Specialized Network Topologies for Efficient Communication in Computer Clusters1

A topology of point-to-point interconnections is an efficient way to network a cluster of computers with well-defined communication patterns. Such a specialized topology allows parallelized programs to run with little penalty. Combining a specialized topology with a local area network (LAN) decreases traffic on the LAN and increases redundancy in the entire combined network. We developed a hierarchical hypercube topology for a cluster of personal computers (PCs). A hier-archical hypercube is a hypercube topology with links of different speeds. Links representing the first dimension are the fastest, whereas those representing higher dimensions are successively slower. This sequence of speeds forms the hierarchy in this topology. The cluster’s topology was designed for the macromolecular mechanics program CHARMM [1], specif-ically the distributed global sum and broadcast operations [2] that account for most of the data exchange among processes in our cluster. CHARMM’s implementation on a hypercube topology has the property that it transmits and receives different amounts of data through different dimensions [2], as depicted in fig. 1(a). The amount of data transferred in each successive dimension is halved. For this communication pattern not all of the links are used efficiently if they are all of the same speed. Only links representin