This benchmark runs a single alignment between a pair of simulated sequences of varying batches sizes. The intention of this benchmark is to measure the performance of a single alignment in CUDA.

To run the benchmark, execute

./benchmarks/cudaaligner/benchmark_cudaaligner_singlebatch_singlealignment

This benchmark runs a varying number of alignments within a single batch, each of varying string sizes. The intention of this benchmark is to measure performanceo of batched alignment.

To the the benchmark, execute

./benchmarks/cudaaligner/benchmark_cudaaligner_singlebatch_multialignment