## Publications

Veronika Strnadova-Neeley, Aydın Buluç, Jarrod Chapman, John R Gilbert, Joseph Gonzalez and Leonid Oliker. **Efficient Data Reduction for Large-Scale Genetic Mapping**.

In *ACM Conference on Bioinformatics, Computational Biology, and Health Informatics*. 2015.

PDF, BibTeX

@inproceedings{datareduction_genmapping, author = "Veronika Strnadova-Neeley and Ayd{\i}n Bulu\c{c} and Jarrod Chapman and John R. Gilbert and Joseph Gonzalez and Leonid Oliker", title = "Efficient Data Reduction for Large-Scale Genetic Mapping", booktitle = "ACM Conference on Bioinformatics, Computational Biology, and Health Informatics", year = 2015, pdf = "http://www.cs.ucsb.edu/~veronika/bcb15.pdf", abstract = "" }

Veronika Strnadova, Aydın Buluç, Jarrod Chapman, John R Gilbert, Joseph Gonzalez, Stefanie Jegelka, Leonid Oliker and Daniel Rokshar. **Efficient and Accurate Clustering for Large-Scale Genetic Mapping**.

In *IEEE International Conference on Bioinformatics and Biomedicine (BIBM)*. 2014.

PDF, BibTeX

@inproceedings{clustering_genmapping, author = "Veronika Strnadova and Ayd{\i}n Bulu\c{c} and Jarrod Chapman and John R. Gilbert and Joseph Gonzalez and Stefanie Jegelka and Leonid Oliker and Daniel Rokshar", title = "Efficient and Accurate Clustering for Large-Scale Genetic Mapping", booktitle = "IEEE International Conference on Bioinformatics and Biomedicine (BIBM)", year = 2014, pdf = "http://www.cs.ucsb.edu/~veronika/geneticmapping/clusteringforgeneticmapping.pdf", abstract = "" }

Adam Lugowski, Shoaib Kamil, Aydın Buluç, Samuel Williams, Erika Duriakova, Leonid Oliker, Armando Fox and John Gilbert. **Parallel Processing of Filtered Queries in Attributed Semantic Graphs**.

*Journal of Parallel and Distributed Computing (JPDC)*, 2014.

In press.

DOI, BibTeX

@article{jpdc14, title = "Parallel Processing of Filtered Queries in Attributed Semantic Graphs", author = "Lugowski, Adam and Kamil, Shoaib and Ayd{\i}n Bulu\c{c} and Williams, Samuel and Duriakova, Erika and Oliker, Leonid and Fox, Armando and Gilbert, John", journal = "Journal of Parallel and Distributed Computing (JPDC)", year = 2014, doi = "10.1016/j.jpdc.2014.08.010", note = "In press" }

Adam Lugowski and John R Gilbert. **Efficient Sparse Matrix-Matrix Multiplication on Multicore Architectures**.

Number UCSB/CS-2014-04, Computer Science Dept., University of California, Santa Barbara, May 2014.

URL, PDF, BibTeX

@techreport{quadmat_TR, author = "Adam Lugowski and John R. Gilbert", title = "Efficient Sparse Matrix-Matrix Multiplication on Multicore Architectures", institution = "Computer Science Dept., University of California, Santa Barbara", year = 2014, month = "May", number = "UCSB/CS-2014-04", url = "http://www.cs.ucsb.edu/research/tech_reports/", pdf = "http://www.cs.ucsb.edu/research/tech_reports/reports/2014-04.pdf" }

Veronika Strnadova, Aydın Buluç, Jarrod Chapman, John R Gilbert, Joseph Gonzalez, Stefanie Jegelka, Leonid Oliker and Daniel Rokshar. **Efficient and Accurate Clustering for Large-Scale Genetic Mapping**.

Number UCSB/CS-2014-03, CS Department, University of California, Santa Barbara, April 2014.

URL, PDF, BibTeX

@techreport{genmapreport, author = "Veronika Strnadova and Ayd{\i}n Bulu\c{c} and Jarrod Chapman and John R. Gilbert and Joseph Gonzalez and Stefanie Jegelka and Leonid Oliker and Daniel Rokshar", title = "Efficient and Accurate Clustering for Large-Scale Genetic Mapping", institution = "CS Department, University of California, Santa Barbara", year = 2014, month = "April", url = "http://www.cs.ucsb.edu/research/tech_reports/", pdf = "http://gauss.cs.ucsb.edu/publication/sdm14clusteringformapping.pdf", number = "UCSB/CS-2014-03", abstract = "" }

Adam Lugowski and John R Gilbert. **Efficient Sparse Matrix-Matrix Multiplication on Multicore Architectures**.

In *SIAM Workshop on Combinatorial Scientific Computing (CSC14)*. July 2014.

PDF, BibTeX

@inproceedings{quadmat_CSC14, author = "Adam Lugowski and John R. Gilbert", title = "Efficient Sparse Matrix-Matrix Multiplication on Multicore Architectures", booktitle = "SIAM Workshop on Combinatorial Scientific Computing (CSC14)", year = 2014, month = "July", pdf = "http://gauss.cs.ucsb.edu/publication/QuadMat_CSC14.pdf" }

Robert W Techentin, Barry K Gilbert, Adam Lugowski, Kevin Deweese, John R Gilbert, Eric Dull, Mike Hinchey and Steven P Reinhardt. **Implementing Iterative Algorithms with SPARQL**.

In *EDBT/ICDT Workshops*. 2014, 216-223.

PDF, BibTeX

@inproceedings{iter_SPARQL, author = "Robert W. Techentin and Barry K. Gilbert and Adam Lugowski and Kevin Deweese and John R. Gilbert and Eric Dull and Mike Hinchey and Steven P. Reinhardt", title = "Implementing Iterative Algorithms with SPARQL", booktitle = "EDBT/ICDT Workshops", year = 2014, pages = "216-223", pdf = "http://ceur-ws.org/Vol-1133/paper-36.pdf" }

Kevin Deweese, John R Gilbert, Adam Lugowski and Steve Reinhardt. **Graph Clustering in SPARQL**.

In *SIAM Workshop on Network Science*. 2013.

PDF, BibTeX

@inproceedings{SIAM-DMA_uRiKA_PP, author = "Kevin Deweese and John R. Gilbert and Adam Lugowski and Steve Reinhardt", title = "Graph Clustering in SPARQL", booktitle = "SIAM Workshop on Network Science", year = 2013, pdf = "http://gauss.cs.ucsb.edu/publication/SIAM-DMA_uRiKA_PP.pdf" }

Aydın Buluç, Erika Duriakova, Armando Fox, John R Gilbert, Shoaib Kamil, Adam Lugowski, Leonid Oliker and Samuel Williams. **High-Productivity and High-Performance Analysis of Filtered Semantic Graphs**.

In *27th IEEE International Symposium on Parallel and Distributed Processing (IPDPS 2013)*. May 2013, 237 - 248.

PDF, DOI, BibTeX

@inproceedings{kdt_ipdps13, author = "Ayd{\i}n Bulu\c{c} and Erika Duriakova and Armando Fox and John R. Gilbert and Shoaib Kamil and Adam Lugowski and Leonid Oliker and Samuel Williams", title = "High-Productivity and High-Performance Analysis of Filtered Semantic Graphs", booktitle = "27th IEEE International Symposium on Parallel and Distributed Processing (IPDPS 2013)", year = 2013, month = "May", pages = "237 - 248", location = "Boston, Massachusetts, USA", doi = "10.1109/IPDPS.2013.52", pdf = "http://gauss.cs.ucsb.edu/publication/kdtsejits_ipdps13.pdf" }

Aydın Buluç and John R Gilbert. **Parallel Sparse Matrix-Matrix Multiplication and Indexing: Implementation and Experiments**.

*SIAM Journal of Scientific Computing (SISC)* 34(4):170 - 191, 2012.

URL, arXiv, DOI, BibTeX

@article{gemmexp, author = "Ayd{\i}n Bulu\c{c} and John R. Gilbert", title = "Parallel Sparse Matrix-Matrix Multiplication and Indexing: Implementation and Experiments", journal = "SIAM Journal of Scientific Computing (SISC)", year = 2012, volume = 34, pages = "170 - 191", number = 4, arxiv = "http://arxiv.org/abs/1109.3739", doi = "10.1137/110848244", url = "http://gauss.cs.ucsb.edu/~aydin/spgemm_sisc12.pdf" }

Aydın Buluç, Armando Fox, John R Gilbert, Shoaib Kamil, Adam Lugowski, Leonid Oliker and Samuel Williams. **High-Performance Analysis of Filtered Semantic Graphs**.

In *Proceedings of the 21st international conference on Parallel architectures and compilation techniques*. 2012, 463–464.

extended abstract.

URL, DOI, BibTeX

@inproceedings{kdt_pact12, author = "Ayd{\i}n Bulu\c{c} and Armando Fox and John R. Gilbert and Shoaib Kamil and Adam Lugowski and Leonid Oliker and Samuel Williams", title = "High-Performance Analysis of Filtered Semantic Graphs", booktitle = "Proceedings of the 21st international conference on Parallel architectures and compilation techniques", series = "PACT '12", year = 2012, isbn = "978-1-4503-1182-3", location = "Minneapolis, Minnesota, USA", pages = "463--464", numpages = 2, url = "http://doi.acm.org/10.1145/2370816.2370897", doi = "10.1145/2370816.2370897", acmid = 2370897, publisher = "ACM", address = "New York, NY, USA", keywords = "domain specific languages, graph analysis, high-performance computing, kdt, sejits", note = "extended abstract" }

Aydın Buluç, Armando Fox, John R Gilbert, Shoaib Kamil, Adam Lugowski, Leonid Oliker and Samuel Williams. **High-Performance Analysis of Filtered Semantic Graphs**.

Number UCB/EECS-2012-61, EECS Department, University of California, Berkeley, May 2012.

URL, PDF, BibTeX

@techreport{sejitskdtreport, author = "Ayd{\i}n Bulu\c{c} and Armando Fox and John R. Gilbert and Shoaib Kamil and Adam Lugowski and Leonid Oliker and Samuel Williams", title = "High-Performance Analysis of Filtered Semantic Graphs", institution = "EECS Department, University of California, Berkeley", year = 2012, month = "May", url = "http://www.eecs.berkeley.edu/Pubs/TechRpts/2012/EECS-2012-61.html", pdf = "http://www.eecs.berkeley.edu/Pubs/TechRpts/2012/EECS-2012-61.pdf", number = "UCB/EECS-2012-61", abstract = {High performance is a crucial consideration when executing a complex analytic query on a massive semantic graph. In a semantic graph, vertices and edges carry "attributes" of various types. Analytic queries on semantic graphs typically depend on the values of these attributes; thus, the computation must either view the graph through a filter that passes only those individual vertices and edges of interest, or else must first materialize a subgraph or subgraphs consisting of only the vertices and edges of interest. The filtered approach is superior due to its generality, ease of use, and memory efficiency, but may carry a performance cost. In the Knowledge Discovery Toolbox (KDT), a Python library for parallel graph computations, the user writes filters in a high-level language, but those filters result in relatively low performance due to the bottleneck of having to call into the Python interpreter for each edge. In this work, we use the Selective Embedded Just-In-Time Specialization (SEJITS) approach to automatically translate filters defined by programmers into a lower-level efficiency language, bypassing the upcall into Python. We evaluate our approach by comparing it with the high-performance C++ /MPI Combinatorial BLAS engine, and show that the productivity gained by using a high-level filtering language comes without sacrificing performance. We also present a new roofline model for graph traversals, and show that our high-performance implementations do not significantly deviate from the roofline.} }

Adam Lugowski, Aydın Buluç, John Gilbert and Steve Reinhardt. **Scalable Complex Graph Analysis with the Knowledge Discovery Toolbox**.

In *IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP)*. March 2012, 5345–5348.

URL, PDF, DOI, BibTeX

@inproceedings{kdt_icassp12, author = "Adam Lugowski and Ayd{\i}n Bulu\c{c} and John Gilbert and Steve Reinhardt", title = "Scalable Complex Graph Analysis with the Knowledge Discovery Toolbox", booktitle = "IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP)", pages = "5345--5348", year = 2012, month = "March", doi = "10.1109/ICASSP.2012.6289128", url = "http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6289128", pdf = "http://gauss.cs.ucsb.edu/publication/ICASSP_12_KDT_filter.pdf" }

Adam Lugowski, David Alber, Aydın Buluç, John R Gilbert, Steve Reinhardt, Yun Teng and Andrew Waranis. **A Flexible Open-Source Toolbox for Scalable Complex Graph Analysis**.

In *Proceedings of the Twelfth SIAM International Conference on Data Mining (SDM12)*. April 2012, 930–941.

Preprint as Technical Report UCSB-CS-2011-10.

URL, pre-print, DOI, BibTeX

@inproceedings{kdt_sdm12, author = "Adam Lugowski and David Alber and Ayd{\i}n Bulu\c{c} and John R. Gilbert and Steve Reinhardt and Yun Teng and Andrew Waranis", title = "A Flexible Open-Source Toolbox for Scalable Complex Graph Analysis", booktitle = "Proceedings of the Twelfth SIAM International Conference on Data Mining (SDM12)", year = 2012, month = "April", pages = "930--941", doi = "10.1137/1.9781611972825.80", url = "http://siam.omnibooksonline.com/2012datamining/data/papers/158.pdf", preprint = "http://www.cs.ucsb.edu/research/tech_reports/reports/2011-10.pdf", note = "Preprint as Technical Report UCSB-CS-2011-10" }

Jeremy Kepner and John R Gilbert (eds.). * Graph Algorithms in the Language of Linear Algebra*.

Society for Industrial and Applied Mathematics, 2011.

URL, DOI, BibTeX

@book{GALLA_book, editor = "Jeremy Kepner and John R. Gilbert", title = "Graph Algorithms in the Language of Linear Algebra", publisher = "Society for Industrial and Applied Mathematics", year = 2011, doi = "10.1137/1.9780898719918", url = "http://epubs.siam.org/doi/abs/10.1137/1.9780898719918" }

Aydın Buluç and John R Gilbert. **The Combinatorial BLAS: Design, Implementation, and Applications**.

*The International Journal of High Performance Computing Applications*, 2011.

URL, DOI, BibTeX

@article{combblas10, author = "Ayd{\i}n Bulu\c{c} and John R. Gilbert", title = "The {C}ombinatorial {BLAS}: Design, Implementation, and Applications", journal = "The International Journal of High Performance Computing Applications", year = 2011, abstract = "http://www.cs.ucsb.edu/research/tech_reports/abstract.php?id=1010", url = "http://www.cs.ucsb.edu/research/tech_reports/reports/2010-18.pdf", doi = "10.1177/1094342011403516" }

Aydın Buluç and John R Gilbert. **Highly Parallel Sparse Matrix-Matrix Multiplication**.

Number UCSB-CS-2010-10, UCSB Computer Science Department, June 2010.

URL, arXiv, BibTeX

@techreport{spgemm:10, author = "Ayd{\i}n Bulu\c{c} and John R. Gilbert", institution = "UCSB Computer Science Department", title = "Highly Parallel Sparse Matrix-Matrix Multiplication", number = "UCSB-CS-2010-10", month = "June", year = 2010, arxiv = "http://arxiv.org/abs/1006.2183", url = "http://www.cs.ucsb.edu/research/tech_reports/reports/2010-10.pdf" }

Aydın Buluç, Jeremy T Fineman, Matteo Frigo, John R Gilbert and Charles E Leiserson. **Parallel Sparse Matrix-Vector and Matrix-Transpose-Vector Multiplication Using Compressed Sparse Blocks**.

In *Proceedings of the Twenty-First ACM Symposium on Parallelism in Algorithms and Architectures (SPAA)*. August 2009, 233–244.

URL, PDF, DOI, BibTeX

@inproceedings{csb:spaa09, author = "Ayd{\i}n Bulu\c{c} and Jeremy T. Fineman and Matteo Frigo and John R. Gilbert and Charles E. Leiserson", title = "Parallel Sparse Matrix-Vector and Matrix-Transpose-Vector Multiplication Using Compressed Sparse Blocks", booktitle = "Proceedings of the Twenty-First {ACM} Symposium on Parallelism in Algorithms and Architectures ({SPAA})", year = 2009, month = "August", pdf = "http://gauss.cs.ucsb.edu/publication/csb2009.pdf", address = "New York, NY, USA", isbn = "978-1-60558-606-9", location = "Calgary, AB, Canada", pages = "233--244", numpages = 12, url = "http://doi.acm.org/10.1145/1583991.1584053", doi = "10.1145/1583991.1584053", acmid = 1584053, publisher = "ACM" }

Aydın Buluç, John R Gilbert and Ceren Budak. **Solving path problems on the GPU**.

*Parallel Computing* 36(5-6):241 - 253, 2010.

Earlier version "Gaussian Elimination Based Algorithms on the GPU" available as UCSB technical report CS-2008-15.

URL, DOI, BibTeX

@article{gpuapsp:2008-15, author = "Ayd{\i}n Bulu\c{c} and John R. Gilbert and Ceren Budak", title = "Solving path problems on the {GPU}", journal = "Parallel Computing", volume = 36, number = "5-6", pages = "241 - 253", year = 2010, url = "http://gauss.cs.ucsb.edu/publication/parco_apsp.pdf", doi = "10.1016/j.parco.2009.12.002", note = {Earlier version "Gaussian Elimination Based Algorithms on the {GPU}" available as UCSB technical report CS-2008-15} }

B H McRae, B G Dickson, T H Keitt and V B Shah.. **Using circuit theory to model connectivity in ecology and conservation**.

*Ecology* (In press)():, 2008.

URL, BibTeX

@article{shahecology08, title = "Using circuit theory to model connectivity in ecology and conservation", author = "B. H. McRae and B. G. Dickson and T. H. Keitt and V. B. Shah.", journal = "Ecology", month = "", year = 2008, volume = "(In press)", number = "", pages = "", url = "http://gauss.cs.ucsb.edu/publication/McRae_et_al_circuit_theory_in_press.pdf" }

Laura Grigori, John R Gilbert and Michel Cosnard. **Symbolic and Exact Structure Prediction for Sparse Gaussian Elimination with Partial Pivoting**.

*SIAM Journal on Matrix Analysis and Applications* 30(4):1520-1545, 2008.

URL, DOI, BibTeX

@article{grigorigilbertcosnard08, title = "Symbolic and Exact Structure Prediction for Sparse Gaussian Elimination with Partial Pivoting", author = "Laura Grigori and John R. Gilbert and Michel Cosnard", publisher = "SIAM", year = 2008, journal = "SIAM Journal on Matrix Analysis and Applications", volume = 30, number = 4, pages = "1520-1545", doi = "10.1137/050629343", url = "http://gauss.cs.ucsb.edu/publication/GrigoriGilbertCosnardStructHall.pdf" }

Viral B Shah and Brad McRae. **Circuitscape: A Tool for Landscape Ecology**.

In *Proceedings of the 7th Python in Science Conference (SciPy2008)*. 2008, 62–65.

URL, BibTeX

@inproceedings{scipy08, title = "Circuitscape: A Tool for Landscape Ecology", author = "Viral B. Shah and Brad McRae", booktitle = "Proceedings of the 7th Python in Science Conference (SciPy2008)", pages = "62--65", year = 2008, url = "http://gauss.cs.ucsb.edu/publication/Circuitscape_Python_Scipy08.pdf" }

J R Gilbert, S Reinhardt and V B Shah. **Distributed Sparse Matrices for Very High Level Languages**.

*Advances in Computers* 72, June 2008.

URL, BibTeX

@article{advances08, title = "Distributed Sparse Matrices for Very High Level Languages", author = "J. R. Gilbert and S. Reinhardt and V. B. Shah", journal = "Advances in Computers", volume = 72, year = 2008, month = "June", url = "http://gauss.cs.ucsb.edu/publication/DistributedSparseMatricesVHLL.pdf" }

Aydın Buluç and John R Gilbert. **Challenges and Advances in Parallel Sparse Matrix-Matrix Multiplication**.

In *The 37th International Conference on Parallel Processing (ICPP'08)*. September 2008, 503-510.

URL, DOI, BibTeX

@inproceedings{icpp08, title = "{Challenges and Advances in Parallel Sparse Matrix-Matrix Multiplication}", author = "Ayd{\i}n Bulu\c{c} and John R. Gilbert", booktitle = "{The 37th International Conference on Parallel Processing (ICPP'08)}", year = 2008, month = "September", pages = "503-510", doi = "10.1109/ICPP.2008.45", address = "Portland, Oregon, USA", url = "http://gauss.cs.ucsb.edu/publication/Buluc-ParallelMatMat.pdf" }

Lorin Hochstein, Victor R Basili, Uzi Vishkin and John R Gilbert. **A pilot study to compare programming effort for two parallel programming models**.

*Journal of Systems and Software* 81(11):1920 - 1930, 2008.

URL, DOI, BibTeX

@article{prammpi08, author = "Lorin Hochstein and Victor R. Basili and Uzi Vishkin and John R. Gilbert", title = "A pilot study to compare programming effort for two parallel programming models", journal = "Journal of Systems and Software", volume = 81, number = 11, pages = "1920 - 1930", year = 2008, doi = "10.1016/j.jss.2007.12.798", url = "http://gauss.cs.ucsb.edu/publication/pram-journal-paper.pdf" }

Lamia Youseff, Alethea Barbaro, Peterson Trethewey, Bjorn Birnir and John R Gilbert. **Parallel Modeling of Fish Interaction**.

In *11th IEEE International Conference on Computational Science and Engineering*. 2008, 234-241.

URL, DOI, BibTeX

@inproceedings{parallelfish08, author = "Lamia Youseff and Alethea Barbaro and Peterson Trethewey and Bjorn Birnir and John R. Gilbert", title = "Parallel Modeling of Fish Interaction", booktitle = "{11th IEEE International Conference on Computational Science and Engineering}", year = 2008, isbn = "978-0-7695-3193-9", pages = "234-241", doi = "10.1109/CSE.2008.8", publisher = "IEEE Computer Society", address = "Los Alamitos, CA, USA", url = "http://gauss.cs.ucsb.edu/publication/parallelModelingOfFishInteraction_YBTBG2008.pdf" }

Aydın Buluç and John R Gilbert. **On the Representation and Multiplication of Hypersparse Matrices**.

In *IEEE International Parallel and Distributed Processing Symposium (IPDPS 2008)*. April 2008, 1-11.

URL, DOI, BibTeX

@inproceedings{hypersparse08, author = "Ayd{\i}n Bulu\c{c} and John R. Gilbert", title = "{On the Representation and Multiplication of Hypersparse Matrices}", booktitle = "{IEEE International Parallel and Distributed Processing Symposium (IPDPS 2008)}", month = "April", year = 2008, pages = "1-11", doi = "10.1109/IPDPS.2008.4536313", location = "Miami, FL", url = "http://gauss.cs.ucsb.edu/publication/hypersparse-ipdps08.pdf" }

John R Gilbert, Steve Reinhardt and Viral B Shah. **A Unified Framework for Numerical and Combinatorial Computing**.

*Computing in Sciences and Engineering* 10(2):20–25, 2008.

URL, BibTeX

@article{cise08, title = "A Unified Framework for Numerical and Combinatorial Computing", author = "John R. Gilbert and Steve Reinhardt and Viral B. Shah", journal = "Computing in Sciences and Engineering", month = "Mar/Apr", year = 2008, volume = 10, number = 2, pages = "20--25", url = "http://gauss.cs.ucsb.edu/publication/cise-graph.pdf" }

Viral B Shah. **An Interactive System for Combinatorial Scientific Computing with an Emphasis on Programmer Productivity**.

University of California, Santa Barbara, June 2007.

URL, BibTeX

@phdthesis{shahthesis, author = "Viral B. Shah", title = "An Interactive System for Combinatorial Scientific Computing with an Emphasis on Programmer Productivity", school = "University of California, Santa Barbara", year = 2007, month = "June", url = "http://gauss.cs.ucsb.edu/publication/Shah_thesis.pdf" }

John R Gilbert, Steven Reinhardt and Viral Shah. **An Interactive Environment to Manipulate Large Graphs**.

In *Proceedings of the 2007 IEEE International Conference on Acoustics, Speech, and Signal Processing* 4. April 2007, IV-1201–IV-1204.

URL, BibTeX

@inproceedings{icassp07, title = "An Interactive Environment to Manipulate Large Graphs", author = "John R. Gilbert and Steven Reinhardt and Viral Shah", booktitle = "Proceedings of the 2007 IEEE International Conference on Acoustics, Speech, and Signal Processing", month = "April", year = 2007, volume = 4, pages = "IV-1201--IV-1204", url = "http://gauss.cs.ucsb.edu/publication/gapdt-icassp07.pdf" }

John R Gilbert, Steve Reinhardt and Viral B Shah. **High performance graph algorithms from parallel sparse matrices**.

In *Applied Parallel Computing. State of the Art in Scientific Computing. 8th International Workshop, PARA 2006.*. 2007, 260–269.

URL, BibTeX

@inproceedings{gapdt, author = "John R. Gilbert and Steve Reinhardt and Viral B. Shah", title = "High performance graph algorithms from parallel sparse matrices", booktitle = "Applied Parallel Computing. State of the Art in Scientific Computing. 8th International Workshop, PARA 2006.", year = 2007, pages = "260--269", url = "http://gauss.cs.ucsb.edu/publication/gapdt-para06.pdf" }

David A Bader, Kamesh Madduri, John R Gilbert, Viral Shah, Jeremy Kepner, Theresa Meuse and Ashok Krishnamurthy. **Designing Scalable Synthetic Compact Applications for Benchmarking High Productivity Computing Systems**.

*Cyberinfrastructure Technology Watch*, November 2006.

URL, BibTeX

@article{ctwatchssca, author = "David A. Bader and Kamesh Madduri and John R. Gilbert and Viral Shah and Jeremy Kepner and Theresa Meuse and Ashok Krishnamurthy", title = "Designing Scalable Synthetic Compact Applications for Benchmarking High Productivity Computing Systems", journal = "Cyberinfrastructure Technology Watch", year = 2006, month = "Nov", url = "http://gauss.cs.ucsb.edu/publication/ctwatch-ssca.pdf" }

Viral Shah and John R Gilbert. **Sparse Matrices in Matlab*P: Design and Implementation.**.

In *High Performance Computing. HiPC 2004.*. 2005, 144–155.

URL, BibTeX

@inproceedings{dsparse, author = "Viral Shah and John R. Gilbert", title = "Sparse Matrices in {M}atlab*{P}: Design and Implementation.", booktitle = "High Performance Computing. HiPC 2004.", year = 2005, pages = "144--155", url = "http://gauss.cs.ucsb.edu/publication/dsparse-hipc04.pdf" }

David R Cheng, Alan Edelman, John R Gilbert and Viral Shah. **A novel parallel sorting algorithm for contemporary architectures**.

*Submitted to ALENEX06*, 2006.

URL, BibTeX

@article{mpisort, author = "David R. Cheng and Alan Edelman and John R. Gilbert and Viral Shah", title = "A novel parallel sorting algorithm for contemporary architectures", journal = "Submitted to ALENEX06", year = 2006, url = "http://gauss.cs.ucsb.edu/publication/psort.pdf" }

Andrew Funk, John R Gilbert, David Mizell and Viral Shah. **Modelling Programmer Workflows with Timed Markov Models**.

*Cyber Technology Watch*, 2006.

URL, BibTeX

@article{ctwatchtmm, author = "Andrew Funk and John R. Gilbert and David Mizell and Viral Shah", title = "Modelling Programmer Workflows with Timed {M}arkov Models", journal = "Cyber Technology Watch", year = 2006, url = "http://gauss.cs.ucsb.edu/publication/ctwatch-tmm.pdf" }

Burton Smith, David Mizell, John Gilbert and Viral Shah. **Towards a timed Markov process model of software development**.

In *SE-HPCS '05: Proceedings of the second international workshop on Software engineering for high performance computing system applications*. 2005, 65–67.

URL, BibTeX

@inproceedings{icsehpc05, author = "Burton Smith and David Mizell and John Gilbert and Viral Shah", title = "Towards a timed {M}arkov process model of software development", booktitle = "SE-HPCS '05: Proceedings of the second international workshop on Software engineering for high performance computing system applications", year = 2005, isbn = "1-59593-117-1", pages = "65--67", location = "St. Louis, Missouri", url = "http://gauss.cs.ucsb.edu/publication/tmm-icsehpc05.pdf", publisher = "ACM Press", address = "New York, NY, USA" }