Processors Clustered

J. Bu and E. Deprettere. Processor clustering for the design of optimal fixed-size systolic arrays. Algorithms and Parallel VLSI Architectures, Vol. A, pages 341-362. North Holland, Elsevier, Amsterdam, 1991. 

J. Bu and E. Deprettere. A constructive procedure for processor clustering and array optimization. Proc, International Symposium on Circuits and Systems pages 248-251,1991. 

The Fourier sum, involving the three dimensional FFT, does not currently run efficiently on more than perhaps eight processors in a network-of-workstations environment. On a more tightly coupled machine such as the Cray T3D/T3E, we obtain reasonable efficiency on 16 processors, as shown in Fig. 5. Our initial production implementation was targeted for a small workstation cluster, so we only parallelized the real-space part, relegating the Fourier component to serial evaluation on the master processor. By Amdahl s principle, the 16% of the work attributable to the serially computed Fourier sum limits our potential speedup on 8 processors to 6.25, a number we are able to approach quite closely. 

As noted above, one of the goals of NAMD 2 is to take advantage of clusters of symmetric multiprocessor workstations and other non-uniform memory access platforms. This can be achieved in the current design by allowing multiple compute objects to run concurrently on different processors via kernel-level threads. Because compute objects interact in a controlled manner with patches, access controls need only be applied to a small number of structures such as force and energy accumulators. A shared memory environment will therefore contribute almost no parallel overhead and generate communication equal to that of a single-processor node. 

Van Vliet et al. (2005) tracked 1x10 computational nodes to obtain a stochastic solution of their FDF equations. In order to deal with the high computational costs, the code was run in parallel on a Linux cluster of 11 dual AMD Athlon (TM) MP 1800 +processors. In this way, about one turbulent macro time scale (or 8,000 computational steps) per 2 days was computed. 

Mainframes are large computers comprised of a cluster of tightly coupled machines or having multiple processors. These units will often be set up for specific applications as database servers, or for handling calculations such as those generated by quantum mechanics-based computational chemistry methods. 

Computer clusters contain a number of processors put together on a motherboard into a unit known as a node. The nodes are then hooked together with other boards via high-speed communications networks. Nodes can be hardwired into supercomputers produced by companies like IBM and Compaq or... 

We also performed a simulation of the HIV accessory protein using the adapted parallel tempering method [13]. We used 20 processors of an INTEL XEON PC cluster and ran the simulation for a total of 30 x 10 energy evaluations for each configuration, which corresponds to approximately 500 CPU hours on an 2.4 GHz INTEL XEON processor. All simulations were started... 

For data evaluation also self-programmed software (mostly in BTCL, Fortran, C) was applied. Data production runs were performed on a 74 processor Opteron Linux Cluster, a SGI Origin 2100 and on SGI Onyx workstation. 

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