Hi Ross
I think the issues such as frequency of writing to disk of various kinds
of data during MD should also be addressed when developing benchmarks.
Btw. what DEShaw paper you are talking about? I think I missed that.
Thanks
Piotr
On Wed, 2007-02-28 at 16:15, Ross Walker wrote:
> Hi All,
>
> Tom C and I spent some time talking about this on Sunday evening. We pretty
> much came to the conclusion that we want to do is design a series of
> calculations that attempt to address the various issues that people simply
> "believe" at present. I.e. find something that is sensitive to single vs
> double precision and see if we can address whether single precision is okay
> or not. In addition we thought about answering PME vs force switch
> simulations. Here a salt water solution simulation might be useful as this
> would be an extreme test of the electrostatics and we could address whether
> a force switch cutoff is actually okay or if you really need pme. There are
> some other options etc in here that we could consider as well, such as
> timesteps etc. Is 2fs really bleeding edge? Note: in the DeShaw paper they
> use a 2.5fs time step with shake on just hydrogens.
>
> This I think is a good plan since we can do these calculations and then put
> something along the lines of - oh btw here is the performance of the
> simulations on all the different codes etc.
>
> A straight benchmark paper is unlikely to get published so I think wrapping
> it up in a paper that attempts to address issues regarding PME, time step,
> single vs double precision etc is a good way to go.
>
> Comments?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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>
> > -----Original Message-----
> > From: owner-amber-developers.scripps.edu
> > [mailto:owner-amber-developers.scripps.edu] On Behalf Of Scott Brozell
> > Sent: Wednesday, February 28, 2007 14:24
> > To: amber-developers.scripps.edu
> > Subject: amber-developers: amber performance
> >
> > Hi,
> >
> > Today Kent Milfeld from TACC asked me about amber performance because
> > he saw that there is work underway for charmm's performance.
> > I told him about pmemd (which he had never heard of), namd,
> > gromacs, etc.
> > He was very receptive to the idea that namd has great advertising
> > and might not be targeting the best science.
> >
> > This follows on the discussion we had at the amber meeting regarding
> > a publication on good vs dubious science, pmemd, single vs
> > double precision,
> > scaling vs throughput, etc. I hope that the ball will be
> > rolling soon.
> > And I'm happy to help out.
> >
> > Scott
> >
> >
> >
>
>
Received on Sun Mar 04 2007 - 06:07:26 PST
