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IEEE/ACM Transactions on Networking (TON)
Parallelization of local BLAST service on workstation clusters
Future Generation Computer Systems
GPFS: A Shared-Disk File System for Large Computing Clusters
FAST '02 Proceedings of the Conference on File and Storage Technologies
TurboBLAST(r): A Parallel Implementation of BLAST Built on the TurboHub
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
High performance RDMA-based MPI implementation over InfiniBand
ICS '03 Proceedings of the 17th annual international conference on Supercomputing
SOSP '03 Proceedings of the nineteenth ACM symposium on Operating systems principles
Efficient Data Access for Parallel BLAST
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Papers - Volume 01
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ALS'00 Proceedings of the 4th annual Linux Showcase & Conference - Volume 4
Parallel genomic sequence-search on a massively parallel system
Proceedings of the 4th international conference on Computing frontiers
IEEE Transactions on Parallel and Distributed Systems
Semantics-based distributed I/O for mpiBLAST
Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of parallel programming
Cell-SWat: modeling and scheduling wavefront computations on the cell broadband engine
Proceedings of the 5th conference on Computing frontiers
Semantic-based distributed i/o with the paramedic framework
HPDC '08 Proceedings of the 17th international symposium on High performance distributed computing
Massively parallel genomic sequence search on the Blue Gene/P architecture
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
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SSDBM '08 Proceedings of the 20th international conference on Scientific and Statistical Database Management
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Proceedings of the 18th ACM international symposium on High performance distributed computing
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Fast and accurate NCBI BLASTP: acceleration with multiphase FPGA-based prefiltering
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DataStager: scalable data staging services for petascale applications
Cluster Computing
Exploiting performance characterization of BLAST in the grid
Cluster Computing
Concurrency and Computation: Practice & Experience
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The Basic Local Alignment Search Tool (BLAST) allows bioinformaticists to characterize an unknown sequence by comparing it against a database of known sequences. The similarity between sequences enables biologists to detect evolutionary relationships and infer biological properties of the unknown sequence.mpiBLAST, our parallel BLAST, decreases the search time of a 300 KB query on the current NT database from over two full days to under 10 minutes on a 128-processor cluster and allows larger query files to be compared. Consequently, we propose to compare the largest query available, the entire NT database, against the largest database available, the entire NT database. The result of this comparison will provide critical information to the biology community, including insightful evolutionary, structural, and functional relationships between every sequence and family in the NT database.Preliminary projections indicated that to complete the above task in a reasonable length of time required more processors than were available to us at a single site. Hence, we assembled GreenGene, an ad-hoc grid that was constructed "on the fly" from donated computational, network, and storage resources during last year's SC|05. GreenGene consisted of 3048 processors from machines that were distributed across the United States. This paper presents a case study of mpiBLAST on GreenGene --- specifically, a pre-run characterization of the computation, the hardware and software architectural design, experimental results, and future directions.