Optimizing and multithreading SNPHAP on a multi-core APU with OpenCL

Optimizing and multithreading SNPHAP on a multi-core APU with OpenCL

In this paper, we have optimized and multithreaded SNPHAP, a bioinformatics program, with OpenCL to reduce the computation time and thus accelerate the execution. Our method is called Radix Comparison algorithm running in sequential and parallel (multithreading). Based on the recent multi-core AMD A...

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Hauptverfasser: Rattanatranurak, A., Kittitornkun, S., Tongsima, S.
Format: Tagungsbericht
Sprache:eng
Schlagworte:
Acceleration
Arrays
Computational modeling
Indexes
Instruction sets
Kernel
Multithreading
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Beschreibung
Zusammenfassung:In this paper, we have optimized and multithreaded SNPHAP, a bioinformatics program, with OpenCL to reduce the computation time and thus accelerate the execution. Our method is called Radix Comparison algorithm running in sequential and parallel (multithreading). Based on the recent multi-core AMD A6-3650 APU (Accelerated Processing Unit), the achieveable Speedups of Sequential Radix and Parallel Radix SNPHAP compared with the original SNPHAP are 260% and 271%, respectively.
DOI:10.1109/JCSSE.2012.6261947