3D-stacked many-core architecture for biological sequence analysis problems

Pei Liu, Ahmed Hemani, Kolin Paul
2015 2015 International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS)  
Sequence analysis plays extremely important role in bioinformatics, and most applications of which have compute intensive kernels consuming over 70% of total execution time. By exploiting the compute intensive execution stages of popular sequence analysis applications, we present and evaluate a VLSI architecture with a focus on those that target at biological sequences directly, including pairwise sequence alignment, multiple sequence alignment, database search, and short read sequence
more » ... Based on coarse grained reconfigurable array we propose the use of many-core and 3D-stacked technologies to gain further improvement over memory subsystem, which gives another order of magnitude speedup from high bandwidth and B Pei Liu Address 0 Dummy Offset 0 Offset 1 Offset 2 0 25 28 36 45 Address 8 Dummy Offset 0 Offset 1 Offset 2 Address 16 Dummy Offset 0 Offset 1 Offset 2 Address 24 Dummy Offset 0 Offset 1 Offset 2 Offset 3 Offset 3 Offset 3 Offset 3 54 63 Address 4 Dummy Offset 0 Offset 1 Offset 2 89 91 100 109 Address 12 Dummy Offset 0 Offset 1 Offset 2 Address 20 Dummy Offset 0 Offset 1 Offset 2 Address 28 Dummy Offset 0 Offset 1 Offset 2 Offset 3 Offset 3 Offset 3 Offset 3 118 127 64 Address n+1 = Address n + offset 0 Address n+2 = Address n + offset 0 + offset 1 Address n+3 = Address n + offset 0 + offset 1 + offset 2 (14)
doi:10.1109/samos.2015.7363678 dblp:conf/samos/LiuHP15 fatcat:xysaiokksbem7cqlnvpqahr7be