ACM SIGOPS Operating Systems Review
In search of clusters: the coming battle in lowly parallel computing
In search of clusters: the coming battle in lowly parallel computing
Efficient distributed shared memory based on multi-protocol release consistency
Efficient distributed shared memory based on multi-protocol release consistency
Scope consistency: a bridge between release consistency and entry consistency
Proceedings of the eighth annual ACM symposium on Parallel algorithms and architectures
Memory consistency and event ordering in scalable shared-memory multiprocessors
ISCA '90 Proceedings of the 17th annual international symposium on Computer Architecture
The DASH Prototype: Logic Overhead and Performance
IEEE Transactions on Parallel and Distributed Systems
JIAJIA: A Software DSM System Based on a New Cache Coherence Protocol
HPCN Europe '99 Proceedings of the 7th International Conference on High-Performance Computing and Networking
Shared virtual memory on loosely coupled multiprocessors
Shared virtual memory on loosely coupled multiprocessors
TreadMarks: distributed shared memory on standard workstations and operating systems
WTEC'94 Proceedings of the USENIX Winter 1994 Technical Conference on USENIX Winter 1994 Technical Conference
Brazos: a third generation DSM system
NT'97 Proceedings of the USENIX Windows NT Workshop on The USENIX Windows NT Workshop 1997
How to Make a Multiprocessor Computer That Correctly Executes Multiprocess Programs
IEEE Transactions on Computers
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Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distributed architectures where no physically shared memory exist. Scope consistent software DSMs provide a relaxed memory model that reduces the coherence overhead by ensuring consistency only at synchronisation operations, on a per-lock basis. Much of the work in DSM systems is validated by benchmarks and there are only a few examples of real parallel applications running on DSM systems. Sequence comparison is a basic operation in DNA sequencing projects, and most of sequence comparison methods used are based on heuristics, that are faster but do not produce optimal alignments. Recently, many organisms had their DNA entirely sequenced, and this reality presents the need for comparing long DNA sequences, which is a challenging task due to its high demands for computational power and memory. In this article, we present and evaluate a parallelisation strategy for implementing a sequence alignment algorithm for long sequences. This strategy was implemented in JIAJIA, a scope consistent software DSM system. Our results on an eight-machine cluster presented good speedups, showing that our parallelisation strategy and programming support were appropriate.