VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 30 2002 - 13:54:55 CDT

Hi,
  I wanted to give some more information on this issue as it appears
that a few people are now having this same problem on Redhat 7.3 systems
and Redhat 6.x systems. The problem is caused by changes in the
shared libraries between different versions of Linux. Up to now we've
been building the Linux versions of VMD on a 7.1 system, which worked
fine until we started using runtime linking for plugins and discovered
these difficulties between versions of Linux. Fortunately, we planned
ahead a bit for this, and we've built VMD such that it has two sets of
plugins:
  1) a built-in statically compiled set of "plugins" for all of the
     core file loader interfaces etc. These plugins are used by default
     unless a dynamically loaded plugin with a higher version number is
     found in the VMD plugin directory or in a user's personal plugin area.

  2) dynamically loaded plugins which are implemented by shared objects
     on Unix systems and DLLs on Windows.

If you get these plugin loading error messages they _should_ be non-fatal.
Despite the errors, I would expect you to be able to use all of the core
features of VMD still, i.e. loading molecules, trajectories, etc. Some
of the non-core features of the new rev of VMD such as psfgen are only
implemented as a dynamically loaded plugin, so they would not be available
in this circumstance, but I think I have some ideas of how to work around
these problems by building sets of plugins specifically for the affected
versions of Linux. This may cure the problems people have been having.

In order to help us get this resolved, I would appreciate it if anyone
that is having these problems could send us email at vmd_at_ks.uiuc.edu
with information on what version of Linux (or any other OS for that matter)
they are running, the VMD errors they are getting, etc. With this information
I think I can make up a list of the platforms that will need to have
special plugin sets built. From there, I'll do some experiments and
have some of you guys try replacing the default plugins we ship with
a new set and see if that cures the problem.

Thanks!!
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 29, 2002 at 02:45:54PM -0600, Kevin Sanbonmatsu wrote:
> Hi Denny, did you ever resolve this problem?
> I'm getting the same messages when I start up
> either vmd-1.7.1 or vmd-1.8 running on rh7.2 out of the box.
> My plugin directories appear in the correct place.
> Thanks in advance,
> Kevin
>
> Date: Sat, 13 Jul 2002 14:16:47 -0400 (EDT)
> > From: Rajiah A Denny <radenny_at_fas.harvard.edu> To: <vmd-l_at_ks.uiuc.edu>
> > --
> > Subject: plugin problems
> >
> > I recently installed VMD on my Linux (Red Hat and Debian) machines. When
> > I try to run it I get the following error messages in both the machines:
> >
> > Unable to open dynamic library
> > '/usr/local/lib/vmd/plugins/LINUX/molfile/webpdbplugin.so'
> > /usr/local/lib/vmd/plugins/LINUX/molfile/webpdbplugin.so: undefined
> > symbol: acos
> > Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUX/molfile/webpdbplugin.so':
> > Unable to dlopen plugin file
> > /usr/local/lib/vmd/plugins/LINUX/molfile/webpdbplugin.so Automatic IMD
> > package could not be loaded: couldn't load file
> > "/usr/local/lib/vmd/plugins/LINUX/tcl/psfgen1.2/libpsfgen.so" :
> > /usr/local/lib/vmd/plugins/LINUX/tcl/psfgen1.2/libpsfgen.so: undefined
> > symbol: acos
> >
> > Can anyone offer any help?
> >
> > Thanks, Denny 

-- 
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