A simple one would be NCBI-Blast, the sources and binaries are readily available, as are
the databases. Normally you search against a database (eg. the nt nucleotide db)
with a set of possibly unknown sequences. It's fairly simple to select a larger/smaller
set of tests, or a different size database to test with larger or longer runs. Do you
have specific hardware that you need to optimise for, or is it fairly "vanilla"?