Scalability Comparison of Bioinformatics for Applications on AIX and Linux on IBM eServer pSeries 690

An IBM Redpaper publication

Published 05 August 2004

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IBM Form #: REDP-3803-00

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Authors: Yinhe Cheng, Joyce Mak, Tzy-Hwa Kathy Tzeng


The scalability performance of several critical bioinformatics applications, including BLAST, FASTA, Smith-Waterman, HMMER, Mascot and ICED, was evaluated on AIX 5.1 and SUSE Linux Enterprise Server 8 for IBM eServer pSeries. These applications are either threaded or OpenMP-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.

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