The scalability performance of several critical bioinformatics applications, including BLAST, FASTA, Smith-Waterman, HMMER, ICED and Mascot, was evaluated on AIX 5.1 and SUSE Linux Enterprise Server 8 for IBM eServer pSeries. These applications are either threaded or Open MP-enabled parallel implementations. The comparison was conducted on the same LPAR of a p690 with 16 CPUs. The results suggested that the scalability of these applications on AIX and Linux are comparable, in general. This paper evaluates how well the leading bioinformatics applications scale on the current offering of Linux on pSeries 690.
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