software

PASQUAL

PArallel SeQUence AssembLer, a Parallel de Novo Genome Sequence Assembler, is designed for shared memory parallelism, using OpenMP due to its good tradeoff between performance and programmer productivity.

Reference:
Xing Liu, Pushkar R. Pande, Henning Meyerhenke, and David A. Bader, ''PASQUAL: Parallel Techniques for Next Generation Genome Sequence Assembly,'' IEEE Transactions on Parallel and Distributed Systems, vol. 24, no. 5, pp. 977-986, May, 2013.

ESB-SpMV

A parallel SpMV code for Intel Xeon Phi using the ELLPACK Sparse Block (ESB) Format. The ESB format has been used in the Intel MKL SpMV Format Prototype Package.

Reference:
Xing Liu, Mikhail Smelyanskiy, Edmond Chow, and Pradeep Dubey, ''Efficient Sparse Matrix-Vector Multiplication on x86-based Many-core Processors,'' In 27th International Conference on Supercomputing (ICS), Eugene, Oregon, June 10-14, 2013.

StokesDT

StokesDT is a parallel toolkit for performing large-scale Brownian and Stokesian dynamics simulations on UNIX/LINUX platforms. StokesDT is written in C++ and is optimized for x86-based multicore and Intel MIC-based manycore architectures.

Reference:
Xing Liu and Edmond Chow, ''Large-scale Hydrodynamic Brownian Simulations on Multicore and Manycore Architectures,'' In 28th IEEE International Parallel & Distributed Processing Symposium (IPDPS), Phoenix, AZ, May 19-23, 2014.