Benchmarking and Tuning the GROMACS Molecular Dynamics Package on Beowulf Clusters

Benchmarking and Tuning the GROMACS Molecular Dynamics Package on Beowulf Clusters

Charles Peck, Josh Hursey, Josh McCoyEarlham College, Indiana University

Charles Peck, Josh Hursey, Josh McCoyEarlham College, Indiana University

Stanford UniversityStanford University

Safe PassageSafe PassageCommunications, IncCommunications, Inc

A Bit of HistoryA Bit of History

Pre- 300 B.C.Babylonians

1632John Napier

1820’sCharles Babbage

1944Harvard Mark I

1939-44Konrad Zuse

1960sIntegrated Circuit

Gordon Moore’s LawGordon Moore’s LawThe number of transistors, per square inch, on The number of transistors, per square inch, on

integrated circuits will double every 18 integrated circuits will double every 18 months for the foreseeable future.months for the foreseeable future.

The number of transistors, per square inch, on The number of transistors, per square inch, on integrated circuits will double every 18 integrated circuits will double every 18

months for the foreseeable future.months for the foreseeable future.

Year Year Memory Contents Physical SizeMemory Contents Physical Size

19501950 32 Bytes One Short Sentence Phone Booth 32 Bytes One Short Sentence Phone Booth

19751975 640 Kbytes 200 Page Thesis Shoe Box 640 Kbytes 200 Page Thesis Shoe Box

20002000 256 Mbytes 300 Books Credit Card 256 Mbytes 300 Books Credit Card

20302030 Approximately the size of a human brain [storage only] Approximately the size of a human brain [storage only]

Year Year Memory Contents Physical SizeMemory Contents Physical Size

19501950 32 Bytes One Short Sentence Phone Booth 32 Bytes One Short Sentence Phone Booth

19751975 640 Kbytes 200 Page Thesis Shoe Box 640 Kbytes 200 Page Thesis Shoe Box

20002000 256 Mbytes 300 Books Credit Card 256 Mbytes 300 Books Credit Card

20302030 Approximately the size of a human brain [storage only] Approximately the size of a human brain [storage only]

High Performance ComputingHigh Performance ComputingHigh Performance ComputingHigh Performance Computing

Parallel ProcessingParallel Processing

Top500 List First 40 [Rmax via LINPACK]

Top500 List First 40 [Rmax via LINPACK]

Top500 List Clusters Marked by Green DotsGreen Dots

Top500 List Clusters Marked by Green DotsGreen Dots

Beowulf ClustersBeowulf Clusters

Computational ScienceComputational Science

Protein Folding &Molecular Dynamics

Protein Folding &Molecular Dynamics

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Performance:Benchmarking & Tuning

Methodology

Performance:Benchmarking & Tuning

Methodology

WeatherDuckWeatherDuck

GROMACS: LayersGROMACS: Layers

1. GROMACS2. FFTW3. LAM-MPI4. OS: Linux5. Network Layer

1. GROMACS2. FFTW3. LAM-MPI4. OS: Linux5. Network Layer

Conclusion

http://cluster.earlham.edu

Conclusion

http://cluster.earlham.edu

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