VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 26 2009 - 14:28:30 CDT

Hi,
  The new version of VMD is multi-core enabled, and also uses GPUs,
so it is conceivable that whatever the cygwin process launching mechanism
is doing is confused by these things in the new VMD.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 25, 2009 at 04:15:25PM -0400, Gustavo Seabra wrote:
> I thought that too, but the strange part is that it only hapens with
> the beta version of VMD. Do yoou reckin anything that changed from the
> 1.8.6 version that could cause it?
>
> On Wed, Jun 24, 2009 at 11:31 PM, John Stone<johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> >  I'm glad that reinstalling cured your plugin issues.
> > I can't comment about your problem with cygwin, that sounds
> > like a problem with cygwin itself rather than with VMD.  VMD doesn't
> > use cygwin.dll for anything, so this must be something about the way
> > cygwin launches processes.
> >
> > Cheers,
> >  John Stone
> >  vmd_at_ks.uiuc.edu
> >
> > On Wed, Jun 24, 2009 at 06:53:26PM -0400, Gustavo Seabra wrote:
> >> Hi John,
> >>
> >> I completely uninstalled the 1.8.6, and reinstalled 1.8.7-beta5. I had
> >> no problems this time, except when I try to launch VMD from within a
> >> Cygwin/X terminal. When I try that, VMD hangs with the message below:
> >>
> >> bash$ vmd
> >> [...info messages...]
> >> Found 69 plugins or data handlers in directory
> >>         'C:/Program Files/University of Illinois/VMD/plugins/WIN32/molfile'.
> >>      51 [main] vmd 5536 C:\Program Files\University of
> >> Illinois\VMD\vmd.exe: *** fatal error - Incompatible cygwin .dll --
> >> incompatible per_process info 0 != 168
> >> Hangup
> >> bash$
> >>
> >> This does not happen with VMD 1.8.6, which works just fine. I'm using
> >> Cygwin 1.7.
> >>
> >> Gustavo.
> >>
> >> On Wed, Jun 24, 2009 at 3:34 PM, John Stone<johns_at_ks.uiuc.edu> wrote:
> >> >
> >> > Gustavo,
> >> >  It sounds like you may have had an existing installation in the same
> >> > target directory, or some other similar issue.  Please uninstall all
> >> > VMD versions, and then after that's done, double-check that there's no
> >> > longer a "C:\program files\university of illinois\" directory tree.  If
> >> > there still any directories or files in that subtree, go ahead and delete
> >> > them manually if necessary.  Once all that is done, please try installing
> >> > the beta 5 version again, and let me know if you still have trouble.
> >> >
> >> > Cheers,
> >> >  John Stone
> >> >  vmd_at_ks.uiuc.edu
> >> >
> >> > On Wed, Jun 24, 2009 at 03:04:25PM -0400, Gustavo Seabra wrote:
> >> >> Hi there,
> >> >>
> >> >> I tried installing VMD 1.8.7 beta 5 (2009-06-01) in my Windows Vista
> >> >> computer but, whenever I launch VMD, I get a huge list of warnings
> >> >> about "Rejecting plugin with incorrect ABI version...", and VMD quits.
> >> >> I then uninstalled that, and installed version 1.8.6. This version
> >> >> does work, but when I open it it still gives me some warnings about
> >> >> plugins with incorrect ABI version (see below). I wonder if those are
> >> >> remainings of the 1.8.7 installation that the uninstaller just didn't
> >> >> get, or is there something really wrong in my install.
> >> >>
> >> >> Thanks,
> >> >> Gustavo.
> >> >>
> >> >> ===
> >> >>
> >> >> Info) VMD for WIN32, version 1.8.6 (April 7, 2007)
> >> >> Info) http://www.ks.uiuc.edu/Research/vmd/
> >> >> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> >> >> Info) Please include this reference in published work using VMD:
> >> >> Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> >> >> Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> >> >> Info) -------------------------------------------------------------
> >> >> Info) Free system memory: 1475MB (72%)
> >> >> Info) OpenGL renderer: Intel 965/963 Graphics Media Accelerator
> >> >> Info)   Features: STENCIL MDE CVA MTX PP
> >> >> Info)   GLSL rendering mode is NOT available.
> >> >> Info)   Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (8)
> >> >> Info) Spaceball driver not installed.  Spaceball interface disabled.
> >> >> Info) No joysticks found.  Joystick interface disabled.
> >> >> Warning) Rejecting plugin with incorrect ABI version: C:/Program
> >> >> Files/University of
> >> >> Illinois/VMD/plugins/WIN32/molfile/basissetplugin.so
> >> >> Warning) Rejecting plugin with incorrect ABI version: C:/Program
> >> >> Files/University of
> >> >> Illinois/VMD/plugins/WIN32/molfile/cpmdlogplugin.so
> >> >> Warning) Rejecting plugin with incorrect ABI version: C:/Program
> >> >> Files/University of Illinois/VMD/plugins/WIN32/molfile/dtrplugin.so
> >> >> Warning) Rejecting plugin with incorrect ABI version: C:/Program
> >> >> Files/University of Illinois/VMD/plugins/WIN32/molfile/dtrplugin.so
> >> >> Warning) Rejecting plugin with incorrect ABI version: C:/Program
> >> >> Files/University of
> >> >> Illinois/VMD/plugins/WIN32/molfile/gaussianplugin.so
> >> >> Warning) Rejecting plugin with incorrect ABI version: C:/Program
> >> >> Files/University of Illinois/VMD/plugins/WIN32/molfile/jsplugin.so
> >> >> Warning) Rejecting plugin with incorrect ABI version: C:/Program
> >> >> Files/University of Illinois/VMD/plugins/WIN32/molfile/maeffplugin.so
> >> >> Found 62 plugins or data handlers in directory
> >> >>         'C:/Program Files/University of Illinois/VMD/plugins/WIN32/molfile'.
> >> >> vmd >
> >> >
> >> > --
> >> > 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
> >> >
> >>
> >>
> >>
> >> --
> >> Gustavo Seabra
> >> Postdoctoral Associate
> >> Quantum Theory Project - University of Florida
> >> Gainesville - Florida - USA
> >> -------------------------------------------------------------------------------------------
> >> Q:      Why do mountain climbers rope themselves together?
> >> A:      To prevent the sensible ones from going home.
> >
> > --
> > 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
> >
>
>
>
> --
> Gustavo Seabra
> Postdoctoral Associate
> Quantum Theory Project - University of Florida
> Gainesville - Florida - USA
> -------------------------------------------------------------------------------------------
> Q: Why do mountain climbers rope themselves together?
> A: To prevent the sensible ones from going home. 

-- 
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