Molecular Dynamics
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Cutoff (bonded) forces (Fij = 0, |ri-rj|>d) and long range (O(N2) non- bonded) forces
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Basic steps in the algorithm:
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1) calculate the non-bonded interaction list. This is done by N2 algorithm. The efficient algorithms based on spatial decomposition are not easily represented in HPF.
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2) Iterate several times
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Calculate bonded interactions
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Calculate non-bonded interactions
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Both of the above steps can be represented in HPF
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Extensions needed:
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Specification of Partitioner
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(and potentially incremental partitioners)
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Extensions of Forall for performing reduction
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Unstructured Finite Element Meshes
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Data structure involves array of pointers
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Use Forall extended for performing reductions
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Interface with static (and incremental) partitioners for optimized performance
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Performance of SIMD or Autonomous SIMD (Maspar) versus MIMD unclear for these irregular applications
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