arXiv subjects

Onur Mutlu

Publications and source records attributed to Onur Mutlu.

At least 91 records · Page 5Linked to original sources

arXiv2025

SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences

Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most fundamental computational steps in most genomic analyses. Due to its high computational complexity, optimized exact and heuristic algorithms are still being developed. We find that these methods are highly sensitive to the underlying data, its quality, and various hyperparameters. Despite their wide use, no in-depth analysis has been performed, potentially falsely discarding genetic sequences from further analysis and unnecessarily inflating computational costs. We provide the first analysis and benchmark of this heterogeneity. We deliver an actionable overview of the 11 most widely used state-of-the-art methods for comparing genomic sequences. We also inform readers about their advantages and downsides using thorough experimental evaluation and different real datasets from all major manufacturers (i.e., Illumina, ONT, and PacBio). SequenceLab is publicly available at https://github.com/CMU-SAFARI/SequenceLab.

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arXiv2025

MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation

Metagenomics, the study of genome sequences of diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological fields. Metagenomic analysis is crucial, for instance, in clinical applications such as infectious disease screening and the diagnosis and early detection of diseases such as cancer. A key task in metagenomics is to determine the species present in a sample and their relative abundances. Currently, the field is dominated by either alignment-based tools, which offer high accuracy but are computationally expensive, or alignment-free tools, which are fast but lack the needed accuracy for many applications. In response to this dichotomy, we introduce MetaTrinity, a tool based on heuristics, to achieve a fundamental improvement in accuracy-runtime tradeoff over existing methods. We benchmark MetaTrinity against two leading metagenomic classifiers, each representing different ends of the performance-accuracy spectrum. On one end, Kraken2, a tool optimized for performance, shows modest accuracy yet a rapid runtime. The other end of the spectrum is governed by Metalign, a tool optimized for accuracy. Our evaluations show that MetaTrinity achieves an accuracy comparable to Metalign while gaining a 4x speedup without any loss in accuracy. This directly equates to a fourfold improvement in runtime-accuracy tradeoff. Compared to Kraken2, MetaTrinity requires a 5x longer runtime yet delivers a 17x improvement in accuracy. This demonstrates a 3.4x enhancement in the accuracy-runtime tradeoff for MetaTrinity. This dual comparison positions MetaTrinity as a broadly applicable solution for metagenomic classification, combining advantages of both ends of the spectrum: speed and accuracy. MetaTrinity is publicly available at https://github.com/CMU-SAFARI/MetaTrinity.

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arXiv2025

pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables

Data movement between the main memory and the processor is a key contributor to execution time and energy consumption in memory-intensive applications. This data movement bottleneck can be alleviated using Processing-in-Memory (PiM). One category of PiM is Processing-using-Memory (PuM), in which computation takes place inside the memory array by exploiting intrinsic analog properties of the memory device. PuM yields high performance and energy efficiency, but existing PuM techniques support a limited range of operations. As a result, current PuM architectures cannot efficiently perform some complex operations (e.g., multiplication, division, exponentiation) without large increases in chip area and design complexity. To overcome these limitations of existing PuM architectures, we introduce pLUTo (processing-using-memory with lookup table (LUT) operations), a DRAM-based PuM architecture that leverages the high storage density of DRAM to enable the massively parallel storing and querying of lookup tables (LUTs). The key idea of pLUTo is to replace complex operations with low-cost, bulk memory reads (i.e., LUT queries) instead of relying on complex extra logic. We evaluate pLUTo across 11 real-world workloads that showcase the limitations of prior PuM approaches and show that our solution outperforms optimized CPU and GPU baselines by an average of 713$\times$ and 1.2$\times$, respectively, while simultaneously reducing energy consumption by an average of 1855$\times$ and 39.5$\times$. Across these workloads, pLUTo outperforms state-of-the-art PiM architectures by an average of 18.3$\times$. We also show that different versions of pLUTo provide different levels of flexibility and performance at different additional DRAM area overheads (between 10.2% and 23.1%). pLUTo's source code is openly and fully available at https://github.com/CMU-SAFARI/pLUTo.

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arXiv2024

Memory-Centric Computing: Recent Advances in Processing-in-DRAM

Memory-centric computing aims to enable computation capability in and near all places where data is generated and stored. As such, it can greatly reduce the large negative performance and energy impact of data access and data movement, by 1) fundamentally avoiding data movement, 2) reducing data access latency & energy, and 3) exploiting large parallelism of memory arrays. Many recent studies show that memory-centric computing can largely improve system performance & energy efficiency. Major industrial vendors and startup companies have recently introduced memory chips with sophisticated computation capabilities. Going forward, both hardware and software stack should be revisited and designed carefully to take advantage of memory-centric computing. This work describes several major recent advances in memory-centric computing, specifically in Processing-in-DRAM, a paradigm where the operational characteristics of a DRAM chip are exploited and enhanced to perform computation on data stored in DRAM. Specifically, we describe 1) new techniques that slightly modify DRAM chips to enable both enhanced computation capability and easier programmability, 2) new experimental studies that demonstrate the functionally-complete bulk-bitwise computational capability of real commercial off-the-shelf DRAM chips, without any modifications to the DRAM chip or the interface, and 3) new DRAM designs that improve access granularity & efficiency, unleashing the true potential of Processing-in-DRAM.

cs.AR↗

arXiv2024

Hardware Acceleration for Knowledge Graph Processing: Challenges & Recent Developments

Knowledge graphs (KGs) have achieved significant attention in recent years, particularly in the area of the Semantic Web as well as gaining popularity in other application domains such as data mining and search engines. Simultaneously, there has been enormous progress in the development of different types of heterogeneous hardware, impacting the way KGs are processed. The aim of this paper is to provide a systematic literature review of knowledge graph hardware acceleration. For this, we present a classification of the primary areas in knowledge graph technology that harnesses different hardware units for accelerating certain knowledge graph functionalities. We then extensively describe respective works, focusing on how KG related schemes harness modern hardware accelerators. Based on our review, we identify various research gaps and future exploratory directions that are anticipated to be of significant value both for academics and industry practitioners.

cs.IR↗

arXiv2024

RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment

Nanopore sequencers generate raw electrical signals representing the contents of a biological sequence molecule passing through the nanopore. These signals can be analyzed directly, avoiding basecalling entirely. We observe that while existing proposals for raw signal analysis typically do well in all metrics for small genomes (e.g., viral genomes), they all perform poorly for large genomes (e.g., the human genome). Our goal is to analyze raw nanopore signals in an accurate, fast, and scalable manner. To this end, we propose RawAlign, the first work to integrate fine-grained signal alignment into the state-of-the-art raw signal mapper. To enable accurate, fast, and scalable mapping with alignment, RawAlign implements three algorithmic improvements and hardware acceleration via a vectorized implementation of fine-grained alignment. Together, these significantly reduce the overhead of typically computationally expensive fine-grained alignment. Our extensive evaluations on different use cases and various datasets show RawAlign provides 1) the most accurate mapping for large genomes and 2) and on-par performance compared to RawHash (between 0.80x-1.08x), while achieving better performance than UNCALLED and Sigmap by on average (geo. mean) 2.83x and 2.06x, respectively. Availability: https://github.com/CMU-SAFARI/RawAlign.

q-bio.GN↗

arXiv2024

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 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. Our thorough experimental evaluations show that TargetCall 1) improves the end-to-end basecalling runtime performance of the state-of-the-art basecaller by 3.31x while maintaining high (98.88%) recall in keeping on-target reads, 2) maintains high accuracy in downstream analysis, and 3) achieves better runtime performance, throughput, recall, precision, and generality compared to prior works. TargetCall is available at https://github.com/CMU-SAFARI/TargetCall.

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arXiv2024

BreakHammer: Enhancing RowHammer Mitigations by Carefully Throttling Suspect Threads

RowHammer is a major read disturbance mechanism in DRAM where repeatedly accessing (hammering) a row of DRAM cells (DRAM row) induces bitflips in other physically nearby DRAM rows. RowHammer solutions perform preventive actions (e.g., refresh neighbor rows of the hammered row) that mitigate such bitflips to preserve memory isolation, a fundamental building block of security and privacy in modern computing systems. However, preventive actions induce non-negligible memory request latency and system performance overheads as they interfere with memory requests. As shrinking technology node size over DRAM chip generations exacerbates RowHammer, the overheads of RowHammer solutions become prohibitively expensive. As a result, a malicious program can effectively hog the memory system and deny service to benign applications by causing many RowHammer-preventive actions. In this work, we tackle the performance overheads of RowHammer solutions by tracking and throttling the generators of memory accesses that trigger RowHammer solutions. To this end, we propose BreakHammer. BreakHammer 1) observes the time-consuming RowHammer-preventive actions of existing RowHammer mitigation mechanisms, 2) identifies hardware threads that trigger many of these actions, and 3) reduces the memory bandwidth usage of each identified thread. As such, BreakHammer significantly reduces the number of RowHammer-preventive actions performed, thereby improving 1) system performance and DRAM energy, and 2) reducing the maximum slowdown induced on a benign application, with near-zero area overhead. Our extensive evaluations demonstrate that BreakHammer effectively reduces the negative performance, energy, and fairness effects of eight RowHammer mitigation mechanisms. To foster further research we open-source our BreakHammer implementation and scripts at https://github.com/CMU-SAFARI/BreakHammer.

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arXiv2024

PIM-Opt: Demystifying Distributed Optimization Algorithms on a Real-World Processing-In-Memory System

Modern Machine Learning (ML) training on large-scale datasets is a very time-consuming workload. It relies on the optimization algorithm Stochastic Gradient Descent (SGD) due to its effectiveness, simplicity, and generalization performance. Processor-centric architectures (e.g., CPUs, GPUs) commonly used for modern ML training workloads based on SGD are bottlenecked by data movement between the processor and memory units due to the poor data locality in accessing large datasets. As a result, processor-centric architectures suffer from low performance and high energy consumption while executing ML training workloads. 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 of popular distributed SGD algorithms on real-world PIM systems to accelerate data-intensive ML training workloads. To this end, we 1) implement several representative centralized parallel SGD algorithms on the real-world UPMEM 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 highlight the need for a shift to an algorithm-hardware codesign. Our results demonstrate three major findings: 1) The UPMEM PIM system can be a viable alternative to state-of-the-art CPUs and GPUs for many memory-bound ML training workloads, especially when operations and datatypes are natively supported by PIM hardware, 2) it is important to carefully choose the optimization algorithms that best fit PIM, and 3) the UPMEM PIM system does not scale approximately linearly with the number of nodes for many data-intensive ML training workloads. We open source all our code to facilitate future research.

cs.AR↗

arXiv2024

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes

AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another similar reference. Users can then quickly run a downstream analysis of read sets for each latest reference release. Compared to the state-of-the-art method for remapping reads (i.e., full mapping), AirLift reduces the overall execution time to remap read sets between two reference genome versions by up to 27.4x. We validate our remapping results with GATK and find that AirLift provides high accuracy in identifying ground truth SNP/INDEL variants AirLift source code and readme describing how to reproduce our results are available at https://github.com/CMU-SAFARI/AirLift.

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arXiv2024

RowPress Vulnerability in Modern DRAM Chips

Memory isolation is a critical property for system reliability, security, and safety. We demonstrate RowPress, a DRAM read disturbance phenomenon different from the well-known RowHammer. RowPress induces bitflips by keeping a DRAM row open for a long period of time instead of repeatedly opening and closing the row. We experimentally characterize RowPress bitflips, showing their widespread existence in commodity off-the-shelf DDR4 DRAM chips. We demonstrate RowPress bitflips in a real system that already has RowHammer protection, and propose effective mitigation techniques that protect DRAM against both RowHammer and RowPress.

cs.AR↗

arXiv2024

RawHash2: Mapping Raw Nanopore Signals Using Hash-Based Seeding and Adaptive Quantization

Summary: Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis. Real-time analysis of raw signals is essential to utilize the unique features that nanopore sequencing provides, enabling the early stopping of the sequencing of a read or the entire sequencing run based on the analysis. The state-of-the-art mechanism, RawHash, offers the first hash-based efficient and accurate similarity identification between raw signals and a reference genome by quickly matching their hash values. In this work, we introduce RawHash2, which provides major improvements over RawHash, including a more sensitive quantization and chaining implementation, weighted mapping decisions, frequency filters to reduce ambiguous seed hits, minimizers for hash-based sketching, and support for the R10.4 flow cell version and various data formats such as POD5 and SLOW5. Compared to RawHash, RawHash2 provides better F1 accuracy (on average by 10.57% and up to 20.25%) and better throughput (on average by 4.0x and up to 9.9x) than RawHash. Availability and Implementation: RawHash2 is available at https://github.com/CMU-SAFARI/RawHash. We also provide the scripts to fully reproduce our results on our GitHub page.

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arXiv2024

Understanding the Security Benefits and Overheads of Emerging Industry Solutions to DRAM Read Disturbance

We present the first rigorous security, performance, energy, and cost analyses of the state-of-the-art on-DRAM-die read disturbance mitigation method, Per Row Activation Counting (PRAC), described in JEDEC DDR5 specification's April 2024 update. Unlike prior state-of-the-art that advises the memory controller to periodically issue refresh management (RFM) commands, which provides the DRAM chip with time to perform refreshes, PRAC introduces a new back-off signal. PRAC's back-off signal propagates from the DRAM chip to the memory controller and forces the memory controller to 1) stop serving requests and 2) issue RFM commands. As a result, RFM commands are issued when needed as opposed to periodically, reducing RFM's overheads. We analyze PRAC in four steps. First, we define an adversarial access pattern that represents the worst-case for PRAC's security. Second, we investigate PRAC's configurations and security implications. Our analyses show that PRAC can be configured for secure operation as long as no bitflip occurs before accessing a memory location 10 times. Third, we evaluate the performance impact of PRAC and compare it against prior works using Ramulator 2.0. Our analysis shows that while PRAC incurs less than 13% performance overhead for today's DRAM chips, its performance overheads can reach up to 94% for future DRAM chips that are more vulnerable to read disturbance bitflips. Fourth, we define an availability adversarial access pattern that exacerbates PRAC's performance overhead to perform a memory performance attack, demonstrating that such an adversarial pattern can hog up to 94% of DRAM throughput and degrade system throughput by up to 95%. We discuss PRAC's implications on future systems and foreshadow future research directions. To aid future research, we open-source our implementations and scripts at https://github.com/CMU-SAFARI/ramulator2.

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arXiv2024

Accelerating Time Series Analysis via Processing using Non-Volatile Memories

Time Series Analysis (TSA) is a critical workload to extract valuable information from collections of sequential data, e.g., detecting anomalies in electrocardiograms. Subsequence Dynamic Time Warping (sDTW) is the state-of-the-art algorithm for high-accuracy TSA. We find that the performance and energy efficiency of sDTW on conventional CPU and GPU platforms are heavily burdened by the latency and energy overheads of data movement between the compute and the memory units. sDTW exhibits low arithmetic intensity and low data reuse on conventional platforms, stemming from poor amortization of the data movement overheads. To improve the performance and energy efficiency of the sDTW algorithm, we propose MATSA, the first Magnetoresistive RAM (MRAM)-based Accelerator for TSA. MATSA leverages Processing-Using-Memory (PUM) based on MRAM crossbars to minimize data movement overheads and exploit parallelism in sDTW. MATSA improves performance by 7.35x/6.15x/6.31x and energy efficiency by 11.29x/4.21x/2.65x over server-class CPU, GPU, and Processing-Near-Memory platforms, respectively.

cs.AR↗

arXiv2024

Genome-on-Diet: Taming Large-Scale Genomic Analyses via Sparsified Genomics

Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the exponential growth of genomic sequencing data. We introduce the concept of sparsified genomics where we systematically exclude a large number of bases from genomic sequences and enable much faster and more memory-efficient processing of the sparsified, shorter genomic sequences, while providing similar or even higher accuracy compared to processing non-sparsified sequences. Sparsified genomics provides significant benefits to many genomic analyses and has broad applicability. We show that sparsifying genomic sequences greatly accelerates the state-of-the-art read mapper (minimap2) by 2.57-5.38x, 1.13-2.78x, and 3.52-6.28x using real Illumina, HiFi, and ONT reads, respectively, while providing up to 2.1x smaller memory footprint, 2x smaller index size, and more truly detected small and structural variations compared to minimap2. Sparsifying genomic sequences makes containment search through very large genomes and large databases 72.7-75.88x faster and 723.3x more storage-efficient than searching through non-sparsified genomic sequences (with CMash and KMC3). Sparsifying genomic sequences enables robust microbiome discovery by providing 54.15-61.88x faster and 720x more storage-efficient taxonomic profiling of metagenomic samples over the state-of-the-art tool (Metalign). We design and open-source a framework called Genome-on-Diet as an example tool for sparsified genomics, which can be freely downloaded from https://github.com/CMU-SAFARI/Genome-on-Diet.

cs.DS↗

arXiv2024

Roadmap to Neuromorphic Computing with Emerging Technologies

The roadmap is organized into several thematic sections, outlining current computing challenges, discussing the neuromorphic computing approach, analyzing mature and currently utilized technologies, providing an overview of emerging technologies, addressing material challenges, exploring novel computing concepts, and finally examining the maturity level of emerging technologies while determining the next essential steps for their advancement.

eess.SP↗

arXiv2024

MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing

Metagenomics has led to significant advances in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large metagenomic databases. Metagenomic analysis suffers from significant data movement overhead due to moving large amounts of low-reuse data from the storage system. In-storage processing can be a fundamental solution for reducing this overhead. However, designing an in-storage processing system for metagenomics is challenging because existing approaches to metagenomic analysis cannot be directly implemented in storage effectively due to the hardware limitations of modern SSDs. We propose MegIS, the first in-storage processing system designed to significantly reduce the data movement overhead of the end-to-end metagenomic analysis pipeline. MegIS is enabled by our lightweight design that effectively leverages and orchestrates processing inside and outside the storage system. We address in-storage processing challenges for metagenomics via specialized and efficient 1) task partitioning, 2) data/computation flow coordination, 3) storage technology-aware algorithmic optimizations, 4) data mapping, and 5) lightweight in-storage accelerators. MegIS's design is flexible, capable of supporting different types of metagenomic input datasets, and can be integrated into various metagenomic analysis pipelines. Our evaluation shows that MegIS outperforms the state-of-the-art performance- and accuracy-optimized software metagenomic tools by 2.7$\times$-37.2$\times$ and 6.9$\times$-100.2$\times$, respectively, while matching the accuracy of the accuracy-optimized tool. MegIS achieves 1.5$\times$-5.1$\times$ speedup compared to the state-of-the-art metagenomic hardware-accelerated (using processing-in-memory) tool, while achieving significantly higher accuracy.

cs.AR↗

arXiv2024

Constable: Improving Performance and Power Efficiency by Safely Eliminating Load Instruction Execution

Load instructions often limit instruction-level parallelism (ILP) in modern processors due to data and resource dependences they cause. Prior techniques like Load Value Prediction (LVP) and Memory Renaming (MRN) mitigate load data dependence by predicting the data value of a load instruction. However, they fail to mitigate load resource dependence as the predicted load instruction gets executed nonetheless. Our goal in this work is to improve ILP by mitigating both load data dependence and resource dependence. To this end, we propose a purely-microarchitectural technique called Constable, that safely eliminates the execution of load instructions. Constable dynamically identifies load instructions that have repeatedly fetched the same data from the same load address. We call such loads likely-stable. For every likely-stable load, Constable (1) tracks modifications to its source architectural registers and memory location via lightweight hardware structures, and (2) eliminates the execution of subsequent instances of the load instruction until there is a write to its source register or a store or snoop request to its load address. Our extensive evaluation using a wide variety of 90 workloads shows that Constable improves performance by 5.1% while reducing the core dynamic power consumption by 3.4% on average over a strong baseline system that implements MRN and other dynamic instruction optimizations (e.g., move and zero elimination, constant and branch folding). In presence of 2-way simultaneous multithreading (SMT), Constable's performance improvement increases to 8.8% over the baseline system. When combined with a state-of-the-art load value predictor (EVES), Constable provides an additional 3.7% and 7.8% average performance benefit over the load value predictor alone, in the baseline system without and with 2-way SMT, respectively.

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