RE: amber-developers: amber performance

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 28 Feb 2007 16:57:26 -0800

For those that don't have the D.E.Shaw paper see attached.

/\
\/
|\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
be read every day, and should not be used for urgent or sensitive issues.

> -----Original Message-----
> From: owner-amber-developers.scripps.edu
> [mailto:owner-amber-developers.scripps.edu] On Behalf Of Piotr Cieplak
> Sent: Wednesday, February 28, 2007 16:16
> To: amber-developers.scripps.edu
> Subject: RE: amber-developers: amber performance
>
> 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
> > be read every day, and should not be used for urgent or
> sensitive issues.
> >
> > > -----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 - 06:07:28 PST
Custom Search