Multicore SIMD ASIP for Next-Generation Sequencing and Alignment Biochip Platforms

Nuno Neves, Nuno Sebastiao, David Matos, Pedro Tomas, Paulo Flores, Nuno Roma
2015 IEEE Transactions on Very Large Scale Integration (vlsi) Systems  
Targeting the development of new biochip platforms capable of autonomously sequencing and aligning biological sequences, a new multicore processing structure is proposed in this manuscript. This multicore structure makes use of a shared memory model and multiple instantiations of a novel applicationspecific instruction-set processor (ASIP) to simultaneously exploit both fine and coarse-grained parallelism and to achieve high performance levels at low-power consumption. The proposed ASIP is
more » ... by extending the instruction set architecture of a synthesizable processor, including both general and specialpurpose single-instruction multiple-data instructions. This allows an efficient exploitation of fine-grained parallelism on the alignment of biological sequences, achieving over 30× speedup when compared with sequential algorithmic implementations. The complete system was prototyped on different field-programmable gate array platforms and synthesized with a 90-nm CMOS process technology. Experimental results demonstrate that the multicore structure scales almost linearly with the number of instantiated cores, achieving performances similar to a quad-core Intel Core i7 3820 processor, while using 25× less energy. Index Terms-Application-specific instruction-set architecture, biochip platforms, biological sequences alignment, multicore architecture, single-instruction-multiple-data (SIMD). 1063-8210
doi:10.1109/tvlsi.2014.2333757 fatcat:twsa7irxnjhkxl3mhqktxdsb4e