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Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth’s diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability. 

This article introduces the first open-source FPGA-based infrastructure, MetaSys, with a prototype in a RISC-V system, to enable the rapid implementation and evaluation of a wide range of cross-layer techniques in real hardware. Hardware-software cooperative techniques are powerful approaches to improving the performance, quality of service, and security of general-purpose processors. They are, however, typically challenging to rapidly implement and evaluate in real hardware as they require full-stack changes to the hardware, system software, and instruction-set architecture (ISA). MetaSys implements a rich hardware-software interface and lightweight metadata support that can be used as a common basis to rapidly implement and evaluate new cross-layer techniques. We demonstrate MetaSys’s versatility and ease-of-use by implementing and evaluating three cross-layer techniques for: (i) prefetching in graph analytics; (ii) bounds checking in memory unsafe languages, and (iii) return address protection in stack frames; each technique requiring only ~100 lines of Chisel code over MetaSys. Using MetaSys, we perform the first detailed experimental study to quantify the performance overheads of using a single metadata management system to enable multiple cross-layer optimizations in CPUs. We identify the key sources of bottlenecks and system inefficiency of a general metadata management system. We design MetaSys to minimize these inefficiencies and provide increased versatility compared to previously proposed metadata systems. Using three use cases and a detailed characterization, we demonstrate that a common metadata management system can be used to efficiently support diverse cross-layer techniques in CPUs. MetaSys is completely and freely available at https://github.com/CMU-SAFARI/MetaSys . 

To process real-world datasets, modern data-parallel systems often require extremely large amounts of memory, which are both costly and energy inefficient. Emerging non-volatile memory (NVM) technologies offer high capacity compared to DRAM and low energy compared to SSDs. Hence, NVMs have the potential to fundamentally change the dichotomy between DRAM and durable storage in Big Data processing. However, most Big Data applications are written in managed languages and executed on top of a managed runtime that already performs various dimensions of memory management. Supporting hybrid physical memories adds a new dimension, creating unique challenges in data replacement. This article proposes Panthera, a semantics-aware, fully automated memory management technique for Big Data processing over hybrid memories. Panthera analyzes user programs on a Big Data system to infer their coarse-grained access patterns, which are then passed to the Panthera runtime for efficient data placement and migration. For Big Data applications, the coarse-grained data division information is accurate enough to guide the GC for data layout, which hardly incurs overhead in data monitoring and moving. We implemented Panthera in OpenJDK and Apache Spark. Based on Big Data applications’ memory access pattern, we also implemented a new profiling-guided optimization strategy, which is transparent to applications. With this optimization, our extensive evaluation demonstrates that Panthera reduces energy by 32–53% at less than 1% time overhead on average. To show Panthera’s applicability, we extend it to QuickCached, a pure Java implementation of Memcached. Our evaluation results show that Panthera reduces energy by 28.7% at 5.2% time overhead on average. 

Many large-scale machine learning (ML) applications need to perform decentralized learning over datasets generated at different devices and locations. Such datasets pose a significant challenge to decentralized learning because their different contexts result in significant data distribution skew across devices/locations. In this paper, we take a step toward better understanding this challenge by presenting a detailed experimental study of decentralized DNN training on a common type of data skew: skewed distribution of data labels across devices/locations. Our study shows that: (i) skewed data labels are a fundamental and pervasive problem for decentralized learning, causing significant accuracy loss across many ML applications, DNN models, training datasets, and decentralized learning algorithms; (ii) the problem is particularly challenging for DNN models with batch normalization; and (iii) the degree of data skew is a key determinant of the difficulty of the problem. Based on these findings, we present SkewScout, a system-level approach that adapts the communication frequency of decentralized learning algorithms to the (skew-induced) accuracy loss between data partitions. We also show that group normalization can recover much of the accuracy loss of batch normalization.