VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 09 2010 - 08:24:14 CST

On Tue, 2010-02-09 at 09:47 +0000, Christopher McLean wrote:

chris,

> Thanks for the feedback Axel,
>
>
>
> The user is on:
>
> · Kernel: 2.6.31-19-generic-pae (i686)
>
> · Distro: Ubuntu 9.10
>
> · VMD for LINUX, version 1.8.7 (August 1, 2009)

ok. so that means it is not only one architecture
(i run on x86_64) and one kind of linux.

>
> It is not possible at this moment to move this user to another
> environment, although we could test dev builds on this machine if

i already tested the latest development sources. it has to be
something that was broken during the development of 1.8.7.
that was a very long development cycle and some changes to how
molecules are initialized were made.

it might be useful to install the previous version of vmd
as vmd-1.8.6 in parallel to the current version (which is
still recommended to use for everything else) so that your
user can keep working (that is what i often do in such cases).

> needed. Should a bug report be filed for this or is this list
> monitored by the devs? Am happy to provide any further information as
> needed

for the most part there is just _the_ "dev", john stone,
and he is very good at keeping track of what is going on.
he is also very busy. it looks like a very odd bug, perhaps
related to some internal state. outside of him there are
very few people that have looked into the intestines of VMD
deep enough and are still actively working on it.

i have uploaded a viewmaster session file to the VMD public
biofs under testfiles/akohlmey/viewmaster-bug/
that will hopefully make it easier to track it down.

cheers,
   axel.

>
>
> Regards
>
>
>
> Chris
>
>
>
> > -----Original Message-----
>
> > From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
>
> > Sent: 08 February 2010 17:48
>
> > To: Christopher McLean
>
> > Cc: 'vmd-l_at_ks.uiuc.edu'
>
> > Subject: Re: vmd-l: Blank thumbnails and non-working snapshots
>
> >
>
> > On Mon, 2010-02-08 at 15:55 +0000, Christopher McLean wrote:
>
> > > Hi,
>
> >
>
> > hi chris,
>
> >
>
> > > One of our students is having issues with the ViewMaster plugin.
> When
>
> > > snapshots are taken, and the project saved, upon reloading, the
>
> > > thumbnails are blank and clicking one of the thumbnails does not
>
> > > reload the view. The thumbnails look fine upon creation before
>
> > > save/reload.
>
> >
>
> > confirmed. i see the same thing here on a fedora 12 x86_64 machine
>
> > with the current development code. after reloading the state, some
>
> > more things seem to be broken. like new representations can only be
>
> > created for lines and points.
>
> >
>
> > unfortunately, i cannot give any pointers as to how to resolve this.
>
> > it looks like something deep inside of VMD is going wrong. using
>
> > valgrind doesn't show anything unusual.
>
> >
>
> > can you please check what platform your user is using, and perhaps
>
> > have him or her try a different platform? that could provide a hint
>
> > where to look.
>
> >
>
> > thanks,
>
> > axel.
>
> > >
>
> > > Any help or pointers would be appreciated.
>
> > >
>
> > >
>
> > >
>
> > > Regards
>
> > >
>
> > >
>
> > >
>
> > > Chris
>
> > >
>
> > >
>
> > >
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.