Can you send some files to see if we can reproduce this on some of our
systems?
All the best,
Jason
On Thu, Dec 16, 2010 at 1:01 AM, Sushil Mishra <sushilbioinfo.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Dec 16 2010 - 07:00:02 PST
