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Enabling the use of Heterogeneous Computing for Bioinformatics

Ramakrishna Bijanapalli Chakri
Virginia Polytechnic Institute
Virginia Polytechnic Institute, 2013

@phdthesis{chakri2013enabling,

   title={Enabling the Use of Heterogeneous Computing for Bioinformatics.},

   author={Chakri, Ramakrishna Bijanapalli},

   year={2013},

   school={Virginia Polytechnic Institute and State University}

}

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The huge amount of information in the encoded sequence of DNA and increasing interest in uncovering new discoveries has spurred interest in accelerating the DNA sequencing and alignment processes. The use of heterogeneous systems, that use different types of computational units, has seen a new light in high performance computing in recent years; However expertise in multiple domains and skills required to program these systems is causing an hindrance to bioinformaticians in rapidly deploying their applications into these heterogeneous systems. This work attempts to make an heterogeneous system, Convey HC-1, with an x86-based host processor and FPGA-based co-processor, accessible to bioinformaticians. First, a highly efficient dynamic programming based Smith-Waterman kernel is implemented in hardware, which is able to achieve a peak throughput of 307.2 Giga Cell Updates per Second (GCUPS) on Convey HC-1. A dynamic programming accelerator interface is provided to any application that uses Smith-Waterman. This implementation is also extended to General Purpose Graphics Processing Units (GP-GPUs), which achieved a peak throughput of 9.89 GCUPS on NVIDIA GTX580 GPU. Second, a well known graphical programming tool, LabVIEW is enabled as a programming tool for the Convey HC-1. A connection is established between the graphical interface and the Convey HC-1 to control and monitor the application running on the FPGA-based co-processor.
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