arXiv subjects

Onur Mutlu

Publications and source records attributed to Onur Mutlu.

At least 109 records · Page 6Linked to original sources

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.

cs.AR↗

arXiv2024

An Experimental Characterization of Combined RowHammer and RowPress Read Disturbance in Modern DRAM Chips

DRAM read disturbance can break memory isolation, a fundamental property to ensure system robustness (i.e., reliability, security, safety). RowHammer and RowPress are two different DRAM read disturbance phenomena. RowHammer induces bitflips in physically adjacent victim DRAM rows by repeatedly opening and closing an aggressor DRAM row, while RowPress induces bitflips by keeping an aggressor DRAM row open for a long period of time. In this study, we characterize a DRAM access pattern that combines RowHammer and RowPress in 84 real DDR4 DRAM chips from all three major DRAM manufacturers. Our key results show that 1) this combined RowHammer and RowPress pattern takes significantly smaller amount of time (up to 46.1% faster) to induce the first bitflip compared to the state-of-the-art RowPress pattern, and 2) at the minimum aggressor row activation count to induce at least one bitflip, the bits that flip are different across RowHammer, RowPress, and the combined patterns. Based on our results, we provide a key hypothesis that the read disturbance effect caused by RowPress from one of the two aggressor rows in a double-sided pattern is much more significant than the other.

cs.AR↗

arXiv2024

Sectored DRAM: A Practical Energy-Efficient and High-Performance Fine-Grained DRAM Architecture

We propose Sectored DRAM, a new, low-overhead DRAM substrate that reduces wasted energy by enabling fine-grained DRAM data transfers and DRAM row activation. Sectored DRAM leverages two key ideas to enable fine-grained data transfers and row activation at low chip area cost. First, a cache block transfer between main memory and the memory controller happens in a fixed number of clock cycles where only a small portion of the cache block (a word) is transferred in each cycle. Sectored DRAM augments the memory controller and the DRAM chip to execute cache block transfers in a variable number of clock cycles based on the workload access pattern with minor modifications to the memory controller's and the DRAM chip's circuitry. Second, a large DRAM row, by design, is already partitioned into smaller independent physically isolated regions. Sectored DRAM provides the memory controller with the ability to activate each such region based on the workload access pattern via small modifications to the DRAM chip's array access circuitry. Activating smaller regions of a large row relaxes DRAM power delivery constraints and allows the memory controller to schedule DRAM accesses faster. Compared to a system with coarse-grained DRAM, Sectored DRAM reduces the DRAM energy consumption of highly-memory-intensive workloads by up to (on average) 33% (20%) while improving their performance by up to (on average) 36% (17%). Sectored DRAM's DRAM energy savings, combined with its system performance improvement, allows system-wide energy savings of up to 23%. Sectored DRAM's DRAM chip area overhead is 1.7% the area of a modern DDR4 chip. We hope and believe that Sectored DRAM's ideas and results will help to enable more efficient and high-performance memory systems. To this end, we open source Sectored DRAM at https://github.com/CMU-SAFARI/Sectored-DRAM.

cs.AR↗

arXiv2024

SpyHammer: Understanding and Exploiting RowHammer under Fine-Grained Temperature Variations

RowHammer is a DRAM vulnerability that can cause bit errors in a victim DRAM row solely by accessing its neighboring DRAM rows at a high-enough rate. Recent studies demonstrate that new DRAM devices are becoming increasingly vulnerable to RowHammer, and many works demonstrate system-level attacks for privilege escalation or information leakage. In this work, we perform the first rigorous fine-grained characterization and analysis of the correlation between RowHammer and temperature. We show that RowHammer is very sensitive to temperature variations, even if the variations are very small (e.g., $\pm 1$ °C). We leverage two key observations from our analysis to spy on DRAM temperature: 1) RowHammer-induced bit error rate consistently increases (or decreases) as the temperature increases, and 2) some DRAM cells that are vulnerable to RowHammer exhibit bit errors only at a particular temperature. Based on these observations, we propose a new RowHammer attack, called SpyHammer, that spies on the temperature of DRAM on critical systems such as industrial production lines, vehicles, and medical systems. SpyHammer is the first practical attack that can spy on DRAM temperature. Our evaluation in a controlled environment shows that SpyHammer can infer the temperature of the victim DRAM modules with an error of less than $\pm 2.5$ °C at the 90th percentile of all tested temperatures, for 12 real DRAM modules (120 DRAM chips) from four main manufacturers.

cs.CR↗

arXiv2024

Simultaneous Many-Row Activation in Off-the-Shelf DRAM Chips: Experimental Characterization and Analysis

We experimentally analyze the computational capability of commercial off-the-shelf (COTS) DRAM chips and the robustness of these capabilities under various timing delays between DRAM commands, data patterns, temperature, and voltage levels. We extensively characterize 120 COTS DDR4 chips from two major manufacturers. We highlight four key results of our study. First, COTS DRAM chips are capable of 1) simultaneously activating up to 32 rows (i.e., simultaneous many-row activation), 2) executing a majority of X (MAJX) operation where X>3 (i.e., MAJ5, MAJ7, and MAJ9 operations), and 3) copying a DRAM row (concurrently) to up to 31 other DRAM rows, which we call Multi-RowCopy. Second, storing multiple copies of MAJX's input operands on all simultaneously activated rows drastically increases the success rate (i.e., the percentage of DRAM cells that correctly perform the computation) of the MAJX operation. For example, MAJ3 with 32-row activation (i.e., replicating each MAJ3's input operands 10 times) has a 30.81% higher average success rate than MAJ3 with 4-row activation (i.e., no replication). Third, data pattern affects the success rate of MAJX and Multi-RowCopy operations by 11.52% and 0.07% on average. Fourth, simultaneous many-row activation, MAJX, and Multi-RowCopy operations are highly resilient to temperature and voltage changes, with small success rate variations of at most 2.13% among all tested operations. We believe these empirical results demonstrate the promising potential of using DRAM as a computation substrate. To aid future research and development, we open-source our infrastructure at https://github.com/CMU-SAFARI/SiMRA-DRAM.

cs.AR↗

arXiv2024

SwiftRL: Towards Efficient Reinforcement Learning on Real Processing-In-Memory Systems

Reinforcement Learning (RL) trains agents to learn optimal behavior by maximizing reward signals from experience datasets. However, RL training often faces memory limitations, leading to execution latencies and prolonged training times. To overcome this, SwiftRL explores Processing-In-Memory (PIM) architectures to accelerate RL workloads. We achieve near-linear performance scaling by implementing RL algorithms like Tabular Q-learning and SARSA on UPMEM PIM systems and optimizing for hardware. Our experiments on OpenAI GYM environments using UPMEM hardware demonstrate superior performance compared to CPU and GPU implementations.

cs.LG↗

arXiv2024

ABACuS: All-Bank Activation Counters for Scalable and Low Overhead RowHammer Mitigation

We introduce ABACuS, a new low-cost hardware-counter-based RowHammer mitigation technique that performance-, energy-, and area-efficiently scales with worsening RowHammer vulnerability. We observe that both benign workloads and RowHammer attacks tend to access DRAM rows with the same row address in multiple DRAM banks at around the same time. Based on this observation, ABACuS's key idea is to use a single shared row activation counter to track activations to the rows with the same row address in all DRAM banks. Unlike state-of-the-art RowHammer mitigation mechanisms that implement a separate row activation counter for each DRAM bank, ABACuS implements fewer counters (e.g., only one) to track an equal number of aggressor rows. Our evaluations show that ABACuS securely prevents RowHammer bitflips at low performance/energy overhead and low area cost. We compare ABACuS to four state-of-the-art mitigation mechanisms. At a near-future RowHammer threshold of 1000, ABACuS incurs only 0.58% (0.77%) performance and 1.66% (2.12%) DRAM energy overheads, averaged across 62 single-core (8-core) workloads, requiring only 9.47 KiB of storage per DRAM rank. At the RowHammer threshold of 1000, the best prior low-area-cost mitigation mechanism incurs 1.80% higher average performance overhead than ABACuS, while ABACuS requires 2.50X smaller chip area to implement. At a future RowHammer threshold of 125, ABACuS performs very similarly to (within 0.38% of the performance of) the best prior performance- and energy-efficient RowHammer mitigation mechanism while requiring 22.72X smaller chip area. ABACuS is freely and openly available at https://github.com/CMU-SAFARI/ABACuS.

cs.CR↗

arXiv2024

Read Disturbance in High Bandwidth Memory: A Detailed Experimental Study on HBM2 DRAM Chips

We experimentally demonstrate the effects of read disturbance (RowHammer and RowPress) and uncover the inner workings of undocumented read disturbance defense mechanisms in High Bandwidth Memory (HBM). Detailed characterization of six real HBM2 DRAM chips in two different FPGA boards shows that (1) the read disturbance vulnerability significantly varies between different HBM2 chips and between different components (e.g., 3D-stacked channels) inside a chip, (2) DRAM rows at the end and in the middle of a bank are more resilient to read disturbance, (3) fewer additional activations are sufficient to induce more read disturbance bitflips in a DRAM row if the row exhibits the first bitflip at a relatively high activation count, (4) a modern HBM2 chip implements undocumented read disturbance defenses that track potential aggressor rows based on how many times they are activated. We describe how our findings could be leveraged to develop more powerful read disturbance attacks and more efficient defense mechanisms. We open source all our code and data to facilitate future research at https://github.com/CMU-SAFARI/HBM-Read-Disturbance.

cs.CR↗

arXiv2024

Functionally-Complete Boolean Logic in Real DRAM Chips: Experimental Characterization and Analysis

Processing-using-DRAM (PuD) is an emerging paradigm that leverages the analog operational properties of DRAM circuitry to enable massively parallel in-DRAM computation. PuD has the potential to reduce or eliminate costly data movement between processing elements and main memory. Prior works experimentally demonstrate three-input MAJ (MAJ3) and two-input AND and OR operations in commercial off-the-shelf (COTS) DRAM chips. Yet, demonstrations on COTS DRAM chips do not provide a functionally complete set of operations. We experimentally demonstrate that COTS DRAM chips are capable of performing 1) functionally-complete Boolean operations: NOT, NAND, and NOR and 2) many-input (i.e., more than two-input) AND and OR operations. We present an extensive characterization of new bulk bitwise operations in 256 off-the-shelf modern DDR4 DRAM chips. We evaluate the reliability of these operations using a metric called success rate: the fraction of correctly performed bitwise operations. Among our 19 new observations, we highlight four major results. First, we can perform the NOT operation on COTS DRAM chips with a 98.37% success rate on average. Second, we can perform up to 16-input NAND, NOR, AND, and OR operations on COTS DRAM chips with high reliability (e.g., 16-input NAND, NOR, AND, and OR with an average success rate of 94.94%, 95.87%, 94.94%, and 95.85%, respectively). Third, data pattern only slightly affects bitwise operations. Our results show that executing NAND, NOR, AND, and OR operations with random data patterns decreases the success rate compared to all logic-1/logic-0 patterns by 1.39%, 1.97%, 1.43%, and 1.98%, respectively. Fourth, bitwise operations are highly resilient to temperature changes, with small success rate fluctuations of at most 1.66% when the temperature is increased from 50C to 95C. We open-source our infrastructure at https://github.com/CMU-SAFARI/FCDRAM

cs.AR↗

arXiv2024

AERO: Adaptive Erase Operation for Improving Lifetime and Performance of Modern NAND Flash-Based SSDs

This work investigates a new erase scheme in NAND flash memory to improve the lifetime and performance of modern solid-state drives (SSDs). In NAND flash memory, an erase operation applies a high voltage (e.g., > 20 V) to flash cells for a long time (e.g., > 3.5 ms), which degrades cell endurance and potentially delays user I/O requests. While a large body of prior work has proposed various techniques to mitigate the negative impact of erase operations, no work has yet investigated how erase latency should be set to fully exploit the potential of NAND flash memory; most existing techniques use a fixed latency for every erase operation which is set to cover the worst-case operating conditions. To address this, we propose AERO (Adaptive ERase Operation), a new erase scheme that dynamically adjusts erase latency to be just long enough for reliably erasing target cells, depending on the cells' current erase characteristics. AERO accurately predicts such near-optimal erase latency based on the number of fail bits during an erase operation. To maximize its benefits, we further optimize AERO in two aspects. First, at the beginning of an erase operation, AERO attempts to erase the cells for a short time (e.g., 1 ms), which enables AERO to always obtain the number of fail bits necessary to accurately predict the near-optimal erase latency. Second, AERO aggressively yet safely reduces erase latency by leveraging a large reliability margin present in modern SSDs. We demonstrate the feasibility and reliability of AERO using 160 real 3D NAND flash chips, showing that it enhances SSD lifetime over the conventional erase scheme by 43% without change to existing NAND flash chips. Our system-level evaluation using eleven real-world workloads shows that an AERO-enabled SSD reduces read tail latency by 34% on average over a state-of-the-art technique.

cs.AR↗

arXiv2024

RowPress: Amplifying Read Disturbance in Modern DRAM Chips

Memory isolation is critical for system reliability, security, and safety. Unfortunately, read disturbance can break memory isolation in modern DRAM chips. For example, RowHammer is a well-studied read-disturb phenomenon where repeatedly opening and closing (i.e., hammering) a DRAM row many times causes bitflips in physically nearby rows. This paper experimentally demonstrates and analyzes another widespread read-disturb phenomenon, RowPress, in real DDR4 DRAM chips. RowPress breaks memory isolation by keeping a DRAM row open for a long period of time, which disturbs physically nearby rows enough to cause bitflips. We show that RowPress amplifies DRAM's vulnerability to read-disturb attacks by significantly reducing the number of row activations needed to induce a bitflip by one to two orders of magnitude under realistic conditions. In extreme cases, RowPress induces bitflips in a DRAM row when an adjacent row is activated only once. Our detailed characterization of 164 real DDR4 DRAM chips shows that RowPress 1) affects chips from all three major DRAM manufacturers, 2) gets worse as DRAM technology scales down to smaller node sizes, and 3) affects a different set of DRAM cells from RowHammer and behaves differently from RowHammer as temperature and access pattern changes. We demonstrate in a real DDR4-based system with RowHammer protection that 1) a user-level program induces bitflips by leveraging RowPress while conventional RowHammer cannot do so, and 2) a memory controller that adaptively keeps the DRAM row open for a longer period of time based on access pattern can facilitate RowPress-based attacks. To prevent bitflips due to RowPress, we describe and evaluate a new methodology that adapts existing RowHammer mitigation techniques to also mitigate RowPress with low additional performance overhead. We open source all our code and data to facilitate future research on RowPress.

cs.CR↗

arXiv2024

PULSAR: Simultaneous Many-Row Activation for Reliable and High-Performance Computing in Off-the-Shelf DRAM Chips

Data movement between the processor and the main memory is a first-order obstacle against improving performance and energy efficiency in modern systems. To address this obstacle, Processing-using-Memory (PuM) is a promising approach where bulk-bitwise operations are performed leveraging intrinsic analog properties within the DRAM array and massive parallelism across DRAM columns. Unfortunately, 1) modern off-the-shelf DRAM chips do not officially support PuM operations, and 2) existing techniques of performing PuM operations on off-the-shelf DRAM chips suffer from two key limitations. First, these techniques have low success rates, i.e., only a small fraction of DRAM columns can correctly execute PuM operations because they operate beyond manufacturer-recommended timing constraints, causing these operations to be highly susceptible to noise and process variation. Second, these techniques have limited compute primitives, preventing them from fully leveraging parallelism across DRAM columns and thus hindering their performance benefits. We propose PULSAR, a new technique to enable high-success-rate and high-performance PuM operations in off-the-shelf DRAM chips. PULSAR leverages our new observation that a carefully crafted sequence of DRAM commands simultaneously activates up to 32 DRAM rows. PULSAR overcomes the limitations of existing techniques by 1) replicating the input data to improve the success rate and 2) enabling new bulk bitwise operations (e.g., many-input majority, Multi-RowInit, and Bulk-Write) to improve the performance. Our analysis on 120 off-the-shelf DDR4 chips from two major manufacturers shows that PULSAR achieves a 24.18% higher success rate and 121% higher performance over seven arithmetic-logic operations compared to FracDRAM, a state-of-the-art off-the-shelf DRAM-based PuM technique.

cs.AR↗

arXiv2024

PUMA: Efficient and Low-Cost Memory Allocation and Alignment Support for Processing-Using-Memory Architectures

Processing-using-DRAM (PUD) architectures impose a restrictive data layout and alignment for their operands, where source and destination operands (i) must reside in the same DRAM subarray (i.e., a group of DRAM rows sharing the same row buffer and row decoder) and (ii) are aligned to the boundaries of a DRAM row. However, standard memory allocation routines (i.e., malloc, posix_memalign, and huge pages-based memory allocation) fail to meet the data layout and alignment requirements for PUD architectures to operate successfully. To allow the memory allocation API to influence the OS memory allocator and ensure that memory objects are placed within specific DRAM subarrays, we propose a new lazy data allocation routine (in the kernel) for PUD memory objects called PUMA. The key idea of PUMA is to use the internal DRAM mapping information together with huge pages and then split huge pages into finer-grained allocation units that are (i) aligned to the page address and size and (ii) virtually contiguous. We implement PUMA as a kernel module using QEMU and emulate a RISC-V machine running Fedora 33 with v5.9.0 Linux Kernel. We emulate the implementation of a PUD system capable of executing row copy operations (as in RowClone) and Boolean AND/OR/NOT operations (as in Ambit). In our experiments, such an operation is performed in the host CPU if a given operation cannot be executed in our PUD substrate (due to data misalignment). PUMA significantly outperforms the baseline memory allocators for all evaluated microbenchmarks and allocation sizes.

cs.AR↗

arXiv2024

MIMDRAM: An End-to-End Processing-Using-DRAM System for High-Throughput, Energy-Efficient and Programmer-Transparent Multiple-Instruction Multiple-Data Processing

Processing-using-DRAM (PUD) is a processing-in-memory (PIM) approach that uses a DRAM array's massive internal parallelism to execute very-wide data-parallel operations, in a single-instruction multiple-data (SIMD) fashion. However, DRAM rows' large and rigid granularity limit the effectiveness and applicability of PUD in three ways. First, since applications have varying degrees of SIMD parallelism, PUD execution often leads to underutilization, throughput loss, and energy waste. Second, most PUD architectures are limited to the execution of parallel map operations. Third, the need to feed the wide DRAM row with tens of thousands of data elements combined with the lack of adequate compiler support for PUD systems create a programmability barrier. Our goal is to design a flexible PUD system that overcomes the limitations caused by the large and rigid granularity of PUD. To this end, we propose MIMDRAM, a hardware/software co-designed PUD system that introduces new mechanisms to allocate and control only the necessary resources for a given PUD operation. The key idea of MIMDRAM is to leverage fine-grained DRAM (i.e., the ability to independently access smaller segments of a large DRAM row) for PUD computation. MIMDRAM exploits this key idea to enable a multiple-instruction multiple-data (MIMD) execution model in each DRAM subarray. We evaluate MIMDRAM using twelve real-world applications and 495 multi-programmed application mixes. Our evaluation shows that MIMDRAM provides 34x the performance, 14.3x the energy efficiency, 1.7x the throughput, and 1.3x the fairness of a state-of-the-art PUD framework, along with 30.6x and 6.8x the energy efficiency of a high-end CPU and GPU, respectively. MIMDRAM adds small area cost to a DRAM chip (1.11%) and CPU die (0.6%).

cs.AR↗

arXiv2024

CoMeT: Count-Min-Sketch-based Row Tracking to Mitigate RowHammer at Low Cost

We propose a new RowHammer mitigation mechanism, CoMeT, that prevents RowHammer bitflips with low area, performance, and energy costs in DRAM-based systems at very low RowHammer thresholds. The key idea of CoMeT is to use low-cost and scalable hash-based counters to track DRAM row activations. CoMeT uses the Count-Min Sketch technique that maps each DRAM row to a group of counters, as uniquely as possible, using multiple hash functions. When a DRAM row is activated, CoMeT increments the counters mapped to that DRAM row. Because the mapping from DRAM rows to counters is not completely unique, activating one row can increment one or more counters mapped to another row. Thus, CoMeT may overestimate, but never underestimates, a DRAM row's activation count. This property of CoMeT allows it to securely prevent RowHammer bitflips while properly configuring its hash functions reduces overestimations. As a result, CoMeT 1) implements substantially fewer counters than the number of DRAM rows in a DRAM bank and 2) does not significantly overestimate a DRAM row's activation count. Our comprehensive evaluations show that CoMeT prevents RowHammer bitflips with an average performance overhead of only 4.01% across 61 benign single-core workloads for a very low RowHammer threshold of 125, normalized to a system with no RowHammer mitigation. CoMeT achieves a good trade-off between performance, energy, and area overheads. Compared to the best-performing state-of-the-art mitigation, CoMeT requires 74.2x less area overhead at the RowHammer threshold 125 and incurs a small performance overhead on average for all RowHammer thresholds. Compared to the best-performing low-area-cost mechanism, at a very low RowHammer threshold of 125, CoMeT improves performance by up to 39.1% while incurring a similar area overhead. CoMeT is openly and freely available at https://github.com/CMU-SAFARI/CoMeT.

cs.CR↗

arXiv2024

Spatial Variation-Aware Read Disturbance Defenses: Experimental Analysis of Real DRAM Chips and Implications on Future Solutions

Read disturbance in modern DRAM chips is a widespread phenomenon and is reliably used for breaking memory isolation, a fundamental building block for building robust systems. RowHammer and RowPress are two examples of read disturbance in DRAM where repeatedly accessing (hammering) or keeping active (pressing) a memory location induces bitflips in other memory locations. Unfortunately, shrinking technology node size exacerbates read disturbance in DRAM chips over generations. As a result, existing defense mechanisms suffer from significant performance and energy overheads, limited effectiveness, or prohibitively high hardware complexity. In this paper, we tackle these shortcomings by leveraging the spatial variation in read disturbance across different memory locations in real DRAM chips. To do so, we 1) present the first rigorous real DRAM chip characterization study of spatial variation of read disturbance and 2) propose Svärd, a new mechanism that dynamically adapts the aggressiveness of existing solutions based on the row-level read disturbance profile. Our experimental characterization on 144 real DDR4 DRAM chips representing 10 chip designs demonstrates a large variation in read disturbance vulnerability across different memory locations: in the part of memory with the worst read disturbance vulnerability, 1) up to 2x the number of bitflips can occur and 2) bitflips can occur at an order of magnitude fewer accesses, compared to the memory locations with the least vulnerability to read disturbance. Svärd leverages this variation to reduce the overheads of five state-of-the-art read disturbance solutions, and thus significantly increases system performance.

cs.CR↗

arXiv2024

GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping

At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the similarities and differences between two sequences is still computationally expensive since approximate string matching techniques traditionally inherit dynamic programming algorithms with quadratic time and space complexity. We introduce GateKeeper-GPU, a fast and accurate pre-alignment filter that efficiently reduces the need for expensive sequence alignment. GateKeeper-GPU provides two main contributions: first, improving the filtering accuracy of GateKeeper (a lightweight pre-alignment filter), and second, exploiting the massive parallelism provided by the large number of GPU threads of modern GPUs to examine numerous sequence pairs rapidly and concurrently. By reducing the work, GateKeeper-GPU provides an acceleration of 2.9x to sequence alignment and up to 1.4x speedup to the end-to-end execution time of a comprehensive read mapper (mrFAST). GateKeeper-GPU is available at https://github.com/BilkentCompGen/GateKeeper-GPU.

q-bio.GN↗