On Wed, Dec 15, 2010 at 10:49 AM, Sushil Mishra <sushilbioinfo.gmail.com>wrote:
> On Wed, Dec 15, 2010 at 4:40 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Wed, Dec 15, 2010 at 6:11 AM, mish <smncbr.gmail.com> wrote:
> >
> > > Hi Bill,
> > > I finished a new simulation where I used 12CPU's, with 48GB of RAM for
> > > the calculation and the problems still persist. I can see the same
> error
> > > "allocation failure in vector: nh = 276948109" in _complex_nm.out file.
> I
> > >
> >
> > This indicates a malloc failure (allocation). It's trying to allocate
> > 276948109 "double" numbers. On a typical machine I think that's 8 bytes
> > (64-bit real), so it's trying to allocate a total of 2.063 GB of memory,
> I
> > think, and for some reason it's failing.
> >
> >
> > > have ran another calculation in 4CPU's with 48 GB of RAM and
> calculation
> > > are
> > > running. However, in that running_MMPBSA_complex.mdcrd.1 calculation I
> > cant
> > > see values of entropy in
> > > the _MMPBSA_complex_nm.out.1, _MMPBSA_complex_nm.out.2,
> > > _MMPBSA_complex_nm.out.3
> > > files. After each minimization is message "allocation failure in
> vector:
> > > nh " in the place of values of entropies. What could be other source of
> > > error ?? is there something wrong with my input file ?
> > >
> >
> > Did you clean all temporary files before re-running? It could be you're
> > seeing the remnants of previous attempts?. Perhaps there's a memory leak
> > as
> > well... can you determine how much memory is being used during the
> > simulation?
> >
>
> Yes I clean all the temporary file before rerunning the calculations. When
> I
> look for the memory use during the simulation its about 8GB where as I had
> assigned 48GB in for the calculations. What could be other possible source
> of such error ?
>
8 GB is being used for how many threads?
>
> Sincerely
> Sushil
>
>
>
> --
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 15 2010 - 10:00:06 PST
