VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Sep 22 2013 - 20:34:01 CDT

Hi,
  Since this is a binary you compiled yourself, and a fairly old version,
it's hard to guess what it might be. I would suggest that if you can
cause it to happen again, that you try attaching to it with 'gdb',
using the -p flag to indicate the process ID, and then once you
attach to it, you should be able to determine what code is encountering
the tight loop you describe. We often leave VMD running for days at a
time in our lab and haven't experienced this, but since you compiled
from source, you're undoubtably using a different version of FLTK,
Tcl, and Tk from what we're using and this may account for some of
what you're seeing. In any case, 'gdb' should be very helpful here.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 23, 2013 at 09:34:46AM +1000, Tristan Croll wrote:
> Hi all,
>
>
>
> I've got another minor(ish) issue to report. I've had a number of
> instances now where I've left VMD open (but not working on anything), and
> come back to find it trapped in some infinite loop state (all VMD windows
> frozen, but ~100% CPU usage). The only way to break it is to kill the
> session. It's a bit tricky to pin down exactly what triggers it, but as
> far as I recall every time this has happened I've had at least one protein
> structure and at least one volumetric map loaded.
>
>
>
> A few other details:
>
>
>
> Version: 1.9 LINUXAMD64, built from source to use Axel Kohlmeyer's VRPN
> version for the Novint Falcon
>
> OS: CentOS 6.4
>
> CUDA boards: Tesla C2050, Quadro 4000
>
>
>
> It's not a memory issue: at present, with a frozen instance of VMD
> running, I'm still registering 11GB free RAM.
>
>
>
> Cheers,
>
>
>
> Tristan
>
>
>
> Tristan Croll
>
> Lecturer
>
> Faculty of Health
>
> Institute of Health and Biomedical Engineering
>
> Queensland University of Technology
>
> 60 Musk Ave
>
> Kelvin Grove QLD 4059 Australia
>
> +61 7 3138 6443
>
>
>
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-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/