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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.

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.

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).