Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are extensive efforts to accelerate genome sequence analysis. In this work, we demonstrate a major bottleneck that greatly limits and diminishes the benefits of state-of-the-art genome sequence analysis accelerators: the data preparation bottleneck, where genomic sequence data is stored in compressed form and needs to be first decompressed and formatted before an accelerator can operate on it. To mitigate this bottleneck, we propose SAGe, an algorithm-architecture co-design for highly-compressed storage and high-performance a ccess of large-scale genomic sequence data. The key challenge is to improve data preparation performance while maintaining high compression ratios (comparable to genomic-specific compression algorithms) at low hardware cost. We address this challenge by leveraging key properties of genomic datasets to co-design (i) a lossless (de)compression algorithm, (ii) hardware that decompresses data with lightweight operations and efficient streaming accesses, (iii) storage data layout, and (iv) interface commands to access data. SAGe is highly versatile, as it supports datasets from different sequencing technologies and species. Due to its lightweight design, SAGe can be seamlessly integrated with a broad range of hardware accelerators for genome sequence analysis to mitigate their data preparation bottlenecks. Our results demonstrate that SAGe improves the average end-to-end performance and energy efficiency of two state-of-the-art genome sequence analysis accelerators by 3.0×-32.1× and 13.0×-34.0×, respectively, compared to when the accelerators rely on state-of-the-art software and hardware decompression tools.

Near-data processing (NDP) mitigates the data movement bottleneck in modern computing systems by performing computation close to where the data resides. Solid-state drives (SSDs) are well suited for NDP because they: (1) store large application datasets that exceed main memory capacity, and (2) contain multiple heterogeneous computation resources, e.g., general-purpose embedded cores in the SSD controller, DRAM chips, and NAND flash chips, which enable three NDP paradigms: in-storage processing (ISP), processing using DRAM in the SSD (PuD-SSD), and in-flash processing (IFP). These resources offer massive internal parallelism and enable in-place computation, which reduces data movement across the memory hierarchy. A large body of prior SSD-based NDP techniques operate in isolation, mapping computations to only one or two NDP paradigms (i.e., ISP, PuD-SSD, or IFP) within the SSD. These techniques (1) are tailored to specific workloads or kernels, (2) do not offload computations across all three NDP paradigms in the SSD and thus fail to exploit the full computational potential of an SSD, and (3) lack programmer-transparency, often requiring significant manual effort to identify offloadable code regions and map them to the SSD computation resources, which limits their general applicability and ease of deployment. While several prior works propose techniques to partition computation between the host and near-memory accelerators, adapting these techniques to SSDs offers limited benefits because they (1) ignore the heterogeneity of the SSD computation resources, and (2) make offloading decisions based on limited factors such as bandwidth utilization, data movement cost, or memory intensity, while ignoring key factors such as resource utilization. We propose Conduit, a general-purpose, programmertransparent NDP framework for SSDs that accelerates a broad range of workloads by leveraging available SSD computation resources. Conduit operates in two stages. At compile time, Conduit executes a custom compiler (e.g., LLVM) pass that (i) vectorizes suitable application code segments into single-instruction multiple-data (SIMD) operations that align with the SSD's page layout, and (ii) embeds metadata (e.g., operation type, operand sizes) into the vectorized instructions to guide runtime offloading decisions. At runtime, within the SSD, Conduit performs instruction-granularity offloading by evaluating six key application and system features (e.g., operation type, computation resource utilization, data dependence delay), and uses a cost function to select the most suitable SSD computation resource to execute each vectorized instruction. We evaluate Conduit and two prior NDP offloading techniques using an in-house event-driven SSD simulator on six data-intensive applications (e.g., large language model inference and training, encryption). Conduit outperforms the best-performing prior offloading policy by$1.8 \times$and reduces energy consumption by 46 %, with small latency and storage overheads, and no additional hardware cost.

Modern high-performance computing (HPC) environments rely on hybrid storage systems (HSS) that combine multiple storage devices with diverse latency, bandwidth, endurance, and capacity characteristics to meet the performance, capacity, and cost requirements of data-intensive applications. The performance of an HSS highly depends on two key data-management policies: (1) data placement, which determines the most suitable storage device to store application data, and (2) data migration, which dynamically reorganizes previously-stored data across storage devices (i.e., prefetching hot data and evicting cold data) to sustain high HSS performance. These policies are tightly interdependent, and thus, improving one without considering the other leads to suboptimal HSS performance. Unfortunately, prior works optimize only one of the policies.

Homomorphic encryption (HE) allows secure computation on encrypted data without revealing the original data, providing significant benefits for privacy-sensitive applications. Many cloud computing applications (e.g., DNA read mapping, biometric matching, web search) use exact string matching as a key operation. However, prior string matching algorithms that use homomorphic encryption are limited by high computational latency caused by the use of complex operations and data movement bottlenecks due to the large encrypted data size. In this work, we provide an efficient algorithm-hardware codesign to accelerate HE-based secure exact string matching. We propose CIPHERMATCH, which (i) reduces the increase in memory footprint after encryption using an optimized software-based data packing scheme, (ii) eliminates the use of costly homomorphic operations (e.g., multiplication and rotation), and (iii) reduces data movement by designing a new in-flash processing (IFP) architecture.

As the memory demands of individual mobile applications continue to grow and the number of concurrently running applications increases, available memory on mobile devices is becoming increasingly scarce. When memory pressure is high, current mobile systems use a RAM-based compressed swap scheme (called ZRAM) to compress unused execution-related data (called anonymous data in Linux) in main memory. This approach avoids swapping data to secondary storage (NAND flash memory) or terminating applications, thereby achieving shorter application relaunch latency.In this paper, we observe that the state-of-the-art ZRAM scheme prolongs relaunch latency and wastes CPU time because it does not differentiate between hot and cold data or leverage different compression chunk sizes and data locality. We make three new observations. First, anonymous data has different levels of hotness. Hot data, used during application relaunch, is usually similar between consecutive relaunches. Second, when compressing the same amount of anonymous data, small-size compression is very fast, while large-size compression achieves a better compression ratio. Third, there is locality in data access during application relaunch.Based on these observations, we propose a hotness-aware and size-adaptive compressed swap scheme, Ariadne, for mobile devices to mitigate relaunch latency and reduce CPU usage. Ariadne incorporates three key techniques. First, a low-overhead hotness-aware data organization scheme aims to quickly identify the hotness of anonymous data without significant overhead. Second, a size-adaptive compression scheme uses different compression chunk sizes based on the data’s hotness level to ensure fast decompression of hot and warm data. Third, a proactive decompression scheme predicts the next set of data to be used and decompresses it in advance, reducing the impact of data swapping back into main memory during application relaunch.We implement and evaluate Ariadne on a commercial smartphone, Google Pixel 7 with the latest Android 14. Our experimental evaluation results show that, on average, Ariadne reduces application relaunch latency by 50% and decreases the CPU usage of compression and decompression procedures by 15% compared to the state-of-the-art compressed swap scheme for mobile devices.

Conventional genome analysis relies on translating the noisy raw electrical signals generated by DNA sequencing technologies into nucleotide bases (i.e., A, C, G, and T) through a computationally-intensive process called basecalling.Raw signal genome analysis (RSGA) has emerged as a promising approach towards enabling real-time genome analysis by directly analyzing raw electrical signals without the need for basecalling.However, rapid advancements in sequencing technologies make it increasingly difficult for softwarebased RSGA to match the throughput of raw signal generation.Hardware-based RSGA acceleration has the potential to bridge the gap between software-based RSGA and sequencing throughput.

Large Language Models (LLMs) face an inherent challenge: their knowledge is confined to the data that they have been trained on.This limitation, combined with the significant cost of retraining renders them incapable of providing up-to-date responses.To overcome these issues, Retrieval-Augmented Generation (RAG) complements the static training-derived knowledge of LLMs with an external knowledge repository.RAG consists of three stages: (i) indexing, which creates a database that facilitates similarity search on text embeddings, (ii) retrieval, which, given a user query, searches and retrieves relevant data from the database and (iii) generation, which uses the user query and the retrieved data to generate a response.The retrieval stage of RAG in particular becomes a significant performance bottleneck in inference pipelines.In this stage, (i) a given user query is mapped to an embedding vector and (ii) an Approximate Nearest Neighbor Search (ANNS) algorithm searches for the most semantically similar embedding vectors in the database to identify relevant items.Due to the large database sizes, ANNS incurs significant data movement overheads between the host and the storage system.To alleviate these overheads, prior works propose In-Storage Processing (ISP) techniques that accelerate ANNS workloads by performing computations inside the storage system.However, existing works that leverage ISP for ANNS (i) employ algorithms that are not tailored to ISP systems, (ii) do not accelerate data retrieval operations for data selected by ANNS, and (iii) introduce significant hardware modifications to the storage system, limiting performance and hindering their adoption.

The performance and capacity of solid-state drives (SSDs) are continuously improving to meet the increasing demands of modern data-intensive applications. Unfortunately, communication between the SSD controller and memory chips (e.g., 2D/3D NAND flash chips) is a critical performance bottleneck for many applications. SSDs use a multi-channel shared bus architecture where multiple memory chips connected to the same channel communicate to the SSD controller with only one path. As a result, path conflicts often occur during the servicing of multiple I/O requests, which significantly limits SSD parallelism. It is critical to handle path conflicts well to improve SSD parallelism and performance.

Hybrid storage systems (HSS) use multiple different storage devices to provide high and scalable storage capacity at high performance. Data placement across different devices is critical to maximize the benefits of such a hybrid system. Recent research proposes various techniques that aim to accurately identify performance-critical data to place it in a "best-fit" storage device. Unfortunately, most of these techniques are rigid, which (1) limits their adaptivity to perform well for a wide range of workloads and storage device configurations, and (2) makes it difficult for designers to extend these techniques to different storage system configurations (e.g., with a different number or different types of storage devices) than the configuration they are designed for. Our goal is to design a new data placement technique for hybrid storage systems that overcomes these issues and provides: (1) adaptivity, by continuously learning from and adapting to the workload and the storage device characteristics, and (2) easy extensibility to a wide range of workloads and HSS configurations.

Bulk bitwise operations, i. e., bitwise operations on large bit vectors, are prevalent in a wide range of important application domains, including databases, graph processing, genome analysis, cryptography, and hyper-dimensional computing. In conventional systems, the performance and energy efficiency of bulk bitwise operations are bottlenecked by data movement between the compute units (e.g., CPUs and GPUs) and the memory hierarchy. In-flash processing (i. e., processing data inside NAND flash chips) has a high potential to accelerate bulk bitwise operations by fundamentally reducing data movement through the entire memory hierarchy, especially when the processed data does not fit into main memory. We identify two key limitations of the state-of-the-art in-flash processing technique for bulk bitwise operations; (i) it falls short of maximally exploiting the bit-level parallelism of bulk bitwise operations that could be enabled by leveraging the unique cell-array architecture and operating principles of NAND flash memory; (ii) it is unreliable because it is not designed to take into account the highly error-prone nature of NAND flash memory. We propose Flash-Cosmos (Flash C omputation with-O ne-S hot M ulti-O perand S ensing), a new in-flash processing technique that significantly increases the performance and energy efficiency of bulk bitwise operations while providing high reliability. Flash-Cosmos introduces two key mechanisms that can be easily supported in modern NAND flash chips: (i) M ulti-W ordline S ensing (MWS), which enables bulk bitwise operations on a large number of operands (tens of operands) with a single sensing operation, and (ii) E nhanced S LC-mode P rogramming (ESP), which enables reliable computation inside NAND flash memory. We demonstrate the feasibility of performing bulk bitwise operations with high reliability in Flash-Cosmos by testing 160 real 3D NAND flash chips. Our evaluation shows that Flash-Cosmos improves average performance and energy efficiency by $3.5 \times /32 \times$ and $3.3 \times /95 \times$, respectively, over the state-of-the-art in-flash/outside-storage processing techniques across three real-world applications.