Re: amber-developers: amber performance

From: Ken Merz <>
Date: Thu, 1 Mar 2007 13:28:38 -0500


  DE Shaw wants to have a big impact (revolutionize drug discovery,
yada, yada.), so they will cut corners to look good. Moreover, they
are merging Desmond into Schrodinger software and they want to sell
this to Biotech and Pharma companies for top dollar, hence, the
marketing materials need to look impressive. Indeed, as Ant Nichols
said at Sanibel, MD is not a killer app in the Biotech and Pharma
industries, so there is a very large show me component if you want to
target that audience for MD. From my perspective, the AMBER MD
aficionado's should keep doing what they are doing so very well and I
think we will be at least as good as any of our competitors and
hopefully demonstrably better! Moreover, in the end MD is a driver to
do science and this requires outstanding force fields just not ns/day
numbers in the stratosphere. The NIH grant along these lines
spearheaded by Yong, Carlos, Tom, et al is going to help insure that
we have the potentials to take advantage of improved MD capabilities.
Great discussion - I for one learned a ton.


On Mar 1, 2007, at 10:52 AM, Ross Walker wrote:

>> taking a very quick eyeball look at temperature drift
>> "without constraints"
>> (I presume this means nve effectively), they drift
>> temperature a whopping
>> 2.0 degrees K per nsec (namd drifts 2.8 K per nsec). I was
>> surprised by
>> this (I am looking at table 5), and maybe I don't understand
>> something.
>> However, in testing out my cutoff methods, I did a bunch of
>> NVE energy drift
>> checks. I did checks on a dna 12mer in a 70 angstrom box.
>> For pme, I had a
>> 0.21 degree drift in 5 nsec, or 0.04 degrees K per nsec.
> Indeed, this same point was made by the IBM Blue Matter guy who
> gave the
> talk after the DE Shaw guy at Supercomputing. He was royally pissed
> and
> probably with good reason as the talk before just trounced all over
> his Blue
> Matter code but with little hard evidence. Besides take a look at the
> Benchmark plot again. The Blue Matter code matches the DE Shaw code
> for
> total throughput. It just needs more cpus because Blue Gene is
> slooowwwww.... But from the talk you'd have thought that the
> Desmond code
> had solved it all and was faster than anything else. Something that
> just
> isn't true and requires some creative benchmarking to show - I.e.
> compare
> apples and oranges.
> Anyway, the guy from IBM said they validate against amber and
> charmm and
> that 0.05 K/nsec drift is the maximum they ever except. He showed a
> nice
> plot of what happens to your temperature over 200ns run (just over
> a days
> simulation if you are at 170ns/day) if you drift by 0.05K vs 2.0K.
> I'm convinced the DE Shaw guys know this but didn't want to let on.
> The
> paper is really an example of where you need to read between the
> lines. For
> example note that they do a lot of benchmark comparissons with namd
> and Blue
> Matter but then in table 5 which shows the energy drift they
> conveniently
> only show namd numbers. I am actually shocked that namd is so bad
> more than
> anything...
> Also note that their communication pattern, described in Figure 4 is
> completely non-standard. The mpi2 standard says nothing about the
> legality
> of recieving a nonblocking send with a blocking receive. I am
> shocked that
> it works at all. It may just be luck based on their mpi
> implementation and
> switch but I would be amazed if it worked on any decent range of
> hardware.
> Also note that they say Desmond uses distributed output files -
> something I
> think we will be in need of in a year or so. Although such
> approaches will
> make little difference on your average NFS mounted cluster disk...
> However,
> also note that the benchmarks section makes no mention of writing
> to output
> or trajectory files so I would suspect that there is no trajectory
> writing
> going on here.
> Just my 2c...
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
> | | PGP Key available on request |
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Professor Kenneth M. Merz, Jr.
Department of Chemistry
Quantum Theory Project
2328 New Physics Building
PO Box 118435
University of Florida
Gainesville, Florida 32611-8435


Phone: 352-392-6973
FAX: 352-392-8722
Cell: 814-360-0376
Received on Sun Mar 04 2007 - 06:07:43 PST
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