Parallelization of Genome Sequence Comparison
Completed for academic work - Queensland University of Technology
cvtree-sequential-original.sh - Original sequential program. Does not compile nor run in this environment.
cvtree-sequential.cpp - Improved sequential program.
cvtree-parallel.cpp - Parallelized program using OpenMP.
The compiled program (either sequential or parallel) takes a single parameter indicating the data directory containing the genome sequences.*
To quickly compile and run the cvtree on sequences within the data/ directory, the scripts sequential.sh and parallel.sh can be used.
These shell scripts run as follows:
rm -f sequential.out
g++ -O2 cvtree-sequential.cpp -o sequential.out
./sequential.out data/
rm -f sequential.out
rm -f parallel.out
g++ -O2 -fopenmp cvtree-parallel.cpp -o parallel.out
./parallel.out data/
rm -f parallel.out
*Please note that a full relative data directory path must be specified, with trailing forward slashes, as seen above.
The program will output a .csv file containing the results of the correlation matrix calculated during execution, for each unique pair of sequences.