
> running
> > fine until
> > >ย ย ย I tried to use the Automatic PSF Builder, which failed to
> > complete the
> > >ย ย ย รข**Iรข**m feeling luckyรข** task and left VMD
> non-responsive.
> > Is this a
> > >ย ย ย known problem?
> > >
> > >ย ย ย The task has always worked fine for me with VMD 1.9.3,
> and it
> > also
> > >ย ย ย worked on a MacBook Air running VMD 1.9.4a51-arm64.Rev9 on
> > macOS Big Sur
> > >ย ย ย 11.2.3. Iรข**ll appreciate any help or suggestions for
> fixing
> > the
> > >ย ย ย problem.
> > >
> > >ย ย ย ร*
> > >
> > >ย ย ย (By the way, pushing the รข**full-screenรข** button for
> the
> > OpenGL Display
> > >ย ย ย crashes VMD 1.9.4, both on the MacBook Pro and MacBook
> Air.)
> > >
> > >ย ย ย ร*
> > >
> > >ย ย ย Thanks,
> > >
> > >ย ย ย ร*
> > >
> > >ย ย ย Patrick Osmer
> > >
> > >ย ย ย Professor Emeritus
> > >
> > >ย ย ย The Ohio State University
> > >
> > >ย ย ย [2][3]osmer.1_at_osu.edu
> > >
> > > References
> > >
> > >ย ย Visible links
> > >ย ย 1. mailto:[4]posmer_at_gmail.com
> > >ย ย 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/ย ย ย ย ย ย Phone:
> 217-244-3349
> > [7]http://www.ks.uiuc.edu/Research/vmd/ย ย ย
> >
> > 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/
>