AMBER Archive (2007)

Subject: AMBER: MPI is slower than single processor with water

From: Mike Summers (summers_at_hhmi.umbc.edu)
Date: Tue Jan 16 2007 - 10:30:18 CST

Protein MD and minimization calculations run much faster
with MPI than with a single processor, as expected,
EXCEPT when I include water (solvateoct with TIP3PBOX).
In this case, the calculations actually run a little
slower compared to using a single processor.

Is this a general problem when performing calculations
with many molecules, or have I misset (or have not used) a
necessary flag?

Mike

*********************************
Michael F. Summers
Department of Chemistry and Biochemistry
  and Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250

Phone: (410)-455-2527
FAX: (410)-455-1174
Email: summers_at_hhmi.umbc.edu
Web: www.hhmi.umbc.edu
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