1. 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

2. Stanford University Safe Passage Communications, Inc

3. A Bit of History

4. Pre- 300 B.C. Babylonians 1632 John Napier 1820’s Charles Babbage 1944 Harvard Mark I 1939-44 Konrad Zuse 1960s Integrated Circuit

5. 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 1950 32 Bytes One Short Sentence Phone Booth 1975 640 Kbytes 200 Page Thesis Shoe Box 2000 256 Mbytes 300 Books Credit Card 2030 Approximately the size of a human brain [storage only] Year Memory Contents Physical Size 1950 32 Bytes One Short Sentence Phone Booth 1975 640 Kbytes 200 Page Thesis Shoe Box 2000 256 Mbytes 300 Books Credit Card 2030 Approximately the size of a human brain [storage only]

6. High Performance Computing Parallel Processing

7. Top500 List First 40 [Rmax via LINPACK]

8. Green Dots Top500 List Clusters Marked by Green Dots

9. Beowulf Clusters

11. Computational Science

13. Protein Folding & Molecular Dynamics

15. Performance: Benchmarking & Tuning Methodology

16. WeatherDuck

17. 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

18. Conclusion http://cluster.earlham.edu

19. Questions

20. 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.