Distance: A New Metric for Controlling Granularity for Parallel Execution

Distance: a New Metric for Controlling Granularity for Parallel Execution Distance: a New Metric for Controlling Granularity for Parallel Execution

Granularity control is a method to improve parallel execution performance by limiting excessive parallelism. The general idea is that if the gain obtained by executing a task in parallel is less than the overheads required to support parallel execution, then the task is better executed sequentially. Traditionally, in logic programming task size is estimated from the sequential time-complexity o...

A New Metric for Controlling Granularity for Parallel Execution

Multi-granularity Parallel Computing in a Genome-Scale Molecular Evolution Application

Previously [1], we reported a coarse-grained parallel computational approach to identifying rare molecular evolutionary events often referred to as horizontal gene transfers. Very high degrees of parallelism (up to 65x speedup on 4,096 processors) were reported, yet the overall execution time for a realistic problem size was still on the order of 12 days. With the availability of large numbers ...

Drug Discovery Acceleration Using Digital Microfluidic Biochip Architecture and Computer-aided-design Flow

A Digital Microfluidic Biochip (DMFB) offers a promising platform for medical diagnostics, DNA sequencing, Polymerase Chain Reaction (PCR), and drug discovery and development. Conventional Drug discovery procedures require timely and costly manned experiments with a high degree of human errors with no guarantee of success. On the other hand, DMFB can be a great solution for miniaturization, int...

Capsules: expressing composable computations in a parallel programming model

A well-known problem in designing high-level parallel programming models and languages is the “granularity problem”, where the execution of parallel task instances that are too fine-grain incur large overheads in the parallel runtime and decrease the speed-up achieved by parallel execution. On the other hand, tasks that are too coarse-grain create load-imbalance and do not adequately utilize th...