VMD-L Mailing List

From: Yamada, Masako (GE Global Research) (yamada_at_research.ge.com)
Date: Wed Feb 08 2012 - 10:37:29 CST

Thanks John -- hope this information helps:

OS: Redhat Enterprise Linux
Architecture: Intel EM64T and AMD64 (tried both)

Just for "kicks" I also tried running on desktop PC, but it froze my
computer.

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Wednesday, February 08, 2012 11:07 AM
To: Yamada, Masako (GE Global Research)
Cc: vmd-l_at_ks.uiuc.edu; Michael Doig; akohlmey_at_gmail.com
Subject: Re: Re: vmd-l: Topotools - limit to size of system it can be
used for?

Hi,
  I just sent the following query to Michael Doig, if you let me know
the same information I may be able to provide some suggestions to
workaround the problem:

  What platform are you running VMD on? This seems to be an issue
related to deep recursion running out of stack space, which is a problem
that tends to crop up some platforms more than others, and sometimes you
can get around it simply by setting an environment variable. If you can
tell me what platforms you're using, I can provide you with some
suggestions to try out.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 08, 2012 at 08:11:21AM -0500, Yamada, Masako (GE Global
Research) wrote:
> I'm facing the same issue that Michael Doig posted recently. I've
tried
> the most recent non-beta VMD 1.9.1 build (Feb 04, 2012) and
continue to
> get a segmentation fault during write-out. Reading the core dump
using a
> debugger, I get similar output to what Michael Doig posted.
>
>
>
> For your reference, I've attached the two Tcl (topotool) scripts
that I've
> been using. Pls run "tip3p_hemisphere.tcl" first to generate the
PDF file
> and then "pdbtolammps_noshift.tcl" to convert to LAMMPS format.
This works
> fine, until the number of atoms becomes on the order of 10^6. To
add to my
> confusion, I could've sworn these exact scripts previously WORKED
using a
> million atoms. I have a million-atom LAMMPS file on hand to prove
it.
>
>
>
> Masako Yamada, Ph.D
>
> GE Global Research 

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