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2009
ACM
15 years 11 months ago
Highly scalable genome assembly on campus grids
Bioinformatics researchers need efficient means to process large collections of sequence data. One application of interest, genome assembly, has great potential for parallelizati...
Christopher Moretti, Michael Olson, Scott J. Emric...
IPPS
2009
IEEE
15 years 11 months ago
Scaling communication-intensive applications on BlueGene/P using one-sided communication and overlap
In earlier work, we showed that the one-sided communication model found in PGAS languages (such as UPC) offers significant advantages in communication efficiency by decoupling d...
Rajesh Nishtala, Paul Hargrove, Dan Bonachea, Kath...
IPPS
2009
IEEE
15 years 11 months ago
Designing multi-leader-based Allgather algorithms for multi-core clusters
The increasing demand for computational cycles is being met by the use of multi-core processors. Having large number of cores per node necessitates multi-core aware designs to ext...
Krishna Chaitanya Kandalla, Hari Subramoni, Gopala...
IPPS
2009
IEEE
15 years 11 months ago
Minimizing startup costs for performance-critical threading
—Using the well-known ATLAS and LAPACK dense linear algebra libraries, we demonstrate that the parallel management overhead (PMO) can grow with problem size on even statically sc...
Anthony M. Castaldo, R. Clint Whaley
IPPS
2009
IEEE
15 years 11 months ago
Building a parallel pipelined external memory algorithm library
Large and fast hard disks for little money have enabled the processing of huge amounts of data on a single machine. For this purpose, the well-established STXXL library provides a...
Andreas Beckmann, Roman Dementiev, Johannes Single...