Multicore SIMD ASIP for Next-Generation Sequencing and Alignment Biochip Platforms
Nuno Neves, Nuno Sebastião, David Martins de Matos, Pedro Tomás, Paulo F. Flores, Nuno Roma · IEEE Transactions on Very Large Scale Integration (VLSI) Systems · 2014
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 application-specific 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 built by extending the instruction set architecture of a synthesizable processor, including both general and special-purpose single-instruction multiple-data instructions. This allows an efficient exploitation of fine-grained parallelism on the alignment of biological sequences, achieving over$30\times $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\times $less energy.