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AINA
2006
IEEE
16 years 20 days ago
Accelerating the HMMER Sequence Analysis Suite Using Conventional Processors
Due to the ever-increasing size of sequence databases it has become clear that faster techniques must be employed to effectively perform biological sequence analysis in a reasonab...
John Paul Walters, Bashar Qudah, Vipin Chaudhary
IPPS
2006
IEEE
16 years 19 days ago
An experimental study of optimizing bioinformatics applications
As bioinformatics is an emerging application of high performance computing, this paper first evaluates the memory performance of several representative bioinformatics application...
Guangming Tan, Lin Xu, Shengzhong Feng, Ninghui Su...
IPPS
2006
IEEE
16 years 19 days ago
A decomposition approach for optimizing the performance of MPI libraries
MPI provides a portable message passing interface for many parallel execution platforms but may lead to inefficiencies for some platforms and applications. In this article we sho...
O. Hartmann, Matthias Kühnemann, Thomas Raube...
IPPS
2006
IEEE
16 years 19 days ago
Tree-based overlay networks for scalable applications
The increasing availability of high-performance computing systems with thousands, tens of thousands, and even hundreds of thousands of computational nodes is driving the demand fo...
Dorian C. Arnold, G. D. Pack, Barton P. Miller
IPPS
2006
IEEE
16 years 19 days ago
Reducing the associativity and size of step caches in CRCW operation
Step caches are caches in which data entered to an cache array is kept valid only until the end of ongoing step of execution. Together with an advanced pipelined multithreaded arc...
M. Forsell