Lifting Sequential Graph Algorithms for Distributed-Memory Parallel Computationhttp://osl.iu.edu/publications/prints/2005/Gregor:OOPSLA:2005.pdf
Efficient Parallel Graph Exploration on Multi-Core CPU and GPU, PACT2011
http://ppl.stanford.edu/papers/pact11-hong.pdf
Accelerating CUDA Graph Algorithms at Maximum Warp, PPOP2007
http://ppl.stanford.edu/papers/ppopp070a-slides.pdf
Efficient Breadth-First Search on the Cell/B.E. Processor
http://www.dais.unive.it/~calpar/AA07-08/bfs.pdf
Optimizing Parallel Sparse Matrix-Vector Multiplication by Corner Partitioning, PARA08
http://www.sandia.gov/~egboman/papers/PARA08.pdf
Fast sparse matrix-vector multiplication by partitioning and reordering
http://igitur-archive.library.uu.nl/dissertations/2011-0913-201603/UUindex.html
More introduction stuff
http://www.cs.berkeley.edu/~skamil/cs267/notes/lect15NoteSpMV_kim.pdf
CACHE-OBLIVIOUS SPARSE MATRIX–VECTOR MULTIPLICATION BY
USING SPARSE MATRIX PARTITIONING METHODS
http://people.cs.kuleuven.be/~albert-jan.yzelman/PDFs/yzelman09-rev.pdf
Parallel Hypergraph Partitioning for Scientific Computing
http://www.cs.sandia.gov/~egboman/papers/IPDPS06.pdf
ON TWO-DIMENSIONAL SPARSE MATRIX PARTITIONING:
MODELS, METHODS, AND A RECIPE∗, 2010
http://graal.ens-lyon.fr/~bucar/papers/ucca2D.pdf
Application to protein-protein interaction network.
A. Vazquez, A. Flammini, A. Maritan, and A. Vespignani.
Global protein function prediction in protein-protein interaction network
http://www.ncbi.nlm.nih.gov/pubmed/12740586
Application to computational phylogenetics
B. Moret, D. Bader, and T. Warnow. High-performance algorithm engineering for computational phylogenetics. In
Proc. Int’l Conf. on Computational Science, volume 2073–
2074 of Lecture Notes in Computer Science, San Francisco,
CA, 2001. Springer-Verlag.
B. M. Moret, D. Bader, T. Warnow, S. Wyman, and M. Yan.
GRAPPA: a high-performance computational tool for phylogeny reconstruction from gene-order data. In Proc.
Botany, Albuquerque, NM, Aug. 2001.
Efficient Parallel Graph Exploration on Multi-Core CPU and GPU, PACT2011
http://ppl.stanford.edu/papers/pact11-hong.pdf
Accelerating CUDA Graph Algorithms at Maximum Warp, PPOP2007
http://ppl.stanford.edu/papers/ppopp070a-slides.pdf
Efficient Breadth-First Search on the Cell/B.E. Processor
http://www.dais.unive.it/~calpar/AA07-08/bfs.pdf
Optimizing Parallel Sparse Matrix-Vector Multiplication by Corner Partitioning, PARA08
http://www.sandia.gov/~egboman/papers/PARA08.pdf
Fast sparse matrix-vector multiplication by partitioning and reordering
http://igitur-archive.library.uu.nl/dissertations/2011-0913-201603/UUindex.html
More introduction stuff
http://www.cs.berkeley.edu/~skamil/cs267/notes/lect15NoteSpMV_kim.pdf
CACHE-OBLIVIOUS SPARSE MATRIX–VECTOR MULTIPLICATION BY
USING SPARSE MATRIX PARTITIONING METHODS
http://people.cs.kuleuven.be/~albert-jan.yzelman/PDFs/yzelman09-rev.pdf
Parallel Hypergraph Partitioning for Scientific Computing
http://www.cs.sandia.gov/~egboman/papers/IPDPS06.pdf
ON TWO-DIMENSIONAL SPARSE MATRIX PARTITIONING:
MODELS, METHODS, AND A RECIPE∗, 2010
http://graal.ens-lyon.fr/~bucar/papers/ucca2D.pdf
Application to protein-protein interaction network.
A. Vazquez, A. Flammini, A. Maritan, and A. Vespignani.
Global protein function prediction in protein-protein interaction network
http://www.ncbi.nlm.nih.gov/pubmed/12740586
Application to computational phylogenetics
B. Moret, D. Bader, and T. Warnow. High-performance algorithm engineering for computational phylogenetics. In
Proc. Int’l Conf. on Computational Science, volume 2073–
2074 of Lecture Notes in Computer Science, San Francisco,
CA, 2001. Springer-Verlag.
B. M. Moret, D. Bader, T. Warnow, S. Wyman, and M. Yan.
GRAPPA: a high-performance computational tool for phylogeny reconstruction from gene-order data. In Proc.
Botany, Albuquerque, NM, Aug. 2001.
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