AMBER Archive (2004)

Subject: Re: AMBER: segmentation fault in Leap

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed Jan 21 2004 - 23:56:10 CST

On Wed, 21 Jan 2004, Bill Ross wrote:

> > Placed Cl- in foo at (34.61, -13.78, 49.32).
> > Segmentation fault (core dumped)
> >
> > Does anyone have any idea what may be wrong in this case? Could it be that
> > there is a memory problem?
>
> There is. As a workaround you could try adding Cl-'s one-by-one
> explicitly.

I am not sure how I could trace this down. I'm running tleap on one
processor, but it does not seem to be eating up memory (swap memory does
not change). I've also tried to run tleap in a pbs job asking for 1Gb of
memory and still I get a segmentation fault.
I've also tried to add Ions one by one but it does not seem to matter.
What seems strange is that the charge calculation over the grid is
completed and only after the ion is placed the segmentation fault happens.

I also remember working some while ago with larger files than the present
one and never got a segmentation fault.

I know this sound very imprecies but I'm looking for help to find a
starting point to try and trace this down.

Thanks,
Ioana

>
> Bill Ross

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu