Hasindu Gamaarachchi

Hasindu Gamaarachchi


Seminar Room 1


An invited talk about Portable and lightweight Nanopore DNA sequence analysis on embedded systems.

DNA sequence analysis is the key to precision medicine. Over the last two decades, DNA sequencing machines have evolved from >500kg machines to pocket-sized devices such as the 87g Oxford Nanopore MinION. However, software tools that analyse the terabytes of data produced by sequencing machines are still dependent on high-performance or cloud computers, which limits the utility of portable sequencers. State-of-the-art DNA analysis software tools are typically designed and developed by biologists, having access to near-unlimited computational and memory resources, and are thus considerably un-optimised. These tools are extremely complex and are collections of dozens of various algorithms and numerous heuristically determined parameters. I will demonstrate how we optimise a complete Nanopore DNA analysis work-flow (a collection of few software tools run sequentially) to execute on portable and lightweight embedded systems. First, we analyse the work-flow and identify, the nature of the workloads (CPU intensive, memory-intensive, I/O intensive) in different portions of the work-flow. Then we systematically re-structure the software and optimise bottlenecks to execute on lightweight System-on-Chip equipped with embedded GPU. We simultaneously use the characteristics of biological data, associated algorithms, and computer software and hardware architecture for re-structuring and optimising. Major bottlenecks are resolved via CPU optimisations, parallelisation for GPU architectures, GPU optimisations (exploiting data access patterns for better cache usage and memory coalescing), and heterogeneous CPU-GPU work-load balancing. Importantly, our re-structuring and optimisations do not alter the accuracy of the results.

Hasindu Gamaarachchi is a PhD candidate at the School of Computer Science and Engineering, University of New South Wales. He is also a visiting research student at Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia.  He has worked as a  lecturer in the Department of Computer Engineering, the University of Peradeniya in 2016. He received his bachelor degree with first-class honours for Computer Engineering from the University of Peradeniya in 2015. His research interests are in embedded systems, bioinformatic algorithms and parallel computing.