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AINA
2008
IEEE
15 years 5 months ago
Communication Protocols and Message Formats for BLAST Parallelization on Cluster Systems
With the widespread use of BLAST, many parallel versions of BLAST on cluster systems are announced, but little work has been done for the parallel execution in the search for indi...
Hong-Soog Kim, Woo-Hyuk Jang, Dong-Soo Han
HIPC
2004
Springer
15 years 10 months ago
A Parallel State Assignment Algorithm for Finite State Machines
This paper summarizes the design and implementation of a parallel algorithm for state assignment of large Finite State Machines (FSMs). High performance CAD tools are necessary to...
David A. Bader, Kamesh Madduri
HIPC
2007
Springer
15 years 11 months ago
Molecular Dynamics Simulations on Commodity GPUs with CUDA
Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the requirement for large system simula...
Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang ...
IPPS
2008
IEEE
15 years 11 months ago
Evaluation of dynamic scheduling methods in simulations of storm-time ion acceleration
In this paper we investigate the applicability of classic dynamic loop scheduling methods on a numerical simulation code that calculates the trajectories of charged particles in t...
Ioannis Riakiotakis, Georgios I. Goumas, Nectarios...
IPPS
2010
IEEE
15 years 2 months ago
Optimization of linked list prefix computations on multithreaded GPUs using CUDA
We present a number of optimization techniques to compute prefix sums on linked lists and implement them on multithreaded GPUs using CUDA. Prefix computations on linked structures ...
Zheng Wei, Joseph JáJá