We present here the design strategy and performance analysis of a large scale scientific application, for the prediction of 3D Protein structures. The unique challenges which will be investigated are the primary objectives of a reduction in wall clock run time through the parallelization process, and the production of an application capable of running and scaling to a massively parallel configuration (currently 1024 nodes of the Intel Paragon) reliably for many non-contiguous days of supercomputer time. Enough flexibility to be reconfigured for a number of different parallel architectures including the CRAY T3E and IBM SP2 was included through the use of MPI as the parallel software layer. The application, GEOCORE, predicts small ensembles of native-like peptide conformations from amino acid sequences. GEOCORE uses a very simple energy function and an extensive conformational search process. The serial program has been tested on around 20 small peptides and is shown to be capable of discriminating native from non-native structures.

Article Free Access Share on Validating system requirements by functional decomposition and dynamic analysis Author: Kaizhi Yue USC/Information Sciences Institute, 4676 Admiralty Way, Marina de1 Rey, CA USC/Information Sciences Institute, 4676 Admiralty Way, Marina de1 Rey, CAView Profile Authors Info & Claims ICSE '89: Proceedings of the 11th international conference on Software engineeringMay 1989 Pages 188–196https://doi.org/10.1145/74587.74613Published:15 May 1989Publication History 4citation831DownloadsMetricsTotal Citations4Total Downloads831Last 12 Months11Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF