Subject: 'raw speed'

From: [email-masked] (Bill Ross )
Date: Mon, 26 Sep 1994 18:30:29 -0700

Richard Walsh of Minnesota Supercomputer Center, Inc. writes:

	I am not sure what you mean by 'raw speed' here ... 
	could you also report C90 parallel times or those for 
	the T3D? It would be helpful and more complete to 
	present these comparisons. 

I certainly should have defined 'raw speed' - it means the best you can
get out of the code we distribute. I look forward to being able to
present such comparisons; we should have T3D results at least for the next 
release of Amber, and I'm hoping for C90 parallelization too. The parallel 
Charmm Web page is the best I have to offer for now along these lines.

	My guess is that your benchmark would run with the most 'raw speed' 
	on a C90 16/512 with a T3D attached. 

I chopped a discussion of possibilities out of my post in the interest
of sticking to data. In support of Richard's notion, I might add that I
believe that even single-cpu Amber could be optimised further on Crays to
get better vector performance and maybe beat these results (the nonbond 
loop only handles 2 residues at a time, so the pipeline setup cost overwhelms 
the vector saving on solvated systems and breaks even in vacuum). Other 
possibilities for the next record time include message-passing on IBM's SP2,
Intel's Paragon, or on a cluster of multi-cpu TFP's.  

	when does a workstation become a supercomputer? ... when it costs 
	$500,000.00, $1,000,000.00. The new SGI systems with multiple CPUs 
	and functionally configured can easily exceed these numbers. Around 
	here anyway a workstation is something that can be purchased for 
	about $50,000.

Good point. My unconscious assumption was that the thing with a main
graphics screen on someone's desk that doesn't need a machine room and
site engineer(s) to service it is a workstation, and I haven't thought
so much about price.

	The SGI TFP performance numbers are impressive, but they should be 
	presented here with as high a regard for completeness as for enthusiasm
	(excepting perhaps by those selling the hardware involved :-)).

Hopefully this will have allayed your worries. I try to be fair by
reporting each new 'speed record' for our code as it happens. (No one 
complained about the earlier announcement about Fujitsu followed by the 
C90 one.) I agree there is some arbitrariness involved in terms of which
machines get optimised when. In this case SGI worked on shared memory
parallelism; Cray could have but didn't choose to, though there has been
talk of them doing it for the next release. My hope is that, on the whole, 
these benchmarks provide a relatively unbiased means of comparing machines.

By the way, I expect that the benchmarks for the next release of Amber will
eliminate some redundancies and more usefully reflect the molecular 
mechanics regimes one might choose, at least by using different cutoff 
sizes.

Bill Ross
University of California, San Francisco