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As experts in science and computing,
Stone Ridge Technology can identify bottleneck code in your software algorithms and provide solutions that accelerate your critical applications by as much as 100X.
Bio-Informatics
| SRT SW publication (pdf) | SRT publication on the Smith Waterman algorithm developed for XtremeData socket FPGA product |
| SRT Blast white paper (pdf) | SRT publication on the BLAST algorithm developed for XtremeData socket FPGA product |
| Li Survey paper (link) | An excellent survey paper on the various algorithms used for sequencing |
| Zoom paper (link) | A leading edge hash table approach to sequencing |
| Bowtie paper (link) | A leading edge Burroughs Wheeler approach to sequencing |
| Schatz website | Mike Schatz's website is an excellent resource for information on sequencing |
Finance
| SRT Barrier Option Valuation on GPU | SRT publication on Barrier Option valuation using GPUs with Jump-Diffusion process and Brownian Bridge (in press). Call for details. |
| SRT High Frequency Trading White paper | Coming soon |
Oil and Gas
| Kirchhoff Time Migration on GPU | SRT publication on Kirchhoff Time migration on GPU |
| Reverse Time Migration on GPU | SRT publication on Reverse Time migration on GPU |
| RTM on GPU | NVidia paper on 3D FDTD done on GPU by P. Micikevicius. Excellent resource for understanding the data flow and optimal use of shared memory |
| Survey of methods of solution for the two-point seismic travel time problem | SRT white paper on solution methods for the two-point seismic travel time problem. |
Sparse Matrix Linear Algebra
| CUSP | CUDA Sparse Linear Algebra Library. Excellent start for Sparse Linear Algebra on GPU including treatment of CSR and Hybrid data formats. |
| Iterative Methods for Sparse Linear Algebra | Classic text on iterative methods by Y. Saad treating simple and Krylov subspace methods, multi-grid and parallelism |
| Numerical Linear Algebra | Excellent text by Trefethen. |
GPU Coding
| CUDAZone | Excellent resource for hundreds of examples of successfull applications run on GPU. Applications include papers, documentation and code. |
| CUDA Download | NVidia CUDA download start. Start here for GPGPU. |
| GPGPU GEMS 2 |
Three volumes of GPGPU examples from a wide variety of disciplines |
| SCVF Download | The Stone Ridge CUDA Visualization Framework (SCVF) is an extensible C++ Framework that can enables users to create compeling visualizations of their simulations. SCVF supports 2D and 3D grid structures and free particles. With SCVF you can easily color particles or grid points with a scalar quantity and custom color pallette. |
| HPCwire article "Heterogeneous Computing Trite or Trend" | HPCwire article by SRT founder Dr. Vincent Natoli that discusses heterogeneous computing, the forces at work that have fomented it and whether it has staying power in the HPC market. |
| HPCwire article "Kudos for CUDA" | HPCwire article by SRT founder Dr. Vincent Natoli extolling the virtues of CUDA and speculating on its evolution as a programming language for parallel computing. |
Multi-Core CPU Coding
| Compute Bound vs Memory Bound | SRT paper by intern Alex Hutcheson which characterizes the standard 2 processor 8 core Nehalem platform looking at memory bandwidth at all levels of cache, bandwidth scaling with cores, contiguous vs non-contiguous access and the transition from memory bound to compute bound. |
| OpenMP |
OpenMP resources including manual and documentation. |
CUDA Tutorial (2011 March aps meeting)
| Parallel Computing with CUDA | Mike Garland (NVIDIA) |
| Programming GPUs for Physics Simulation Part I |
David Dembeck (Stone Ridge Technology) |
| Programming GPUs for Physics Simulation Part II | Ken Esler (Stone Ridge Technology) |
| Quantum Chemistry and First Principles Molecular Dynamics on GPUs | Todd Martinez (Stanford University) |
| Hands on Tutorial for Molecular Dynamics (Slides) | |
| Hands on Tutorial for Molecular Dynamics (Code) |