Systolic loop algorithm

Windemuth and Schulten described a further variant of the systolic loop algorithm, the replicated systolic loop for the efficient calculation of macromolecular force fields on the Connection Machine (e.g., CM-1, CM-2, CM-5). The full force field was separated into bond interactions and nonbonding interactions only the latter were implemented on the Connection Machine, and parallelized by the replicated systolic loop algorithm. The former, less computationally intensive tasks were performed by an existing, conventional MD code on the front end. 

Which one of these variations one should use is mostly a question of the balance between communication and calculation of the parallel computer being used. In any case as the systems grow larger the RD method will be limited by the all-to-all global communication steps. However, there is an improvement of the RD method which avoids global all-to-all communication [102]. Also it is possible to combine the ideas of RD with systolic loop algorithms. The main reason to do this would be to decrease the need for node memory and it also opens up the possibility for overlapping communication and calculation [46,103-105]. 

Data movement in systolic loop algorithm for aU-to-aU broadcast involving four processes, P0-P3. Using p processes, the algorithm requires p - 1 steps. Initially, process Pi owns data Di, and upon completion, the full data set Do, Di, D2, D3 has been copied to every process. 

Smith has also described the implementation of MD on parallel machines, with particular reference to hypercube computers. In work designed to introduce a novice to the main aspects of parallel computing in MD, Smith described three particular algorithms replicated data (RD), systolic loop (SLS-G), and parallelized link cells (PLC), all of which have good load balancing. The performance characteristics of each algorithm and the factors affecting... 

Two categories of force decomposition algorithm have appeared in the literature those that systolically cycle atom data around a ring, and those based on the force-matrix formalism discussed by Plimpton.i o A variety of systolic loop methods have been implemented on both and... 

FIGURE 8-2. General treatment algorithm for acute decompensated heart failure (ADHF) based on clinical presentation. IV vasodilators that may be used include nitroglycerin, nesiritide, or nitroprusside. Metolazone or spironolactone may be added if the patient fails to respond to loop diuretics and a second diuretic is required. IV inotropes that may be used include dobutamine or milrinone. (D/C, discontinue HF, heart failure SBP, systolic blood pressure.) (Reprinted and adapted from J Cardiac Fail, Vol 12, pages el-el 22, copyright 2006, with permission from Elsevier.)... 

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