Benchmarking and Tuning the GROMACS Molecular Dynamics Package on Beowulf Clusters Charles Peck, Josh Hursey, Josh McCoy Earlham College, Indiana University.

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Presentation transcript:

Benchmarking and Tuning the GROMACS Molecular Dynamics Package on Beowulf Clusters Charles Peck, Josh Hursey, Josh McCoy Earlham College, Indiana University Charles Peck, Josh Hursey, Josh McCoy Earlham College, Indiana University

Stanford University Safe Passage Communications, Inc

A Bit of History

Pre- 300 B.C. Babylonians 1632 John Napier 1820’s Charles Babbage 1944 Harvard Mark I Konrad Zuse 1960s Integrated Circuit

Gordon Moore’s Law The number of transistors, per square inch, on integrated circuits will double every 18 months for the foreseeable future. Year Memory Contents Physical Size Bytes One Short Sentence Phone Booth Kbytes 200 Page Thesis Shoe Box Mbytes 300 Books Credit Card 2030 Approximately the size of a human brain [storage only] Year Memory Contents Physical Size Bytes One Short Sentence Phone Booth Kbytes 200 Page Thesis Shoe Box Mbytes 300 Books Credit Card 2030 Approximately the size of a human brain [storage only]

High Performance Computing Parallel Processing

Top500 List First 40 [Rmax via LINPACK]

Green Dots Top500 List Clusters Marked by Green Dots

Beowulf Clusters

Computational Science

Protein Folding & Molecular Dynamics

Performance: Benchmarking & Tuning Methodology

WeatherDuck

GROMACS: Layers 1.GROMACS 2.FFTW 3.LAM-MPI 4.OS: Linux 5.Network Layer 1.GROMACS 2.FFTW 3.LAM-MPI 4.OS: Linux 5.Network Layer

Conclusion

Questions

Methodology  Create Benchmarking Suite  Generate a list of Parallel Structures 1.Choose a Test Case 2.Choose a Parallel Structure 3.Determine Optimal Option Profile for each Layer 4.Test Optimal Option Profile for all Parallel Structures 5.Test Optimal Option Profile for each Test Case in the Benchmarking Suite.  Create Benchmarking Suite  Generate a list of Parallel Structures 1.Choose a Test Case 2.Choose a Parallel Structure 3.Determine Optimal Option Profile for each Layer 4.Test Optimal Option Profile for all Parallel Structures 5.Test Optimal Option Profile for each Test Case in the Benchmarking Suite.