Hi,
That is definitely a memory issue, however without some more information
it's hard to diagnose what exactly is going wrong. Dan's suggestions of
reducing the grid size should help, but if the crash is occurring
immediately something else may be going on. Some information would really
help us get an idea of the situation: could you link the gist command from
your cpptraj input script and provide a little information regarding the
simulation (in particular the solvent model in use)?
In general the GIST memory bottleneck is in saving water coordinates within
the region of interest at every frame being analyzed so that entropies can
be calculated after all frames have been read. A ballpark estimate for the
memory usage (of entropy alone) would be Nframe * Nwater (in the region of
interest) * 7 * 8 bytes. It can get out of hand quickly with larger grids.
Happy to help,
--Steve
On Fri, Sep 23, 2016 at 8:22 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I suspect this is a memory issue. GIST tends to be pretty memory
> hungry since it has many grids and has to store some information for
> each voxel. As a first step try reducing your grid size and/or grid
> spacing and see if the error goes away.
>
> -Dan
>
> PS - As Hai suggested it may be worthwhile to try the GitHub version
> of GIST anyway as it is a bit faster.
>
> On Fri, Sep 23, 2016 at 2:40 AM, <peter.schmidtke.discngine.servier.com>
> wrote:
> > Dear all,
> >
> > I'm using cpptraj to perform gist calculations. Nearly immediately after
> starting a calculation I get the following error message :
> > Terminate called after throwing an instance of 'std::length_error'
> > What(): vector::_M_fill_insert
> > Aborted (core dumped)
> >
> > I would be greatful for any guidance of how to avoid that error.
> >
> > Cpptraj version 15 is used.
> >
> > Cheers.
> >
> > Peter
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 23 2016 - 09:00:04 PDT
