Hi Ross,
All simulations have been carried out with constant pressure. For
historical reasons it is all isotropic for AMBER.
I haven't mentioned the compiler and libraries for AMBER 11 because the
binaries were not compiled by us. We do not have a license for this
version. It is very likely that an older version of gcc was used and
possibly an older version of the MPI library.
A ns/day plot is certainly more user friendly. I will consider that.
Cheers,
Hannes.
On Thu, 5 Jul 2012 09:23:14 -0700
Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Hannes,
>
> This is excellent and very comprehensive work, thanks for sharing
> this.
>
> With regards to the AMBER 12 vs AMBER 11 numbers, are these all
> constant pressure runs (with isotropic or anisotropic pressure
> scaling?) - Some of the code was reworked as part of adding the
> constant surface tension code and this may account for some of the
> differences seen. I'd be interested to know if the same differences
> are observed for NVT.
>
> Also the Addendum mentions the MPI and compiler versions used for
> AMBER 12 but the original report (Mar 2012) doesn't give this info.
> Did you use the exact same MPI and compiler versions for AMBER 11 as
> AMBER 12 in these tests? That might also be causing a difference,
> especially if some of the collectives over large core counts improved
> in a new MPI version.
>
> One minor comment as well if I may. I know the standard approach used
> for benchmarking in computer science is to plot log of execution time
> against core count but I tend to find this very difficult to
> interpret since time is an inverse scale and so the differences as
> you move to the right of the plot become harder and harder to see.
> Can I suggest plotting throughput (ns/day) against core count since
> this is then a linear scale and is much easier to interpret. It is
> also what people really want to know, how much simulation can I get
> done in a given time.
--
Scanned by iCritical.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 11 2012 - 01:30:02 PDT
