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GTC On-Demand

Bioinformatics & Genomics
Presentation
Media
Implementing Modern Short Read DNA Alignment Algorithms in CUDA
Jonathan Cohen (NVIDIA)
Because of their inherently parallel and high-throughput nature, NVIDIA GPUs are a natural fit for the types of data-intensive computing required in bioinformatics applications. For many genomics applications, the primary challenge is to map hig ...Read More

Because of their inherently parallel and high-throughput nature, NVIDIA GPUs are a natural fit for the types of data-intensive computing required in bioinformatics applications. For many genomics applications, the primary challenge is to map highly divergent and control flow-heavy code to a SIMD architecture. By transforming complex serial flow of control into a sequence of communicating sequential processors running in parallel, we are able to achieve high throughput on very branchy code, while maintaining memory coherence and avoiding execution divergence. I will present initial results from NVIDIA''s internal "nvbio" project to develop efficient computational building blocks for analysis of Next-Generation Sequencing data, with a focus on implementations of BWA and Bowtie2-type aligners.

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Keywords:
Bioinformatics & Genomics, GTC 2013 - ID S3580
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Introducing NVBIO: High Performance Primitives for Computational Genomics
Jonathan Cohen (NVIDIA), Nuno Subtil (NVIDIA)
Learn about NVIDIA's new open source CUDA/C++ library for high-performance computational genomics, NVBIO. NVBIO includes primitives for fast alignment using many variants of Smith-Waterman, text indexing via an FM-Index and related data structures, ...Read More
Learn about NVIDIA's new open source CUDA/C++ library for high-performance computational genomics, NVBIO. NVBIO includes primitives for fast alignment using many variants of Smith-Waterman, text indexing via an FM-Index and related data structures, and approximate string matching with backtracking. It also provides basic services like file IO and inter-thread communication. The design of NVBIO supports pipeline parallelism, where computation is expressed as a sequence of stages with queues to communicate between stages. Using this design concept, we have engineered an implementation of the Bowtie2 aligner on top of NVBIO, which aligns short read data 2-7x faster than the original Bowtie2 running on a high-end multicore CPU at comparable quality. In this talk we will introduce the codebase and demonstrate how to use it for your own applications.  Back
 
Keywords:
Bioinformatics & Genomics, GTC 2014 - ID S4741
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Computational Fluid Dynamics
Presentation
Media
Solving PDEs on Regular Grids with OpenCurrent
Jonathan Cohen
- NVIDIA Research
OpenCurrent is an open source library with support for structured 3D grids and various PDE solvers that operate on them, including a multigrid Poisson solver and an incompressible Navier-Stokes solver. ...Read More
OpenCurrent is an open source library with support for structured 3D grids and various PDE solvers that operate on them, including a multigrid Poisson solver and an incompressible Navier-Stokes solver. It also includes extensions for splitting grids across multiple GPUs. This talk will provide a basic introduction to the code base and its design principles.  Back
 
Keywords:
Computational Fluid Dynamics, GTC 2010 - ID 2022
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Developer - Algorithms
Presentation
Media
Efficient Graph Matching and Coloring on the GPU
Patrice Castonguay (NVIDIA), Jonathan Cohen (NVIDIA)
The goal of this session is to compare the performance of graph matching and graph coloring algorithms on massively parallel devices such as GPUs. We present novel algorithms, which produce superior results for certain graphs and also discuss th ...Read More

The goal of this session is to compare the performance of graph matching and graph coloring algorithms on massively parallel devices such as GPUs. We present novel algorithms, which produce superior results for certain graphs and also discuss the techniques used to efficiently implement these algorithms on the GPU.

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Keywords:
Developer - Algorithms, GTC 2012 - ID S2332
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High Performance Algebraic Multigrid for Commercial Applications
Jonathan Cohen (NVIDIA)
NVIDIA has been developing a library of high-performance parallel sparse iterative linear solvers, with an emphasis on multilevel and multigrid methods. In this presentation, I will provide an overview of the library''s design and outlin ...Read More

NVIDIA has been developing a library of high-performance parallel sparse iterative linear solvers, with an emphasis on multilevel and multigrid methods. In this presentation, I will provide an overview of the library''s design and outline many of the challenges we have faced in balancing numerical behavior against parallel scalability. Our library has been integrated into ANSYS Fluent 14.5, and will be released as a fully supported feature in the upcoming Fluent 15. I will describe the collaboration between ANSYS and NVIDIA, and present benchmarking results across a variety of test problems from CFD and other fields. Finally, I will talk about our future plans and discuss some of the open research problems in the area of algebraic multigrid on massively parallel processors.

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Keywords:
Developer - Algorithms, Computational Fluid Dynamics, Energy Exploration, GTC 2013 - ID S3579
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Developer - Programming Languages
Presentation
Media
Processing Device Arrays with C++ Metaprogramming
Jonathan Cohen
I will describe tricks for building APIs using C++ metaprogramming that generate custom kernels for complex manipulation of device-side arrays in CUDA. Using a variation of Expression Templates, multiple operations can be fused into a single ker ...Read More

I will describe tricks for building APIs using C++ metaprogramming that generate custom kernels for complex manipulation of device-side arrays in CUDA. Using a variation of Expression Templates, multiple operations can be fused into a single kernel that executes with reasonable efficiency.

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Keywords:
Developer - Programming Languages, Developer - Tools & Libraries, GTC 2010 - ID S1020230
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Developer - Tools & Libraries
Presentation
Media
CUDA 5 Math Library Performance Overview
Jonathan Cohen (NVIDIA)
 
Keywords:
Developer - Tools & Libraries, GTC Webinars 2013 - ID GTCE028
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CUDA 6 - Performance Overview
Jonathan Cohen (NVIDIA)
Please join Jonathan Cohen supported by other members of the NVIDIA engineering team responsible for the new high performance libraries which are part of the CUDA 6 Toolkit. In this webinar, the team will present the latest performance improveme ...Read More

Please join Jonathan Cohen supported by other members of the NVIDIA engineering team responsible for the new high performance libraries which are part of the CUDA 6 Toolkit. In this webinar, the team will present the latest performance improvements and give attendees a chance to ask questions and even make suggestions for future enhancements - a must attend webinar for any serious GPU Computing Developer. CUDA 6.0 Production is now available download : www.nvidia.com/getcuda

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Keywords:
Developer - Tools & Libraries, GTC Webinars 2014 - ID GTCE087
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High Performance Computing
Presentation
Media
The Next Generation CUDA Architecture, Code Named Fermi - The Soul of a Supercomputer in the Body of a GPU
Jonathan Cohen, Michael Garland
- NVIDIA
 
Keywords:
High Performance Computing, Supercomputing 2009 - ID SC0914
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The Next Generation CUDA Architecture, Code Named Fermi - The Soul of a Supercomputer in the Body of a GPU
Jonathan Cohen, Michael Garland
- NVIDIA
 
Keywords:
High Performance Computing, Supercomputing 2009 - ID SC0914
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