VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 09 2008 - 01:22:13 CST

Oliver,
  I was checking on the crash symptoms you describe, and these
sound like the known problem with older Linux kernels and multithreading
on Linux kernels earlier than 2.6.9-42. As you are apparently running
2.6.9-22, that would explain the crash problems you've described, as
each of the crashes you mention are in pieces of code that are
heavily multithreaded. The MacOS X oddity you mention sounds like a but
in their X server. Let me know if you have more questions about these
issues.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 20, 2007 at 04:50:10PM -0500, Oliver Beckstein wrote:
> John,
>
> > I've posted two Linux builds with 64 bonds per atom in the alpha
> >directory in the VMD Public project on BioCoRE:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> thanks for the Linux builds. I only tested the 32bit one
> (vmd-1.8.7a14extrabonds.bin.LINUX.opengl). It works in principle. In
> particular, I get all my 'bonds' displayed.
>
> I'm having a few stability issues. Although they won't prevent me from
> using the build I'll mention them nevertheless.
>
> For testing, I ran Linux-VMD remotely (bad, I know) through X11 on my
> PowerBook laptop:
>
> VMD: 1.8.7a14extrabonds (December 19, 2007)
>
> remote:
> Linux: CentOs 4.2 (Rocks 4.1)
> Linux 2.6.9-22.ELsmp #1 SMP Sat Oct 8 19:11:43 CDT 2005 i686 i686 i386
> GNU/Linux
>
> local:
> Mac OS X 10.3.9, Apple's X11
>
> VMD's startup output:
> Info) ATI Linux driver detected, limiting features to avoid driver bugs.
> Info) Set the environment variable VMDDISABLEATILINUXWORKAROUND
> Info) to enable full functionality on a known-safe driver version.
> Info) OpenGL renderer: ATI Radeon 9600 XT OpenGL Engine
> Info) Features: STENCIL MDE MTX
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (2048x2048), Multitexture (8)
>
>
> The following operations crashed VMD:
> * Render -> Tachyon Internal
> (Tachyon external works)
> * Trying to load any pdb file on its own (psf + pdb works)
> * Trying to load a pdb from the web
>
> (Also, when I resize the VMD OpenGL window with a molecule present my
> local MacOS X freezes (either hangs or the display becomes brighter and
> brighter while hanging until the user panics and hits the power-off
> button...). This happens with both 1.8.5 and 1.8.7a14extrabonds running
> remotely on Linux (and it doesn't matter if I do 'export
> VMDDISABLEATILINUXWORKAROUND=1' ). --- I suspect that's more a problem
> with my ancient version of MacOS X than with VMD per se, though; native
> MacOS X ppc VMD 1.8.6 has no problems.)
> >
> >Give those a spin and let me know if all is well. I can do a MacOS
> >build
> >for you tomorrow if the Linux builds work for you.
>
> I'd like to test the OS X build as well, please (hoping that it works
> around the OpenGL problems and so that I can run VMD locally).
>
> Many thanks,
> Oliver
>
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Dec 18, 2007 at 05:05:02PM -0500, Oliver Beckstein wrote:
> >>Hello John,
> >>
> >>> I can make you special builds with larger max bond counts.
> >>
> >>I appreciate this very much.
> >>
> >>>Will 30 be adequate? I can make it any number you like
> >>>up to 255, but the larger the number the more memory VMD will use
> >>>on a per-atom basis.
> >>
> >>To be on the safe side let's choose 64 – more are really not going to
> >>come up in my problems.
> >>
> >>Thank you,
> >>Oliver
> >>
> >>>
> >>>Cheers,
> >>> John Stone
> >>> vmd_at_ks.uiuc.edu
> >>>
> >>>
> >>>On Mon, Dec 17, 2007 at 02:37:42PM -0500, Oliver Beckstein wrote:
> >>>>Hello,
> >>>>
> >>>>is there a way to obtain binaries for Mac OS X and Linux i686 that
> >>>>have
> >>>>MAXATOMBONDS increased to, say, 30? I am (ab)using VMD for graph
> >>>>plotting and some of my nodes simply don't behave like atoms
> >>>>although
> >>>>I'd like to keep using atom-like representations instead of drawing
> >>>>bonds as graphics objects because it makes it so much easier to
> >>>>change
> >>>>colors, materials etc.
> >>>>
> >>>>As I understand it, MAXATOMBONDS is defined to be 12 in Atom.h:
> >>>>http://www.ks.uiuc.edu/Research/vmd/doxygen/Atom_8h.html
> >>>>
> >>>>I don't have the VMD source and as I understand it, it can be a bit
> >>>>complicated compiling it, though I'd give it a shot if this is too
> >>>>much
> >>>>work for the developers (which I would certainly understand).
> >>>>
> >>>>Thanks,
> >>>>Oliver
> >>>>
> >
> --
> Oliver Beckstein * orbeckst_at_jhmi.edu
>
> Johns Hopkins University, School of Medicine
> Dept. of Physiology, Biophysics 206
> 725 N. Wolfe St
> Baltimore, MD 21205, USA
>
> Tel.: +1 (410) 614-4435
>
> 

-- 
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