On Fri, 2013-11-22 at 11:47 -0800, yunshi11 . wrote:
> On Fri, Nov 22, 2013 at 10:59 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> > Hi Yun,
> >
> > To expand a little bit on what Jason wrote. There are ways to tweak the QM
> > performance a bit - you might be able to get a factor of 2 or 3
> > improvement in performance but that's more or less it.
> >
> > Firstly: Compile with the Intel compiler and link to one of the latest
> > versions of MKL.
> >
> > Second: set diag_routine=0 in the qmmm namelist. This will then try the
> > various diagonalizers in MKL and select the fastest one. For QM atom
> > counts above 40 or so the default diagonalizer is not the most efficient.
> > - Timing info on each of the diagonalizers will be give in the mdout file.
> >
> > All the best
> > Ross
> >
> > Hi Ross,
>
> I also read the J Phys Chem A (2007) paper about SCC-DFTB in AMBER 9, which
> states that "Extensive work is underway to make DFTB fully parallel in the
> next AMBER release and it is anticipated that by that time the same DFTB
> calculations as above will be no more than 2.0 times slower than the
> corresponding all-classical simulation."
>
> So I wonder if SCC-DFTB, also semi-empirical, would run faster than PM3 in
> AMBER 12.
You can try it. I'm not sure, though.
> > >Semi-empirical QM is not particularly parallelizable, in stark contrast
> > >to high-level ab-initio techniques. Unlike HF, DFT, and the more
> > >expensive correlated methods, the bottleneck of semi-empirical
> > >techniques is diagonalization of the Fock matrix rather than computing
> > >the integrals. Diagonalization is not efficiently parallelized, which
> > >means the slowest part of the QM calculation must be run by 1 CPU. You
> > >can throw more CPUs at it, but they will all end up waiting for the
> > >slowest CPU to finish diagonalizing the matrix.
> > >
> >
>
>
> Does this mean that if I have some parallel computational power (100-200
> CPU cores), I would get better performance when using HF or DFT (with
> external QM programs rather than amber itself) for my QM region?
Definitely not. HF or DFT will be much slower. HF and DFT will scale
better, but the absolute performance will always be worse than
semi-empirical.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 22 2013 - 12:30:02 PST
