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Optimizing AMBER for the CRAY T3E and IBM SP

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AMBER is the collective name for a suite of programs that allow users to carry ... AMBER not only accounts for the greatest usage of CPU time on the SDSC CRAY T3E, ... – PowerPoint PPT presentation

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Title: Optimizing AMBER for the CRAY T3E and IBM SP


1
Strategic Application Collaboration AMBER
Collaborators Peter Kollman (UCSF), Dave Case,
Mike Crowley (TSRI)
Robert Sinkovits, Jerry Greenberg (SDSC)
AMBER is the collective name for a suite of
programs that allow users to carry out molecular
dynamics simulations, particularly on
biomolecules.
AMBER not only accounts for the greatest usage of
CPU time on the SDSC CRAY T3E, but is used
extensively by researchers in the biochemistry
and pharmaceutical communities worldwide.
2
AMBER Accomplishments
  • Improved performance of AMBER 5.0 pairlist
    calculations by up to 70
  • Integrated work done at SDSC and UCSF to nearly
    double code performance
  • Optimized particle mesh Ewald calculations for
    speedups of 25
  • Tuned Extended Generalized Born (EGB)
    calculations for up to 2.2x speedup
  • Provided detailed documentation on all code
    changes

Code modifications already included in AMBER
pre-release (v 5.0.1),slated for inclusion in
next major AMBER release (v 6.0, summer 99)
3
Comparison of original and hand tuned codes
AMBER 5.0 - current release version of code SDSC
AMBER - tuned version of AMBER 5.0 UCSF AMBER -
UC San Francisco modifications Merged AMBER -
combined SDSC and UCSF optimizations
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