Some projects I've worked on at D. E. Shaw Research

D. E. Shaw Research does scientific research in computational biochemistry and molecular dynamics. (See an up-to-date list of D. E. Shaw Research papers and publications in various leading science and engineering journals and conferences)

David Shaw's 2006 talk at Stanford University's Computer Systems Colloquium has both video and slides which provide background, context and elaboration for our lab's work.

We have designed and built Anton 2 and previously, Anton, the fastest biomolecular simulation machines in the world. Some papers describing science done on Anton:

Papers describing Anton 2:

Papers describing Anton:

A side-project that emerged from Anton is a class of "counter-based" random number generators (CBRNGs), which we presented at SC11 (awarded Best Paper). CBRNGs are fast, stateless functions that are great for modern multi-core or distributed applications -- the source code is available for download. It was interesting getting them to work in C, C++0X as well as OpenCL (on an AMD HD6970) and CUDA (on an NVIDIA GTX580). NVIDIA includes one of these generators in their CURAND library, starting with version 6, they've been described in books like Numerical Computation with GPUS, and papers like Random number generators for massively parallel simulations on GPU. There's also a Haskell port of Random123, and a Julia implementation. There's a version of Random123 in Fujitsu's Open Petascale library. GitHub has a Boost-compatible implementation of Random123.

Another of our projects is Desmond, a scalable molecular dynamics (MD) program for commodity clusters (aka Beowulfs). We first described the performance of Desmond on a 2005-vintage Infiniband+Opteron cluster in Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters, (SuperComputing 2006, Best Paper). We also released a tech report with updated Desmond performance numbers on our 2nd generation (2008-vintage) Infiniband+Xeon cluster, and Desmond performance numbers on modern NVIDIA GPUs.

I gave a talk on D. E. Shaw Research's experience with deploying our first generation (vintage 2005) Infiniband+Opteron cluster at the 2007 OpenFabrics Sonoma Workshop

The D. E. Shaw Research publications page.

More general articles about D. E. Shaw Research:

My home page.

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