FM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, resulting in a memory bound problem. This paper analyzes different FM-index versions presented in the literature, focusing on those computing aspects related to the data access. As a result of the analysis, we propose a new organization of FM-index that minimizes the demand for memory bandwidth, allowing a great improvement of performance on processors with high-bandwidth memory, such as the second-generation Intel Xeon Phi (Knights Landing, or KNL), integrating ultra high-bandwidth stacked memory technology. As the roofline model shows, our implementation reaches 95% of the peak random access bandwidth limit when executed on the KNL and almost all the available bandwidth when executed on other Intel Xeon architectures with conventional DDR memory. In addition, the obtained throughput in KNL is much higher than the results reported for GPUs in the literature.
Because of the growing importance of decimal floating-point (DFP) arithmetic, specifications for it are included in the IEEE Draft Standard for Floating-point Arithmetic (IEEE P754). In this paper, we present a novel algorithm and hardware design for a DFP adder. The adder performs addition and subtraction on 64-bit operands that use the IEEE P754 binary encoding of DFP numbers, widely known as the Binary Integer Decimal (BID) encoding. The BID adder uses a novel hardware component for decimal digit counting and an enhanced version of a previously published BID rounding unit. By adding more sophisticated control, operations are performed with variable latency to optimize for common cases. We show that a BID-based DFP adder design can be achieved with a modest area increase compared to a single 2-stage pipelined 64-bit fixed-point multiplier. Over 70% of the BID adder's area is due the 64-bit fixed-point multiplier, which can be shared with a binary floating-point multiplier and hardware for other DFP operations. To our knowledge, this is the first hardware design for adding and subtracting IEEE P754 BID-encoded DFP numbers.
Because of the growing importance of decimal floating-point (DFP) arithmetic, specifications for it were recently added to the draft revision of the IEEE 754 Standard (IEEE P754). In this paper, we present a hardware design for a rounding unit for 64-bit DFP numbers (decimal64) that use the IEEE P754 binary encoding of DFP numbers, which is widely known as the Binary Integer Decimal (BID) encoding. We summarize the technique used for rounding, present the theory and design of the BID rounding unit, and evaluate its critical path delay, latency, and area for combinational and pipelined designs. Over 86% of the rounding unit's area is due to a 55-bit by 54-bit binary multiplier, which can be shared with a double-precision binary floating-point multiplier. To our knowledge, this is the first hardware design for rounding IEEE P754 BID-encoded DFP numbers.
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