AMBER Archive (2005)

Subject: Re: AMBER: amber8 parallel sander

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Sep 22 2005 - 11:57:53 CDT

Kathleen -
Don't know who you were talking to on this one. PMEMD 8, which offers a subset of sander functionality (primarily pme explicit solvent calcs) scales well on good hardware out to about 128 procs, and has been competitive with namd on various platforms for top-end scaling. Versions under current development scale well out past 128 procs, depending once again on the h/w, though going over 200 procs is impractical with the current parallelization infrastructure. There has been an emphasis on getting good per processor performance, followed by scaling well up to reasonable numbers of processors, to yield good simulation througput. We can achieve on the order of 6-7 nsec/day simulating large (~100K atoms) explicit solvent systems with pme electrostatics; this is nothing to sneeze at. I don't actually know of many places where folks can get 256, 512, 1024 procs for days on end without obliterating their compute allocation.
Regards - Bob Duke
  ----- Original Message -----
  From: Kathleen Erickson
  To: amber_at_scripps.edu
  Sent: Thursday, September 22, 2005 12:44 PM
  Subject: Re: AMBER: amber8 parallel sander

  Peter: So are you saying that scaling efficiencies beyond 8 CPUs are better achieved with NAMD? In other words, is 8 CPUs the limit for most effiencient scaling on AMBER? I'd like to know at which point AMBER users find they need to switch to NAMD or some other MD package. -Kathleen

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