DSPatch: Dual Spatial Pattern Prefetcher

High main memory latency continues to limit performance of modern high-performance out-of-order cores. While DRAM latency has remained nearly the same over many generations, DRAM bandwidth has grown significantly due to higher frequencies, newer architectures (DDR4, LPDDR4, GDDR5) and 3D-stacked memory packaging (HBM). Current state-of-the-art prefetchers do not do well in extracting higher performance when higher DRAM bandwidth is available. Prefetchers need the ability to dynamically adapt to available bandwidth, boosting prefetch count and prefetch coverage when headroom exists and throttling down to achieve high accuracy when the bandwidth utilization is close to peak. To this end, we present the Dual Spatial Pattern Prefetcher (DSPatch) that can be used as a standalone prefetcher or as a lightweight adjunct spatial prefetcher to the state-of-the-art delta-based Signature Pattern Prefetcher (SPP). DSPatch builds on a novel and intuitive use of modulated spatial bit-patterns. The key idea is to: (1) represent program accesses on a physical page as a bit-pattern anchored to the first "trigger" access, (2) learn two spatial access bit-patterns: one biased towards coverage and another biased towards accuracy, and (3) select one bit-pattern at run-time based on the DRAM bandwidth utilization to generate prefetches. Across a diverse set of workloads, using only 3.6KB of storage, DSPatch improves performance over an aggressive baseline with a PC-based stride prefetcher at the L1 cache and the SPP prefetcher at the L2 cache by 6% (9% in memory-intensive workloads and up to 26%). Moreover, the performance of DSPatch+SPP scales with increasing DRAM bandwidth, growing from 6% over SPP to 10% when DRAM bandwidth is doubled.Comment: This work is to appear in MICRO 201

ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis

Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequences. In pHMMs, sequences are represented as graph structures. These probabilities are subsequently used to compute the similarity score between a sequence and a pHMM graph. The Baum-Welch algorithm, a prevalent and highly accurate method, utilizes these probabilities to optimize and compute similarity scores. However, the Baum-Welch algorithm is computationally intensive, and existing solutions offer either software-only or hardware-only approaches with fixed pHMM designs. We identify an urgent need for a flexible, high-performance, and energy-efficient HW/SW co-design to address the major inefficiencies in the Baum-Welch algorithm for pHMMs. We introduce ApHMM, the first flexible acceleration framework designed to significantly reduce both computational and energy overheads associated with the Baum-Welch algorithm for pHMMs. ApHMM tackles the major inefficiencies in the Baum-Welch algorithm by 1) designing flexible hardware to accommodate various pHMM designs, 2) exploiting predictable data dependency patterns through on-chip memory with memoization techniques, 3) rapidly filtering out negligible computations using a hardware-based filter, and 4) minimizing redundant computations. ApHMM achieves substantial speedups of 15.55x - 260.03x, 1.83x - 5.34x, and 27.97x when compared to CPU, GPU, and FPGA implementations of the Baum-Welch algorithm, respectively. ApHMM outperforms state-of-the-art CPU implementations in three key bioinformatics applications: 1) error correction, 2) protein family search, and 3) multiple sequence alignment, by 1.29x - 59.94x, 1.03x - 1.75x, and 1.03x - 1.95x, respectively, while improving their energy efficiency by 64.24x - 115.46x, 1.75x, 1.96x.Comment: Accepted to ACM TAC

Early Prediction of DNN Activation Using Hierarchical Computations

Deep Neural Networks (DNNs) have set state-of-the-art performance numbers in diverse fields of electronics (computer vision, voice recognition), biology, bioinformatics, etc. However, the process of learning (training) from the data and application of the learnt information (inference) process requires huge computational resources. Approximate computing is a common method to reduce computation cost, but it introduces loss in task accuracy, which limits their application. Using an inherent property of Rectified Linear Unit (ReLU), a popular activation function, we propose a mathematical model to perform MAC operation using reduced precision for predicting negative values early. We also propose a method to perform hierarchical computation to achieve the same results as IEEE754 full precision compute. Applying this method on ResNet50 and VGG16 shows that up to 80% of ReLU zeros (which is 50% of all ReLU outputs) can be predicted and detected early by using just 3 out of 23 mantissa bits. This method is equally applicable to other floating-point representations