Implementing and Accelerating HMMER3 Protein Sequence Search on CUDA-Enabled GPU Lin Cheng The recent emergence of multi-core CPU and many-core GPU architectures has made parallel computing more accessible. Hundreds of industrial and research applications have been mapped onto GPUs to further utilize the extra computing resource. In bioinformatics, HMMER isâ€¦ (More)

In this paper, we present a heuristic for broadcasting in arbitrary networks. This heuristic generates optimal broadcast time for ring, tree and grid graphs when the originator is a corner vertex. In practice, the new heuristic outperforms the best known broadcast algorithms for three different network models. The time complexity of one round of theâ€¦ (More)

We continue the investigation of k-broadcasting, a variant of broadcasting in which an informed vertex can call up to k of its neighbors in each time unit. A focus of the investigation into broadcasting is the function Bk(n), which is the minimum number of edges in any n vertex graph such that each vertex can originate a k-broadcast that completes inâ€¦ (More)

2014 IEEE Intl Conf on High Performance Computingâ€¦

2014

Performance of a multicomputer largely depends on that of the underlying network communications such as multicast, which is essential for processors in multicomputer to exchange data and messages. Two major parameters used to evaluate multicast routing are the time it takes to deliver the message to all destinations and the traffic which refers to the totalâ€¦ (More)