AMBER Archive (2004)

Subject: Re: AMBER: Computing psec/day using Amber 8

From: Craig TOEPFER (
Date: Thu May 06 2004 - 14:19:01 CDT


A couple of points of clarification.

First, what time do I use to compute seconds per step. Do I use the
total runtime(i.e., time pmemd....) or some subset of the total time?
At the end of the output file, I see a breakdown of time spent per
component. Do I use one of these?

Finally, does the value of 86.4 only apply to the "jac" benchmark, or is
this a generic value? I saw on the Amber 8 benchmarks page that the
value for the "factor_ix" benchmark is 129.6, not 86.4.



David A. Case wrote:
> On Thu, May 06, 2004, Craig TOEPFER wrote:
>>On the Amber website, there are some benchmark results from various
>>machines/compilers. The results are listed as "ps per day". I am not
>>sure how to compute this value from the output produced by these set of
>>benchmarks that are included in the Amber8 distribution. Can you help
>>me or point me in the right direction.
> The fourth "Note" at the top of the benchmark page gives the conversion:
> The value of ps per day = 86.4/(seconds per step), for a time step of 1 fs.
> Double this value if you plan to use 2 fs time steps.
> The "jac" benchmark uses a 1 fs time step, for example, and it is 1000 steps
> long. So you figure out your seconds per step, and use the above equation.
> ..good luck...dac

Craig Toepfer                          
Advanced Compilers and Tools           
AST Portland Lab, STMicroelectronics             Phone:  +1-503-682-2806
9150 SW Pioneer Ct, Suite H                      FAX:    +1-503-682-2637
Wilsonville, OR USA 97070

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