My two cents:
In the latest release (or at least the development version for the last
several months) when d-orbital support was added, we had to re-visit some
default parameters to ensure energy conservation during dynamics. For
charged d-orbital systems this meant being quite conservative with the
Ewald reciprocal space parameters (kmaxqx, kmaxqy, kmaxqz, ksqmaxq). The
old defaults (5, 5, 5, 40 or something like that) were a little bit too
small. The new defaults (8, 8, 8, 100 I think?) are a bit
*too*conservative if you ask me. I've been running with 7, 7, 7, 98
based on
comparisons to vary large settings (up to kmax = 13). This is of course
highly system dependent, but you can probably get a little bit of speed up
from it.
Regards,
Brian
On Fri, Nov 22, 2013 at 1:59 PM, 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
>
>
> On 11/22/13 10:32 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
> >On Fri, 2013-11-22 at 10:19 -0800, yunshi11 . wrote:
> >> Dear all,
> >>
> >> I have a enzyme-substrate system that includes 80 QM+link atoms (with
> >>PM3,
> >> TIP3P water, PME implemented).
> >>
> >> As suggested in Amber12 manual, the scaling of such calculations are not
> >> good. In my test, both 24-core run and 12-core run gave me 20 ps per
> >>day,
> >> which means 50 days for 1 ns. Thus I wonder how to improve the
> >>performance.
> >
> >Stop using QM. As long as you are using QM on a part of your system,
> >there is a severe limit to how fast simulations will run. In fact, as
> >you have seen the best you can get is 20 ps/day, regardless of how many
> >CPUs you use.
> >
> >
> >> Should I adjust the number of cores according to the number of QM/link
> >> atoms? It seems kind of inefficient that NO QM atoms have been assigned
> >>to
> >> 4 of the 24 cores, while the other 20 cores take 4 QM atoms each.
> >
> >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.
> >
> >> How about using GPUs?
> >
> >No. First, Amber does not have GPU support for QM. Also, the matrix
> >diagonalization makes semi-empirical QM methods difficult to port to
> >GPUs efficiently, making it unlikely that Amber's QM will ever be ported
> >to GPUs.
> >
> >HTH,
> >Jason
> >
> >--
> >Jason M. Swails
> >BioMaPS,
> >Rutgers University
> >Postdoctoral Researcher
> >
> >
> >_______________________________________________
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> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Fri Nov 22 2013 - 12:00:05 PST
