AMBER Archive (2003)

Subject: RE: anyone have AMBER benchmarks with gigabit ethernet?

From: Ross Walker (r.c.walker_at_ic.ac.uk)
Date: Thu Apr 24 2003 - 04:42:57 CDT

Dear Carlos,

If you go to http://www.rosswalker.co.uk/files/amber7_bench.xls there is
an excel spreadsheet of a range of amber 7 tests I have conducted using
dual processor athlon 2200MP's with gigabit and scali.

Using lam 6.5.9 with the intel v7.0 ifc compilers with -D_REENTRANT,
-O3, -tpp6 options and including -DMPI, -DROWAT and -DRLE in the system
flags at compilation I can get (for LADH ca 76000 atoms) 9.58x speed up
over 16 cpus with scali and 8.69x speedup for gigabit.

For the JAC benchmark I get 7.68x speedup over scali (16 cpus) and 6.14x
over gigabit which is essentially the same as those quoted for redfish
on the amber website.

I hope this helps

All the best
Ross

/\
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|\oss Walker

| Imperial College London |
| Department of Biological and Biophysical Chemistry |
| Tel:- +44 20 759(45851) |
| EMail:- ross_at_rosswalker.co.uk | http://www.rosswalker.co.uk/ |
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> -----Original Message-----
> From: Carlos Simmerling [mailto:carlos_at_csb.sunysb.edu]
> Sent: 23 April 2003 19:37
> To: amber_at_heimdal.compchem.ucsf.edu
> Subject: anyone have AMBER benchmarks with gigabit ethernet?
>
>
> does anyone have benchmarks for AMBER7 using
> gigabit ethernet? There are numbers on the AMBER
> benchmark page but we are unable to reproduce the
> scaling values (ours are much worse). I'd like to hear
> from anyone else what they have tried.
> Note that this is for gigabit ethernet, not Myrinet or Giganet.
> thanks
> Carlos
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Assistant Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web:
> http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115
> E-mail: carlos.simmerling_at_stonybrook.edu
> ===================================================================
>
>
>
>
>