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Research Software

The Combinatorial BLAS: Distributed memory implementation of sparse linear algebra routines that can be used as building blocks for large scale graph and data analysis.

HipMCL clusters protein similarity networks with 70 billion edges in a couple of hours. This highly-scalable implementation of the Markov Cluster algorithm is available open source.

HipMer: Extreme-scale de novo genome assembler for large complex genomes. Primarily written in UPC with some MPI/C++ pieces.

Compressed Sparse Blocks: A small Cilk Plus library that performs sparse matrix times dense vector and sparse matrix transpose times dense vector using compressed sparse blocks.

SpDM^3 and HP-CONCORD: SpDM^3 does communication-avoiding Sparse-Dense Matrix-Matrix Multiplication on distributed-memory parallel computers and HP-CONCORD is high-performance inverse covariance matrix estimation using the CONCORD-ISTA algorithm.

High-performance sparse-sparse matrix products on multicores and KNL

Implementing Push-Pull Efficiently in GraphBLAS: Mapping direction-optimization to the language of linear algebra.

Sparse matrix multi-vector (aka tall-skinny dense matrix) products on the GPU

MS-BFS-Graft: Multithreaded OpenMP code for computing maximum cardinality matching on bipartite graphs. Performs multi-source breadth-first search with tree-grafting for exploiting parallelism.

Genetic Mapping: MarkerReduce (based on the BCB paper) and BubbleCluster (based on the BIBM paper) are available from the CSC@UCSB Website.

The Knowledge Discovery Toolbox (KDT): High-performance parallel graph analysis and mining in a very-high-level language (Python).

GPU-APSP: A CUDA program that computes the distances for all pairs shortest paths in a dense directed graph (represented in adjacency matrix form).