(Georgia Institute of Technology, 2006-02-26)
Bader, David A.; Chandu, Vaddadi P.; Yan, Mi
Constructing phylogenetic trees in the study of the evolutionary history of a group
organisms is an extremely challenging problem in computational biology. The problem
becomes intractable with growing number of organisms. In this paper, we design and
implement an efficient parallel solver (ExactMP) using a parsimony based approach for
solving this problem. We create a testbed consisting of eighteen datasets of varying size
(up to 27 taxa) and difficulty level (easy to hard), containing real (Eukaryotes, Metazoan, and rbcL) and randomly-generated synthetic genome sequences. We demonstrate
our ExactMP Solver against this testbed and achieve a parallel speedup of up to 7.26
with 8 processors using an 8-way symmetric multiprocessor. The main contributions of
this work are: (1) an efficient parallel solver ExactMP for the problem of phylogenetic
tree reconstruction using maximum parsimony, (2) a new upper bounding methodology for this problem using heuristic and randomization techniques, and (3) a highly
optimized branch and bound algorithm for this problem.
(Georgia Institute of Technology, 2006-02-25)
Sottile, Matthew J.; Chandu, Vaddadi P.; Bader, David A.
The ability to understand the factors contributing to parallel program performance
are vital for understanding the impact of machine parameters on the performance of
specific applications. We propose a methodology for analyzing the performance characteristics
of parallel programs based on message-passing traces of their execution on a
set of processors. Using this methodology, we explore how perturbations in both single
processor performance and the messaging layer impact the performance of the traced
run. This analysis provides a quantitative description of the sensitivity of applications
to a variety of performance parameters to better understand the range of systems upon
which an application can be expected to perform well. These performance parameters
include operating system interference and variability in message latencies within the
interconnection network layer.