RE: AMBER: meaningful tax for sander question

From: Ross Walker <>
Date: Tue, 31 May 2005 13:12:10 -0700

Another idea, if you just want a "BIG" test case would be to solvate
something in a HUGE box of water. You can just do a periodic water system if
you want. E.g. in Leap:
watersystem = copy WAT
solvatebox watersystem TIP3PBOX 60
will get you a system of well over 100,000 atoms.
Then you can just run as much MD on this system as you want and on as many
cpus as you want. If you want it to run for months then just ask for
billions of steps and a big cut off.
E.g. nstlim=1000000000,cut=25.0,
This will want lots and lots of memory and will run for ages.
Although I'm not sure what you hope to learn from very long benchmarks -
except to test the stability of your machine...
Typically a benchmark that runs for 10 minutes or so should easily be long
enough to avoid issues associated with start up time etc.
I hope this helps.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
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From: [] On Behalf Of
Cordova, Luis E.
Sent: 31 May 2005 12:20
Subject: AMBER: meaningful tax for sander question



I am trying to benchmark/tax an experimental processor running Amber8, in
particular the sander link.

Does anyone know/could point me to other meaningful examples or benchmarks
that tax the sander link significantly?

Some example that is reported on the literature with results and can be
extended in size and also studied in regards to its scalability varying for
instance the number of processors. One example coming with the source code
of Amber is /benchmarks/dhfr but it takes only seconds to run on a single
processor and there is no documentation for how to make it bigger or how to
extend it or if it is meaningful to the biochemistry/&c. community.

The problem has to tax the processor preferably while going through the
Ewald and FFT parts of the sander link.

I am particularly interested in problems which demands resources or time
beyond realistic computational constraints.


Many thanks, and I will post back the responses I get,



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Received on Tue May 31 2005 - 21:53:00 PDT
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