Phylogenetic analysis combining information from different data partitions

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Test Platforms
MrBayes Computational Biology Code
Understanding parallel environments and focusing
on performance of a computational biology code on
two supercomputing systems.

• Read the Nexus data file
• Set the evolutionary model
• Running the analysis
• Summarize the samples

• Phylogenetic analysis combining information from
  different data partitions
• Evaluates trees and reconstructs DNA structure
• Estimates how much confidence one can have in
  different branches of the tree
• Leads to more efficient drug development by
  understanding optimal combinations
• Includes 6 data sets with ranging set problem
  sizes determined by the taxonomy.

• Collect performance results from MrBayes
  computational biology code on two systems using
  PAIDE
• Analyze performance results on both systems by
  processor partitioning and analyzing overhead
• Model results using online prophesy modeling
  system

Chip Architecture

• In the power 5 chip architecture, the L3 cache
  is on chip compared to the off chip architecture
  in the power 4 system
• L3 cache serves as a victim cache

http//www.research.ibm.com/journal/rd/494/sinha1.
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• Parallel processing and multicore systems
• Computational biology applications
• Better drug development
• More efficient drugs
• Performance results
• Chip architecture
• Resource contention
• Communication affecting execution time
• Future work
• Fine tune application to improve scalability

PAIDE
I would like to thank the CRA-W DMP Program from
which this research is funded. Also to Dr.
Valerie Taylor and special thanks to Dr. Xingfu
Wu.
http//prophesy.cs.tamu.edu/