Basic HTML version of Foils prepared April 7,1995

Foil 31 Difficult but (almost) possible for HPF

From Programming Paradigms B CRPC/MCNC Workshop -- April 10-13 1995. by Geoffrey C. Fox
1 Molecular Dynamics
  • Cutoff (bonded) forces (Fij = 0, |ri-rj|>d) and long range (O(N2) non- bonded) forces
2 Basic steps in the algorithm:
  • 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.
  • 2) Iterate several times
    • Calculate bonded interactions
    • Calculate non-bonded interactions
  • Both of the above steps can be represented in HPF
  • Extensions needed:
    • Specification of Partitioner
    • (and potentially incremental partitioners)
    • Extensions of Forall for performing reduction
3 Unstructured Finite Element Meshes
  • Data structure involves array of pointers
  • Use Forall extended for performing reductions
  • Interface with static (and incremental) partitioners for optimized performance
4 Performance of SIMD or Autonomous SIMD (Maspar) versus MIMD unclear for these irregular applications
in Table To:

Northeast Parallel Architectures Center, Syracuse University, npac@npac.syr.edu

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