Parallelising Molecular Dynamics for Message Passing Systems by Martin Gerber

By Martin Gerber

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Standard microprocessor performance increases about 50–70% per year, and the memory capacity about 30–50%. Parallel machines must follow this curve of performance growth to remain competitive. Because the DRAM access time is not growing as fast as the operating frequency of microprocessors, sophisticated cache structures are required to bridge this timing gap. To follow this technological progress popular manufacturers of high performance parallel machines started to use off-the-shelf microprocessors or even full workstation nodes in their latest parallel computers.

If a satisfactory schedule fulfilling the optimisation or design goal may not be found, the proposed implementation is not a valid system. 2), or try different allocations and bindings until a valid schedule may be developed. This iterative characteristic was the motivation to apply a semi-automated approach which is described in the next section. Complex operations are represented by a functional node mapped on, for example, a dedicated hardware chip. Of course an exact prediction of cost, execution time and memory demand is not possible for such bindings, and an exact measurement implies the synthesis of these components.

The modified logP model which was presented here can accurately predict communication performance with long messages of constant length. g. IBM SP-2 [53], Paragon, and most message passing libraries). This dependence could easily be included in the model by making the bandwidth a function of the message length. An alternative extension to the original logP model proposes a linear model for long messages, this way accurately modelling short and long messages, at the expense of an additional communication parameter [27].

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