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Estimation of the pose in which two given molecules might bind together to form a potential complex is a crucial task in structural biology. To solve this so-called "docking problem", most algorithms initially generate large numbers of candidate poses (or decoys) which are then clustered to allow for subsequent computationally expensive evaluations of reasonable representatives. Since the...
We investigate the problem of partitioning finite difference meshes in two dimensions among the processors of a parallel computer. The objective is to achieve a perfect load balance while minimizing the communication cost. There are well-known graph, hypergraph, and geometry-based partitioning algorithms for this problem. The known geometric algorithms have linear running time and obtain the best...
With the end of Moore's Law in sight, parallelism became the main means for speeding up computationally intensive applications, especially in the cases where large collections of tasks need to be performed. Network supercomputing -- taking advantage of very large numbers of computers in a distributed environment is an effective approach to massive parallelism that harnesses the processing power inherent...
Unstructured peer-to-peer (P2P) architectures offer several benefits to implement semantic discovery and composition in future-generation service registries. However, their success strongly depends on the adoption of efficient techniques for disseminating semantic queries over the network. Gossip strategies significantly reduce the amount of messages with respect to flooding, but they need a predefined...
Modern multicore systems offer huge computing potential. Exploiting large parallel systems is still a very challenging task, however, especially as many software developers still use overly-sequential programming models. refactoring tool support that allows the programmer to introduce and tune parallelism in an easy and effective way, exploiting high-level parallel patterns such as farms and pipelines...
In this paper, we recall the methodology, proposed in [7], for constructing correct and efficient routing strategies for distributed memory multicomputers. As the methodology is based on a primary communication scheme, we choose routing by Eulerian cycle rules [9] as the primary one. We first propose an improvement of this latter routing scheme. Then, we apply the general routing strategy to the torus...
Traditionally, skeleton based parallel programming frameworks support data parallelism by providing the programmer with a comprehensive set of data parallel skeletons, based on different variants of map and reduce patterns. On the other side, more conventional parallel programming frameworks provide application programmers with the possibility to introduce parallelism in the execution of loops with...
The advent of emergent System-on-Chip (SoCs) and multiprocessor System-on-Chip (MPSocs) opens a new era on the small mobile devices (Smartphones, Tablets, ...) in terms of computing capabilities and applications to be addressed. The efficient use of such devices, including the parallel power, is still a challenge for general purpose programmers due to the very high learning curve demanding very specific...
In this paper we explore machine-learning approaches for dynamically selecting the well suited amount of concurrent threads in applications relying on Software Transactional Memory (STM). Specifically, we present a solution that dynamically shrinks or enlarges the set of input features to be exploited by the machine-learner. This allows for tuning the concurrency level while also minimizing the overhead...
This paper proposes an effective barrier synchronization implementations for shared memory-based parallel programming models (e.g. OpenMP) on the Intel SCC non-cache- coherent platform. Barrier synchronization primitives are key components of these programming models to coordinate the parallel threads. Therefore, we need an efficient implementation of the underlying synchronization algorithms to allow...
The hamming weight (also known as population count) of a bitstring is the number of 1's in the bitstring. It has applications in scopes like cryptography, chemical informatics and information theory. Typical bitstring lengths range from the processor's word length to several thousands of bits. A plethora of hamming weight algorithms have been pro- posed. While some implementations expose just scalar...
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