VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 28 2007 - 15:38:50 CDT

Hi,
  Yes, just to add to what Axel mentioned, there are some Linux
kernels out there that don't properly handle child thread completions
or terminations, and they cause bogus SIGHUP signals to be sent to the
multithreaded process. VMD 1.8.6 now makes much more extensive use of
multithreading by default, such that this kind of problem will be
fatal to VMD 1.8.6, but older versions would run along without trouble
except in certain rare circumstances. I should point out that this type
of kernel flaw will be fatal to any non-trivial multithreaded program,
so it's best to get your system patched up.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 28, 2007 at 02:17:22PM -0400, Axel Kohlmeyer wrote:
> On Mon, 28 May 2007, Philippe Roche wrote:
>
> philippe,
>
> this is a know problem (of the kernel on your machine). see:
> http://www.ks.uiuc.edu/Research/vmd/current/linuxrelnotes.html
>
> salut,
> axel.
>
> PR> Dear all,
> PR> I have just installed vmd-1.8.6 on a LINUX system and it crashes when I
> PR> load a pdb file.
> PR> The problem seems to come from the determination of bond structure since
> PR> VMD works fine when I load both a PSF file and a PDB file.
> PR> If I run 'mol bondsrecalc 0' after loading the PSF and PDB files it
> PR> crashes again.
> PR> (although it works in the vmd text mode (with 'vmd -dispdev text').
> PR>
> PR> I have tried vmd -debug mode and I get this message.
> PR>
> PR> Info) Determining bond structure from distance search ...
> PR> [New Thread 1436548016 (LWP 7454)]
> PR> [Thread 1436548016 (LWP 7454) exited]
> PR> Info) Bond count: 65
> PR>
> PR> Any suggestion ?
> PR>
> PR> Cheers
> PR>
> PR> Philippe
> PR>
> PR> PS : VMD-1.8.5 works on the same machine
> PR>
> PR>
> PR>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
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