Abstract
In order to handle the massive raw data generated by next generation sequencing (NGS) platforms, GPUs are widely used by many genetic analysis tools to speed up the used algorithms. In this paper, we use GPUs to accelerate the pair-HMMs forward algorithm, which is used to calculate the overall alignment probability in many genomics analysis tools. We firstly evaluate two different implementation methods to accelerate the pair-HMMs forward algorithm according to their effectiveness on GPU platforms. Based on these two methods, we present several implementations of the pair-HMMs forward algorithm.
We execute these implementations on the NVIDIA Tesla K40 card using different datasets to compare the performance. Experimental results show that the intra-task implementation has the highest throughput in most cases, achieving pure computational throughput as high as 23.56 GCUPS for synthetic datasets.
On a real dataset, the inter-task implementation achieves 4.82x speedup compared with a vectorized implementation executed on a 20-core POWER8 system.
We execute these implementations on the NVIDIA Tesla K40 card using different datasets to compare the performance. Experimental results show that the intra-task implementation has the highest throughput in most cases, achieving pure computational throughput as high as 23.56 GCUPS for synthetic datasets.
On a real dataset, the inter-task implementation achieves 4.82x speedup compared with a vectorized implementation executed on a 20-core POWER8 system.
Original language | English |
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Title of host publication | Proceedings 3rd International Workshop on High Performance Computing on Bioinformatics |
Pages | 1-8 |
Number of pages | 8 |
DOIs | |
Publication status | Published - 2016 |
Event | The 3rd International Workshop on High Performance Computing on Bioinformatics (HPCB 2016) - Shenzhen, China Duration: 15 Dec 2016 → 18 Dec 2016 |
Workshop
Workshop | The 3rd International Workshop on High Performance Computing on Bioinformatics (HPCB 2016) |
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Abbreviated title | HPCB 2016 |
Country/Territory | China |
City | Shenzhen |
Period | 15/12/16 → 18/12/16 |