Analysis of Distributed Optimization Algorithms on a Real Processing-In-Memory System

Machine Learning (ML) training on large-scale datasets is a very expensive and time-consuming workload. Processor-centric architectures (e.g., CPU, GPU) commonly used for modern ML training workloads are limited by the data movement bottleneck, i.e., due to repeatedly accessing the training dataset. As a result, processor-centric systems suffer from performance degradation and high energy consumption. Processing-In-Memory (PIM) is a promising solution to alleviate the data movement bottleneck by placing the computation mechanisms inside or near memory. Our goal is to understand the capabilities and characteristics of popular distributed optimization algorithms on real-world PIM architectures to accelerate data-intensive ML training workloads. To this end, we 1) implement several representative centralized distributed optimization algorithms on UPMEM's real-world general-purpose PIM system, 2) rigorously evaluate these algorithms for ML training on large-scale datasets in terms of performance, accuracy, and scalability, 3) compare to conventional CPU and GPU baselines, and 4) discuss implications for future PIM hardware and the need to shift to an algorithm-hardware codesign perspective to accommodate decentralized distributed optimization algorithms. Our results demonstrate three major findings: 1) Modern general-purpose PIM architectures can be a viable alternative to state-of-the-art CPUs and GPUs for many memory-bound ML training workloads, when operations and datatypes are natively supported by PIM hardware, 2) the importance of carefully choosing the optimization algorithm that best fit PIM, and 3) contrary to popular belief, contemporary PIM architectures do not scale approximately linearly with the number of nodes for many data-intensive ML training workloads. To facilitate future research, we aim to open-source our complete codebase.

Accelerating Graph Neural Networks on Real Processing-In-Memory Systems

Graph Neural Networks (GNNs) are emerging ML models to analyze graph-structure data. Graph Neural Network (GNN) execution involves both compute-intensive and memory-intensive kernels, the latter dominates the total time, being significantly bottlenecked by data movement between memory and processors. Processing-In-Memory (PIM) systems can alleviate this data movement bottleneck by placing simple processors near or inside to memory arrays. In this work, we introduce PyGim, an efficient ML framework that accelerates GNNs on real PIM systems. We propose intelligent parallelization techniques for memory-intensive kernels of GNNs tailored for real PIM systems, and develop handy Python API for them. We provide hybrid GNN execution, in which the compute-intensive and memory-intensive kernels are executed in processor-centric and memory-centric computing systems, respectively, to match their algorithmic nature. We extensively evaluate PyGim on a real-world PIM system with 1992 PIM cores using emerging GNN models, and demonstrate that it outperforms its state-of-the-art CPU counterpart on Intel Xeon by on average 3.04x, and achieves higher resource utilization than CPU and GPU systems. Our work provides useful recommendations for software, system and hardware designers. PyGim will be open-sourced to enable the widespread use of PIM systems in GNNs.

Topologies of Reasoning: Demystifying Chains, Trees, and Graphs of Thoughts

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and others parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

TransPimLib: A Library for Efficient Transcendental Functions on Processing-in-Memory Systems

Processing-in-memory (PIM) promises to alleviate the data movement bottleneck in modern computing systems. However, current real-world PIM systems have the inherent disadvantage that their hardware is more constrained than in conventional processors (CPU, GPU), due to the difficulty and cost of building processing elements near or inside the memory. As a result, general-purpose PIM architectures support fairly limited instruction sets and struggle to execute complex operations such as transcendental functions and other hard-to-calculate operations (e.g., square root). These operations are particularly important for some modern workloads, e.g., activation functions in machine learning applications. In order to provide support for transcendental (and other hard-to-calculate) functions in general-purpose PIM systems, we present \emph{TransPimLib}, a library that provides CORDIC-based and LUT-based methods for trigonometric functions, hyperbolic functions, exponentiation, logarithm, square root, etc. We develop an implementation of TransPimLib for the UPMEM PIM architecture and perform a thorough evaluation of TransPimLib's methods in terms of performance and accuracy, using microbenchmarks and three full workloads (Blackscholes, Sigmoid, Softmax). We open-source all our code and datasets at~\url{https://github.com/CMU-SAFARI/transpimlib}.

RedBit: An End-to-End Flexible Framework for Evaluating the Accuracy of Quantized CNNs

In recent years, Convolutional Neural Networks (CNNs) have become the standard class of deep neural network for image processing, classification and segmentation tasks. However, the large strides in accuracy obtained by CNNs have been derived from increasing the complexity of network topologies, which incurs sizeable performance and energy penalties in the training and inference of CNNs. Many recent works have validated the effectiveness of parameter quantization, which consists in reducing the bit width of the network's parameters, to enable the attainment of considerable performance and energy efficiency gains without significantly compromising accuracy. However, it is difficult to compare the relative effectiveness of different quantization methods. To address this problem, we introduce RedBit, an open-source framework that provides a transparent, extensible and easy-to-use interface to evaluate the effectiveness of different algorithms and parameter configurations on network accuracy. We use RedBit to perform a comprehensive survey of five state-of-the-art quantization methods applied to the MNIST, CIFAR-10 and ImageNet datasets. We evaluate a total of 2300 individual bit width combinations, independently tuning the width of the network's weight and input activation parameters, from 32 bits down to 1 bit (e.g., 8/8, 2/2, 1/32, 1/1, for weights/activations). Upwards of 20000 hours of computing time in a pool of state-of-the-art GPUs were used to generate all the results in this paper. For 1-bit quantization, the accuracy losses for the MNIST, CIFAR-10 and ImageNet datasets range between [0.26%, 0.79%], [9.74%, 32.96%] and [10.86%, 47.36%] top-1, respectively. We actively encourage the reader to download the source code and experiment with RedBit, and to submit their own observed results to our public repository, available at https://github.com/IT-Coimbra/RedBit.

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering

Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art basecallers employ complex deep learning models to achieve high basecalling accuracy. This makes basecalling computationally-inefficient and memory-hungry; bottlenecking the entire genome analysis pipeline. However, for many applications, the majority of reads do no match the reference genome of interest (i.e., target reference) and thus are discarded in later steps in the genomics pipeline, wasting the basecalling computation. To overcome this issue, we propose TargetCall, the first fast and widely-applicable pre-basecalling filter to eliminate the wasted computation in basecalling. TargetCall's key idea is to discard reads that will not match the target reference (i.e., off-target reads) prior to basecalling. TargetCall consists of two main components: (1) LightCall, a lightweight neural network basecaller that produces noisy reads; and (2) Similarity Check, which labels each of these noisy reads as on-target or off-target by matching them to the target reference. TargetCall filters out all off-target reads before basecalling; and the highly-accurate but slow basecalling is performed only on the raw signals whose noisy reads are labeled as on-target. Our thorough experimental evaluations using both real and simulated data show that TargetCall 1) improves the end-to-end basecalling performance of the state-of-the-art basecaller by 3.31x while maintaining high (98.88%) sensitivity in keeping on-target reads, 2) maintains high accuracy in downstream analysis, 3) precisely filters out up to 94.71% of off-target reads, and 4) achieves better performance, sensitivity, and generality compared to prior works. We freely open-source TargetCall at https://github.com/CMU-SAFARI/TargetCall.

NEON: Enabling Efficient Support for Nonlinear Operations in Resistive RAM-based Neural Network Accelerators

Resistive Random-Access Memory (RRAM) is well-suited to accelerate neural network (NN) workloads as RRAM-based Processing-in-Memory (PIM) architectures natively support highly-parallel multiply-accumulate (MAC) operations that form the backbone of most NN workloads. Unfortunately, NN workloads such as transformers require support for non-MAC operations (e.g., softmax) that RRAM cannot provide natively. Consequently, state-of-the-art works either integrate additional digital logic circuits to support the non-MAC operations or offload the non-MAC operations to CPU/GPU, resulting in significant performance and energy efficiency overheads due to data movement. In this work, we propose NEON, a novel compiler optimization to enable the end-to-end execution of the NN workload in RRAM. The key idea of NEON is to transform each non-MAC operation into a lightweight yet highly-accurate neural network. Utilizing neural networks to approximate the non-MAC operations provides two advantages: 1) We can exploit the key strength of RRAM, i.e., highly-parallel MAC operation, to flexibly and efficiently execute non-MAC operations in memory. 2) We can simplify RRAM's microarchitecture by eliminating the additional digital logic circuits while reducing the data movement overheads. Acceleration of the non-MAC operations in memory enables NEON to achieve a 2.28x speedup compared to an idealized digital logic-based RRAM. We analyze the trade-offs associated with the transformation and demonstrate feasible use cases for NEON across different substrates.

Accelerating Neural Network Inference with Processing-in-DRAM: From the Edge to the Cloud

Neural networks (NNs) are growing in importance and complexity. A neural network's performance (and energy efficiency) can be bound either by computation or memory resources. The processing-in-memory (PIM) paradigm, where computation is placed near or within memory arrays, is a viable solution to accelerate memory-bound NNs. However, PIM architectures vary in form, where different PIM approaches lead to different trade-offs. Our goal is to analyze, discuss, and contrast DRAM-based PIM architectures for NN performance and energy efficiency. To do so, we analyze three state-of-the-art PIM architectures: (1) UPMEM, which integrates processors and DRAM arrays into a single 2D chip; (2) Mensa, a 3D-stack-based PIM architecture tailored for edge devices; and (3) SIMDRAM, which uses the analog principles of DRAM to execute bit-serial operations. Our analysis reveals that PIM greatly benefits memory-bound NNs: (1) UPMEM provides 23x the performance of a high-end GPU when the GPU requires memory oversubscription for a general matrix-vector multiplication kernel; (2) Mensa improves energy efficiency and throughput by 3.0x and 3.1x over the Google Edge TPU for 24 Google edge NN models; and (3) SIMDRAM outperforms a CPU/GPU by 16.7x/1.4x for three binary NNs. We conclude that the ideal PIM architecture for NN models depends on a model's distinct attributes, due to the inherent architectural design choices.