FourierPIM: High-Throughput In-Memory Fast Fourier Transform and Polynomial Multiplication

The Discrete Fourier Transform (DFT) is essential for various applications ranging from signal processing to convolution and polynomial multiplication. The groundbreaking Fast Fourier Transform (FFT) algorithm reduces DFT time complexity from the naive O(n^2) to O(n log n), and recent works have sought further acceleration through parallel architectures such as GPUs. Unfortunately, accelerators such as GPUs cannot exploit their full computing capabilities as memory access becomes the bottleneck. Therefore, this paper accelerates the FFT algorithm using digital Processing-in-Memory (PIM) architectures that shift computation into the memory by exploiting physical devices capable of storage and logic (e.g., memristors). We propose an O(log n) in-memory FFT algorithm that can also be performed in parallel across multiple arrays for high-throughput batched execution, supporting both fixed-point and floating-point numbers. Through the convolution theorem, we extend this algorithm to O(log n) polynomial multiplication - a fundamental task for applications such as cryptography. We evaluate FourierPIM on a publicly-available cycle-accurate simulator that verifies both correctness and performance, and demonstrate 5-15x throughput and 4-13x energy improvement over the NVIDIA cuFFT library on state-of-the-art GPUs for FFT and polynomial multiplication

ClaPIM: Scalable Sequence CLAssification using Processing-In-Memory

DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important. This paper introduces ClaPIM, a scalable DNA sequence classification architecture based on the emerging concept of hybrid in-crossbar and near-crossbar memristive processing-in-memory (PIM). We enable efficient and high-quality classification by uniting the filter and search stages within a single algorithm. Specifically, we propose a custom filtering technique that drastically narrows the search space and a search approach that facilitates approximate string matching through a distance function. ClaPIM is the first PIM architecture for scalable approximate string matching that benefits from the high density of memristive crossbar arrays and the massive computational parallelism of PIM. Compared with Kraken2, a state-of-the-art software classifier, ClaPIM provides significantly higher classification quality (up to 20x improvement in F1 score) and also demonstrates a 1.8x throughput improvement. Compared with EDAM, a recently-proposed SRAM-based accelerator that is restricted to small datasets, we observe both a 30.4x improvement in normalized throughput per area and a 7% increase in classification precision

The Bitlet model: a parameterized analytical model to compare PIM and CPU systems

Currently, data-intensive applications are gaining popularity. Together with this trend, processing-in-memory (PIM)-based systems are being given more attention and have become more relevant. This article describes an analytical modeling tool called Bitlet that can be used in a parameterized fashion to estimate the performance and power/energy of a PIM-based system and, thereby, assess the affinity of workloads for PIM as opposed to traditional computing. The tool uncovers interesting trade-offs between, mainly, the PIM computation complexity (cycles required to perform a computation through PIM), the amount of memory used for PIM, the system memory bandwidth, and the data transfer size. Despite its simplicity, the model reveals new insights when applied to real-life examples. The model is demonstrated for several synthetic examples and then applied to explore the influence of different parameters on two systems - IMAGING and FloatPIM. Based on the demonstrations, insights about PIM and its combination with a CPU are provided.This work was supported by the European Research Council through the European Union’s Horizon 2020 Research and Innovation Programme under Grant No. 757259 and by the Israel Science Foundation under Grant No. 1514/17