AMBER Archive (2005)

Subject: Re: AMBER: amber on sgi

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Mar 09 2005 - 07:32:29 CST

Mathew -
Look at the amber 8 benchmarks page at amber.scripps.edu. The 1.5 GHz altix
is about 4 times faster than an SGI Origin 3800. I don't know whether this
machine is an R12000 or R14000, but the 3800 at UNC is an R14000 at 500 MHz.

For Factor ix (90906 atoms - I use const pressure), on the UNC SGI Origin
3800 I get (using pmemd rel 8):

# procs psec/day
  1 31.2
  4 108.2
  8 198.3

For a 1.3 GHz altix itanium, the California gang got:

# procs psec/day
  1 114
  4 368
  8 709

Roberto Gomperts of SGI has a nice series of benchmarks for pmemd and sander
on the altix; the link is:
www.sgi.com/industries/sciences/chembio/resources/amber/amber040928.html
There are newer versions of the altix with faster chips and bigger caches
that are even bigger screamers (over 5 nsec/day with pmemd 8 on 64 procs for
factor ix - 90906 atoms - pme). Roberto would probably also be able to
expound more on relative speed between the R14000 and R16000 as well as
relative benefits of the two machines. I personally think the altix is an
incredible compute engine for MD. Roberto has a "contact" link out under
the SGI benchmarks.

Regards - Bob Duke

----- Original Message -----
From: "mathew k varghese" <mathew_kvarghese_at_yahoo.co.in>
To: <amber_at_scripps.edu>
Sent: Wednesday, March 09, 2005 6:23 AM
Subject: AMBER: amber on sgi

> Dear amber community,
>
> Our university is planning to purchase an sgi
> machine.What is your openion about a machine with
> R16000 processor? Is it suitable for the calculations?
> What about the altix350 system with itanium processor?
> Which one is better?
> Thanks in advance
>
>
>
> ===========================================================================
>
> /\/\athew
>
> Mathew K Varghese
> Research Scholar
> School of Pure and Applied Physics
> M.G.University
> Kottayam, Kerala
> India
>
> email mathew_kvarghese_at_yahoo.co.in
>
> ===========================================================================
>
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