On Wed, Dec 15, 2010 at 9:39 PM, Jason Swails <jason.swails.gmail.com>wrote:
> What do you get when you just run the serial version? Does it work?
>
> When I run serial version, I am facing same problem, calculation run fine
> for ligand but for complex and receptor there is same error " allocation
> failure in vector: nh = 280631737" , Where as I ran this simulation in 1CPU
> by allocating 8GB of RAM.
> On Wed, Dec 15, 2010 at 3:26 PM, Sushil Mishra <sushilbioinfo.gmail.com
> >wrote:
>
> > On Wed, Dec 15, 2010 at 6:47 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > 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?
> > > by 4 all the threads.
> > >
> > > >
> > > > Sincerely
> > > > Sushil
> > > >
> > > >
> > > >
> > > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
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>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Dec 15 2010 - 23:30:02 PST
