Re: AMBER: amber 8 benchmarks dec alpha

From: Robert Duke <>
Date: Mon, 24 Jan 2005 17:27:50 -0500

Sergio -
PMEMD benchmarks are out on the amber web site, If you
follow the pmemd link and look at the old release notes for pmemd 3.0 and
3.1, there are fairly complete benchmarks for pmemd 3.0/3.1, which are
maybe a little slower than pmemd 8. The only numbers I published for pmemd
8 is on the benchmarks page; I just copied it below. These two sources give
you some starting points; if you are not interested in using pmemd, you
should probably not run sander at really high processor count as it is not
very efficient. All my numbers were produced on PSC machines.
Regards - Bob Duke


LEMIEUX PERFORMANCE, Compaq 1 GHz ES45 alphaserver, Quadrics interconnect

With the Quadrics interconnect, it is possible to use one or two
"rails", with one rail being the default. Performance may be improved by
of two rails by on the order of 10-20%, but at the time of benchmarking,
appeared to be system problems associated with using two rails. Thus, at
present we only present data for one rail, and only recommend the use of one
rail. PMEMD optimization is the default optimization (no DIRFRC_*)
which produced the best results over a range of values.

90906 Atoms, Constant Pressure Molecular Dynamics (Factor IX)

#procs PMEMD Sander 8
              psec/day psec/day

  64 (4x16) 1745 500
 128 (4x32) 2615 1172

Benchmarks were run on NCSA's Itanium 1 Linux cluster, which has a Myrinet
interconnect. The Itanium 1 is significantly slower than the Itanium 2, but
the benchmarks show good PMEMD scaling on the Myrinet interconnect out to
about 32 processors, which is fairly typical. The Itanium chips have a huge
L3 cache, so PMEMD is best optimized using DIRFRC_BIGCACHE_OPT (the
----- Original Message -----
From: "Sergio E. Wong" <>
To: <>
Sent: Monday, January 24, 2005 5:08 PM
Subject: AMBER: amber 8 benchmarks dec alpha

> Dear sirs;
> I was wondering if anyone had any sort of amber 8 benchmark on dec
> alphas (compiled with the compaq f90 compiler). Thanks
> -Sergio
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Received on Mon Jan 24 2005 - 22:53:00 PST
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