APM

INF560_Project_APM

Different versions are kept in different branches with corresponded name. Compilation is done by make command.

Usage:

seq branch:

./apm approximation_factor dna_database pattern1 pattern2 ...

MPI branch:

salloc -N 1 -n 4 mpirun ./apm approximation_factor dna_database pattern1 pattern2

salloc -N 1 -n 9 mpirun ./apm 2 ./dna/chr9.fa AAAA AAAA AAAA AAAA AAAA AAAA AAAA AAAA

openMP branch:

salloc -n 1 ./apm approximation_factor dna_database pattern1 pattern2

salloc -n 1 ./apm 2 ./dna/chr9.fa AAAA AAAA AAAA AAAA AAAA AAAA AAAA AAAA

hybrid branch:

salloc -N 1 -n 4 mpirun ./apm approximation_factor dna_database pattern1 pattern2

salloc -N 1 -n 9 mpirun ./apm 2 ./dna/chr9.fa AAAA AAAA AAAA AAAA AAAA AAAA AAAA AAAA

gpu branch:

./apm_gpu approximation_factor dna_database pattern1 pattern2

./apm_gpu 2 ./dna/chr9.fa AAAA AAAA AAAA AAAA AAAA AAAA AAAA AAAA