Re: segmentation fault?

From: Giacomo Fiorin (
Date: Wed Nov 05 2008 - 17:46:19 CST

Hello Bin, for a system of that size the memory usage is of the order
of few tens of Mb, certainly too small to explain. Also, most of the
times you shouldn't get a segmentation fault (which means that there's
an internal error when accessing data), but an operating system error

Are you concatenating minimization and dynamics with Tcl? If you have
a Tcl library that doesn't behave properly on your Cray's operating
system, you may be better off just running separate input files for
NAMD that don't use Tcl, and investigate the problem in the meantime.
Unless you're using tclForces, results are completely equivalent with
and without Tcl. It's just a little less convenient for you to set up
separate inputs :-(


---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
 phone: (+1)-215-573-4773
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 mail: giacomo.fiorin_<at>
---- ----

On Wed, Nov 5, 2008 at 4:58 PM, BIN ZHANG <> wrote:
> Hi, there:
> Is there an upper limit of atom number that NAMD can handle?
> I was running a simulation with first 1000 step minimization and then
> dynamics. But NAMD existed after the minimization with error
> Application 471018 exit signals: Segmentation fault, Killed
> And the error in the output file is:
> APINFO_NIDTERM: compute node initiated termination, possible out of memory
> condition
> Is this a problem of limited compute memory? or, the namd itself(wrong
> scripts, et al)? How can I estimate the memory needed for a given atom
> number?
> BTW, the atom numbers of my system is about 15,000
> Thanks a lot.
> Bin
> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood of
> patriots and tyrants.

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