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Unformatted text preview: (or unset): use shared memory –  CHPL_COMM=gasnet: use distributed memory •  Depending on your plaworm, you may also need to tell GASNet how to launch an SPMD program –  Brandon has prepared READMEs for the VM and UW cluster •  One snafu: The pre- built Chapel I gave you embedded my paths into your build – so you’ll need to rebuild it –  Sorry… though GASNet gets the blame CSEP 524: Parallel ComputaIon Winter 2013: Chamberlain 69 Smith- Waterman Algorithm for Sequence Alignment Smith- Waterman Goal: Determine the similariIes/differences between two protein sequences/nucleoIdes. –  e.g., ACACACTA and AGCACACA* Basis of Computa3on: Defined via a recursive formula: H(i,0) = 0 H(0,j) = 0 H(i,j) = f(H(i-1, j-1), H(i-1, j), H(i, j-1)) Caveat: This is a classic, rather than cuyng- edge...
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This document was uploaded on 04/04/2014.

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