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 27.4×. We validate our remapping results with GATK and find that AirLift provides high accuracy in identifying ground truth SNP/INDEL variants.

Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequences. In pHMMs, sequences are represented as graph structures, where states and edges capture modifications (i.e., insertions, deletions, and substitutions) by assigning probabilities to them. These probabilities are subsequently used to compute the similarity score between a sequence and a pHMM graph. The Baum-Welch algorithm, a prevalent and highly accurate method, utilizes these probabilities to optimize and compute similarity scores. Accurate computation of these probabilities is essential for the correct identification of sequence similarities. However, the Baum-Welch algorithm is computationally intensive, and existing solutions offer either software-only or hardware-only approaches with fixed pHMM designs. When we analyze state-of-the-art works, we identify an urgent need for a flexible, high-performance, and energy-efficient hardware-software co-design to address the major inefficiencies in the Baum-Welch algorithm for pHMMs. We introduce ApHMM , the first flexible acceleration framework designed to significantly reduce both computational and energy overheads associated with the Baum-Welch algorithm for pHMMs. ApHMM employs hardware-software co-design to tackle the major inefficiencies in the Baum-Welch algorithm by (1) designing flexible hardware to accommodate various pHMM designs, (2) exploiting predictable data dependency patterns through on-chip memory with memoization techniques, (3) rapidly filtering out unnecessary computations using a hardware-based filter, and (4) minimizing redundant computations. ApHMM achieves substantial speedups of 15.55×–260.03×, 1.83×–5.34×, and 27.97× when compared to CPU, GPU, and FPGA implementations of the Baum-Welch algorithm, respectively. ApHMM outperforms state-of-the-art CPU implementations in three key bioinformatics applications: (1) error correction, (2) protein family search, and (3) multiple sequence alignment, by 1.29×–59.94×, 1.03×–1.75×, and 1.03×–1.95×, respectively, while improving their energy efficiency by 64.24×–115.46×, 1.75×, and 1.96×.

Read mapping is a fundamental step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome (called a reference genome). Read mapping is costly because it needs to perform approximate string matching (ASM) on large amounts of data. To address the computational challenges in genome analysis, many prior works propose various approaches such as accurate filters that select the reads within a dataset of genomic reads (called a read set) that must undergo expensive computation, efficient heuristics, and hardware acceleration. While effective at reducing the amount of expensive computation, all such approaches still require the costly movement of a large amount of data from storage to the rest of the system, which can significantly lower the end-to-end performance of read mapping in conventional and emerging genomics systems.

RowHammer is a circuit-level DRAM vulnerability, where repeatedly activating and precharging a DRAM row, and thus alternating the voltage of a row’s wordline between low and high voltage levels, can cause bit flips in physically nearby rows. Recent DRAM chips are more vulnerable to RowHammer: with technology node scaling, the minimum number of activate-precharge cycles to induce a RowHammer bit flip reduces and the RowHammer bit error rate increases. Therefore, it is critical to develop effective and scalable approaches to protect modern DRAM systems against RowHammer. To enable such solutions, it is essential to develop a deeper understanding of the RowHammer vulnerability of modern DRAM chips. However, even though the voltage toggling on a wordline is a key determinant of RowHammer vulnerability, no prior work experimentally demonstrates the effect of wordline voltage (VPP) on the RowHammer vulnerability. Our work closes this gap in understanding.This is the first work to experimentally demonstrate on 272 real DRAM chips that lowering VPPreduces a DRAM chip’s RowHammer vulnerability. We show that lowering VPP1) increases the number of activate-precharge cycles needed to induce a RowHammer bit flip by up to 85.8 % with an average of 7.4 % across all tested chips and 2) decreases the RowHammer bit error rate by up to 66.9 % with an average of 15.2 % across all tested chips. At the same time, reducing VPPmarginally worsens a DRAM cell’s access latency, charge restoration, and data retention time within the guardbands of system-level nominal timing parameters for 208 out of 272 tested chips. We conclude that reducing VPPis a promising strategy for reducing a DRAM chip’s RowHammer vulnerability without requiring modifications to DRAM chips.

Random number generation is an important task in a wide variety of critical applications including cryptographic algorithms, scientific simulations, and industrial testing tools. True Random Number Generators (TRNGs) produce cryptographically-secure truly random data by sampling a physical entropy source that typically requires custom hardware and suffers from long latency. To enable high-bandwidth and low-latency TRNGs on widely-available commodity devices, recent works propose hardware TRNGs that generate random numbers using commodity DRAM as an entropy source. Although prior works demonstrate promising TRNG mechanisms using DRAM, practical integration of such mechanisms into real systems poses various challenges.We identify three key challenges for using DRAM-based TRNGs in current systems: (1) generating random numbers with DRAM-based TRNGs can degrade overall system performance by slowing down concurrently-running applications due to the interference between RNG and regular memory operations in the memory controller (i.e., RNG interference), (2) this RNG interference can degrade system fairness by causing unfair prioritization of applications that intensively use random numbers (i.e., RNG applications), and (3) RNG applications can experience significant slowdown due to the high latency of DRAM-based TRNGs.To address these challenges, we propose DR-STRaNGe, an end-to-end system design for DRAM-based TRNGs that (1) reduces the RNG interference by separating RNG requests from regular memory requests in the memory controller, (2) improves fairness across applications with an RNG-aware memory request scheduler, and (3) hides the large TRNG latencies using a random number buffering mechanism combined with a new DRAM idleness predictor that accurately identifies idle DRAM periods.We evaluate DR-STRaNGe using a comprehensive set of 186 multi-programmed workloads. Compared to an RNG-oblivious baseline system, DR-STRaNGe improves the performance of non-RNG and RNG applications on average by 17.9% and 25.1%, respectively. DR-STRaNGe improves system fairness by 32.1% on average when generating random numbers at a 5 Gb/s throughput. DR-STRaNGe reduces energy consumption by 21% compared to the RNG-oblivious baseline design by reducing the time spent for RNG and non-RNG memory accesses by 15.8%.

To reduce the leakage power of inactive (dark) silicon components, modern processor systems shut-off these components' power supply using low-leakage transistors, called power-gates. Unfortunately, power-gates increase the system's power-delivery impedance and voltage guardband, limiting the system's maximum attainable voltage (i.e., Vmax) and, thus, the CPU core's maximum attainable frequency (i.e., Fmax). As a result, systems that are performance constrained by the CPU frequency (i.e., Fmax-constrained), such as high-end desktops, suffer significant performance loss due to power-gates.To mitigate this performance loss, we propose DarkGates, a hybrid system architecture that increases the performance of Fmax-constrained systems while fulfilling their power efficiency requirements. DarkGates is based on three key techniques: i) bypassing on-chip power-gates using package-level resources (called bypass mode), ii) extending power management firmware to support operation either in bypass mode or normal mode, and iii) introducing deeper idle power states.We implement DarkGates on an Intel Skylake microprocessor for client devices and evaluate it using a wide variety of workloads. On a real 4-core Skylake system with integrated graphics, DarkGates improves the average performance of SPEC CPU2006 workloads across all thermal design power (TDP) levels (35W–91W) between 4.2% and 5.3%. DarkGates maintains the performance of 3DMark workloads for desktop systems with TDP greater than 45W while for a 35W-TDP (the lowest TDP) desktop it experiences only a 2% degradation. In addition, DarkGates fulfills the requirements of the ENERGY STAR and the Intel Ready Mode energy efficiency benchmarks of desktop systems.

A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the linear reference sequence with a graph-based representation of the reference genome, which captures the genetic variations and diversity across many individuals in a population. Mapping reads to the graph-based reference genome (i.e., sequence-to-graph mapping) results in notable quality improvements in genome analysis. Unfortunately, while sequence-to-sequence mapping is well studied with many available tools and accelerators, sequence-to-graph mapping is a more difficult computational problem, with a much smaller number of practical software tools currently available.

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 base-lines 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 and all scripts required to reproduce the results of this paper are openly and fully available at https://github.com/CMU-SAFARI/pLUTo.

User-facing applications running in modern datacenters exhibit irregular request patterns and are implemented using a multitude of services with tight latency requirements (30–250$\mu$s). These characteristics render existing energy-conserving techniques ineffective when processors are idle due to the long transition time (order of 100$\mu$s) from a deep CPU core idle power state (C-state). While prior works propose management techniques to mitigate this inefficiency, we tackle it at its root with AgileWatts (AW): a new deep CPU core C-state architecture optimized for datacenter server processors targeting latency-sensitive applications.AW drastically reduces the transition latency from deep CPU core idle power states while retaining most of their power savings based on three key ideas. First, AW eliminates the latency (several microseconds) of savinglrestoring the core context when powering-off/-on the core in a deep idle state by i) implementing medium-grained power-gates, carefully distributed across the CPU core, and ii) reraining context in the power-ungated domain. Second, AW eliminates rhe flush latency (several tens of microseconds) of the LllL2 caches when entering a deep idle state by keeping LllL2 content power-ungated. A small control logic also remains ungated to serve cache coherence traffic. AW implements cache sleep-mode and leakage reduction for the power-ungated domain by lowering a core’s voltage to the minimum operational level. Third, using a state-of-the-art power efficient all-digital phase-locked loop (ADPLL) clock generator, AW keeps the PLL active and locked during the idle state, cutting microseconds of wake-up latency at negligible power cost.Our evaluation with an accurate industrial-grade simulator calibrated against an Intel Skylake server shows that AW reduces the energy consumprion of Memcached by up to 71% (35% on average) with<1% end-to-end performance degradation. We observe similar trends for other evaluated services (MySQL and Kafka). AW’s new deep C-states C6A and C6AE reduce transition-time by up to 900$\times$ as compared to the deepest existing idle state C6, while consuming only 7% and 5% of the active state (C0) power, respectively.

MOTIVATION: A genome read dataset can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly used CrossMap tool. With the explosion of available genomic datasets and references, high-performance remapping tools will be even more important for keeping up with the computational demands of genome assembly and analysis. RESULTS: We provide FastRemap, a fast and efficient tool for remapping reads between genome assemblies. FastRemap provides up to a 7.82× speedup (6.47×, on average) and uses as low as 61.7% (80.7%, on average) of the peak memory consumption compared to the state-of-the-art remapping tool, CrossMap. AVAILABILITY AND IMPLEMENTATION: FastRemap is written in C++. Source code and user manual are freely available at: github.com/CMU-SAFARI/FastRemap. Docker image available at: https://hub.docker.com/r/alkanlab/fastremap. Also available in Bioconda at: https://anaconda.org/bioconda/fastremap-bio.

Aggressive memory density scaling causes modern DRAM devices to suffer from RowHammer, a phenomenon where rapidly activating (i.e., hammering) a DRAM row can cause bit-flips in physically-nearby rows. Recent studies demonstrate that modern DDR4/LPDDR4 DRAM chips, including chips previously marketed as RowHammer-safe, are even more vulnerable to RowHammer than older DDR3 DRAM chips. Many works show that attackers can exploit RowHammer bit-flips to reliably mount system-level attacks to escalate privilege and leak private data. Therefore, it is critical to ensure RowHammersafe operation on all DRAM-based systems as they become increasingly more vulnerable to RowHammer. Unfortunately, state-of-the-art RowHammer mitigation mechanisms face two major challenges. First, they incur increasingly higher performance and/or area overheads when applied to more vulnerable DRAM chips. Second, they require either closely-guarded proprietary information about the DRAM chips' physical circuit layouts or modifications to the DRAM chip design.In this paper, we show that it is possible to efficiently and scalably prevent RowHammer bit-flips without knowledge of or modification to DRAM internals. To this end, we introduce BlockHammer, a low-cost, effective, and easy-to-adopt RowHammer mitigation mechanism that prevents all RowHammer bit-flips while overcoming the two key challenges. BlockHammer selectively throttles memory accesses that could otherwise potentially cause RowHammer bit-flips. The key idea of BlockHammer is to (1) track row activation rates using area-efficient Bloom filters, and (2) use the tracking data to ensure that no row is ever activated rapidly enough to induce RowHammer bit-flips. By guaranteeing that no DRAM row ever experiences a RowHammer-unsafe activation rate, BlockHammer (1) makes it impossible for a RowHammer bit-flip to occur and (2) greatly reduces a RowHammer attack's impact on the performance of co-running benign applications. Our evaluations across a comprehensive range of 280 workloads show that, compared to the best of six state-of-the-art RowHammer mitigation mechanisms (all of which require knowledge of or modification to DRAM internals), BlockHammer provides (1) competitive performance and energy when the system is not under a RowHammer attack and (2) significantly better performance and energy when the system is under a RowHammer attack.

DRAM is the dominant main memory technology used in modern computing systems. Computing systems implement a memory controller that interfaces with DRAM via DRAM commands. DRAM executes the given commands using internal components (e.g., access transistors, sense amplifiers) that are orchestrated by DRAM internal timings, which are fixed for each DRAM command. Unfortunately, the use of fixed internal timings limits the types of operations that DRAM can perform and hinders the implementation of new functionalities and custom mechanisms that improve DRAM reliability, performance and energy. To overcome these limitations, we propose enabling programmable DRAM internal timings for controlling in-DRAM components.To this end, we design CODIC, a new low-cost DRAM substrate that enables fine-grained control over four previously fixed internal DRAM timings that are key to many DRAM operations. We implement CODIC with only minimal changes to the DRAM chip and the DDRx interface. To demonstrate the potential of CODIC, we propose two new CODIC-based security mechanisms that outperform state-of-the-art mechanisms in several ways: (1) a new DRAM Physical Unclonable Function (PUF) that is more robust and has significantly higher throughput than state-of-the-art DRAM PUFs, and (2) the first cold boot attack prevention mechanism that does not introduce any performance or energy overheads at runtime.

To operate efficiently across a wide range of workloads with varying power requirements, a modern processor applies different current management mechanisms, which briefly throttle instruction execution while they adjust voltage and frequency to accommodate for power-hungry instructions (PHIs) in the instruction stream. Doing so 1) reduces the power consumption of non-PHI instructions in typical workloads and 2) optimizes system voltage regulators’ cost and area for the common use case while limiting current consumption when executing PHIs.However, these mechanisms may compromise a system’s confidentiality guarantees. In particular, we observe that multilevel side-effects of throttling mechanisms, due to PHI-related current management mechanisms, can be detected by two different software contexts (i.e., sender and receiver) running on 1) the same hardware thread, 2) co-located Simultaneous Multi-Threading (SMT) threads, and 3) different physical cores.Based on these new observations on current management mechanisms, we develop a new set of covert channels, IChannels, and demonstrate them in real modern Intel processors (which span more than 70% of the entire client and server processor market). Our analysis shows that IChannels provides more than 24× the channel capacity of state-of-the-art power management covert channels. We propose practical and effective mitigations to each covert channel in IChannels by leveraging the insights we gain through a rigorous characterization of real systems.

True random number generators (TRNG) sample random physical processes to create large amounts of random numbers for various use cases, including security-critical cryptographic primitives, scientific simulations, machine learning applications, and even recreational entertainment. Unfortunately, not every computing system is equipped with dedicated TRNG hardware, limiting the application space and security guarantees for such systems. To open the application space and enable security guarantees for the overwhelming majority of computing systems that do not necessarily have dedicated TRNG hardware (e.g., processing-in-memory systems), we develop QUAC-TRNG, a new high-throughput TRNG that can be fully implemented in commodity DRAM chips, which are key components in most modern systems.QUAC-TRNG exploits the new observation that a carefully-engineered sequence of DRAM commands activates four consecutive DRAM rows in rapid succession. This QUadruple ACtivation (QUAC) causes the bitline sense amplifiers to non-deterministically converge to random values when we activate four rows that store conflicting data because the net deviation in bitline voltage fails to meet reliable sensing margins.We experimentally demonstrate that QUAC reliably generates random values across 136 commodity DDR4 DRAM chips from one major DRAM manufacturer. We describe how to develop an effective TRNG (QUAC-TRNG) based on QUAC. We evaluate the quality of our TRNG using the commonly-used NIST statistical test suite for randomness and find that QUAC-TRNG successfully passes each test. Our experimental evaluations show that QUAC-TRNG reliably generates true random numbers with a throughput of 3.44 Gb/s (per DRAM channel), outperforming the state-of-the-art DRAM-based TRNG by 15.08× and 1.41× for basic and throughput-optimized versions, respectively. We show that QUAC-TRNG utilizes DRAM bandwidth better than the state-of-the-art, achieving up to 2.03× the throughput of a throughput-optimized baseline when scaling bus frequencies to 12 GT/s.

RowHammer is a circuit-level DRAM vulnerability where repeatedly accessing (i.e., hammering) a DRAM row can cause bit flips in physically nearby rows. The RowHammer vulnerability worsens as DRAM cell size and cell-to-cell spacing shrink. Recent studies demonstrate that modern DRAM chips, including chips previously marketed as RowHammer-safe, are even more vulnerable to RowHammer than older chips such that the required hammer count to cause a bit flip has reduced by more than 10X in the last decade. Therefore, it is essential to develop a better understanding and in-depth insights into the RowHammer vulnerability of modern DRAM chips to more effectively secure current and future systems.

Conventional planar video streaming is the most popular application in mobile systems. The rapid growth of 360° video content and virtual reality (VR) devices is accelerating the adoption of VR video streaming. Unfortunately, video streaming consumes significant system energy due to high power consumption of major system components (e.g., DRAM, display interfaces, and display panel) involved in the video streaming process. For example, in conventional planar video streaming, the video decoder (in the processor) decodes video frames and stores them in the DRAM main memory before the display controller (in the processor) transfers decoded frames from DRAM to the display panel. This system architecture causes large amount of data movement to/from DRAM as well as high DRAM bandwidth usage. As a result, DRAM by itself consumes more than 30% of the video streaming energy.

The RowHammer vulnerability in DRAM is a critical threat to system security. To protect against RowHammer, vendors commit to security-through-obscurity: modern DRAM chips rely on undocumented, proprietary, on-die mitigations, commonly known as Target Row Refresh (TRR). At a high level, TRR detects and refreshes potential RowHammer-victim rows, but its exact implementations are not openly disclosed. Security guarantees of TRR mechanisms cannot be easily studied due to their proprietary nature.

There are three domains in a modern thermally-constrained mobile system-on-chip (SoC): compute, IO, and memory. We observe that a modern SoC typically allocates a fixed power budget, corresponding to worst-case performance demands, to the IO and memory domains even if they are underutilized. The resulting unfair allocation of the power budget across domains can cause two major issues: 1) the IO and memory domains can operate at a higher frequency and voltage than necessary, increasing power consumption and 2) the unused power budget of the IO and memory domains cannot be used to increase the throughput of the compute domain, hampering performance. To avoid these issues, it is crucial to dynamically orchestrate the distribution of the SoC power budget across the three domains based on their actual performance demands. We propose SysScale, a new multi-domain power management technique to improve the energy efficiency of mobile SoCs. SysScale is based on three key ideas. First, SysScale introduces an accurate algorithm to predict the performance (e.g., bandwidth and latency) demands of the three SoC domains. Second, SysScale uses a new DVFS (dynamic voltage and frequency scaling) mechanism to distribute the SoC power to each domain according to the predicted performance demands. This mechanism is designed to minimize the significant latency overheads associated with applying DVFS across multiple domains. Third, in addition to using a global DVFS mechanism, SysScale uses domain-specialized techniques to optimize the energy efficiency of each domain at different operating points. We implement SysScale on an Intel Skylake microprocessor for mobile devices and evaluate it using a wide variety of SPEC CPU2006, graphics (3DMark), and battery life workloads (e.g., video playback). On a 2-core Skylake, SysScale improves the performance of SPEC CPU2006 and 3DMark workloads by up to 16% and 8.9% (9.2% and 7.9% on average), respectively. For battery life workloads, which typically have fixed performance demands, SysScale reduces the average power consumption by up to 10.7% (8.5% on average), while meeting performance demands.

RowHammer is a circuit-level DRAM vulnerability, first rigorously analyzed and introduced in 2014, where repeatedly accessing data in a DRAM row can cause bit flips in nearby rows. The RowHammer vulnerability has since garnered significant interest in both computer architecture and computer security research communities because it stems from physical circuit-level interference effects that worsen with continued DRAM density scaling. As DRAM manufacturers primarily depend on density scaling to increase DRAM capacity, future DRAM chips will likely be more vulnerable toRowHammer than those of the past. Many RowHammer mitigation mechanisms have been proposed by both industry and academia, but it is unclear whether these mechanisms will remain viable solutions forfuture devices, as their overheads increase with DRAM's vulnerability to RowHammer. In order to shed more light on how RowHammer affects modern and future devices at the circuit-level, wefirst present an experimental characterization of RowHammer on 1580 DRAM chips (408X DDR3, 652X DDR4, and 520X LPDDR4) from 300 DRAM modules (60X DDR3, 110X DDR4, and 130X LPDDR4) with RowHammer protection mechanisms disabled, spanning multiple different technology nodes from across each of the three major DRAM manufacturers. Our studies definitively show that newer DRAM chips are more vulnerable to RowHammer: as device feature size reduces, the number of activations needed to induce a RowHammer bit flip also reduces, to as few as 9.6k (4.8k to two rows each) in the most vulnerable chip we tested. We evaluate five state-of-the-art RowHammer mitigation mechanisms using cycle-accurate simulation in the context of real data taken from our chips to study how the mitigation mechanisms scale with chip vulnerability. Wefind that existing mechanisms either are not scalable or suffer from prohibitively large performance overheads in projected future devices given our observed trends of RowHammer vulnerability. Thus, it is critical to research more effective solutions to RowHammer.

Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. To perform genome sequencing, devices extract small random fragments of an organism's DNA sequence (known as reads). The first step of genome sequence analysis is a computational process known as read mapping. In read mapping, each fragment is matched to its potential location in the reference genome with the goal of identifying the original location of each read in the genome. Unfortunately, rapid genome sequencing is currently bottlenecked by the computational power and memory bandwidth limitations of existing systems, as many of the steps in genome sequence analysis must process a large amount of data. A major contributor to this bottleneck is approximate string matching (ASM), which is used at multiple points during the mapping process. ASM enables read mapping to account for sequencing errors and genetic variations in the reads. We propose GenASM, the first ASM acceleration framework for genome sequence analysis. GenASM performs bitvectorbased ASM, which can efficiently accelerate multiple steps of genome sequence analysis. We modify the underlying ASM algorithm (Bitap) to significantly increase its parallelism and reduce its memory footprint. Using this modified algorithm, we design the first hardware accelerator for Bitap. Our hardware accelerator consists of specialized systolic-array-based compute units and on-chip SRAMs that are designed to match the rate of computation with memory capacity and bandwidth, resulting in an efficient design whose performance scales linearly as we increase the number of compute units working in parallel. We demonstrate that GenASM provides significant performance and power benefits for three different use cases in genome sequence analysis. First, GenASM accelerates read alignment for both long reads and short reads. For long reads, GenASM outperforms state-of-the-art software and hardware accelerators by 116× and 3.9×, respectively, while reducing power consumption by 37× and 2.7×. For short reads, GenASM outperforms state-of-the-art software and hardware accelerators by 111× and 1.9×. Second, GenASM accelerates pre-alignment filtering for short reads, with 3.7× the performance of a state-of-the-art pre-alignment filter, while reducing power consumption by 1.7× and significantly improving the filtering accuracy. Third, GenASM accelerates edit distance calculation, with 22-12501× and 9.3-400× speedups over the state-of-the-art software library and FPGA-based accelerator, respectively, while reducing power consumption by 548-582× and 67×. We conclude that GenASM is a flexible, high-performance, and low-power framework, and we briefly discuss four other use cases that can benefit from GenASM.

Modern client processors typically use one of three commonly-used power delivery network (PDN) architectures: 1) motherboard voltage regulators (MBVR), 2) integrated voltage regulators (IVR), and 3) low dropout voltage regulators (LDO). We observe that the energy-efficiency of each of these PDNs varies with the processor power (e.g, thermal design power (TDP) and dynamic power-state) and workload characteristics (e.g., work-load type and computational intensity). This leads to energy-inefficiency and performance loss, as modern client processors operate across a wide spectrum of power consumption and execute a wide variety of workloads. To address this inefficiency, we propose FlexWatts, a hybrid adaptive PDN for modern client processors whose goal is to provide high energy-efficiency across the processor's wide range of power consumption and workloads. FlexWatts provides high energy-efficiency by intelligently and dynamically allocating PDNs to processor domains depending on the processor's power consumption and workload. FlexWatts is based on three key ideas. First, FlexWatts combines IVRs and LDOs in a novel way to share multiple on-chip and off-chip resources and thus reduce cost, as well as board and die area overheads. This hybrid PDN is allocated for processor domains with a wide power consumption range (e.g., CPU cores and graphics engines) and it dynamically switches between two modes: IVR-Mode and LDO-Mode, depending on the power consumption. Second, for all other processor domains (that have a low and narrow power range, e.g., the IO domain), FlexWatts statically allocates off-chip VRs, which have high energy-efficiency for low and narrow power ranges. Third, FlexWatts introduces a novel prediction algorithm that automatically switches the hybrid PDN to the mode (IVR-Mode or LDO-Mode) that is the most beneficial based on processor power consumption and workload characteristics. To evaluate the tradeoffs of PDNs, we develop and open-source PDNspot, the first validated architectural PDN model that enables quantitative analysis of PDN metrics. Using PDNspot, we evaluate FlexWatts on a wide variety of SPEC CPU2006, graphics (3DMark06), and battery life (e.g., video playback) workloads against IVR, the state-of-the-art PDN in modern client processors. For a 4 W thermal design power (TDP) processor, FlexWatts improves the average performance of the SPEC CPU2006 and 3DMark06 workloads by 22% and 25%, respectively. For battery life workloads, FlexWatts reduces the average power consumption of video playback by 11% across all tested TDPs (4W-50W). FlexWatts has comparable cost and area overhead to IVR. We conclude that FlexWatts provides high energy-efficiency across a modern client processor's wide range of power consumption and wide variety of workloads, with minimal overhead.

Increasing single-cell DRAM error rates have pushed DRAM manufacturers to adopt on-die error-correction coding (ECC), which operates entirely within a DRAM chip to improve factory yield. The on-die ECC function and its effects on DRAM reliability are considered trade secrets, so only the manufacturer knows precisely how on-die ECC alters the externally-visible reliability characteristics. Consequently, on-die ECC obstructs third-party DRAM customers (e.g., test engineers, experimental researchers), who typically design, test, and validate systems based on these characteristicsTo give third parties insight into precisely how on-die ECC transforms DRAM error patterns during error correction, we introduce Bit-Exact ECC Recovery (BEER), a new methodology for determining the full DRAM on-die ECC function (i.e., its parity-check matrix) without hardware tools, prerequisite knowledge about the DRAM chip or on-die ECC mechanism, or access to ECC metadata (e.g., error syndromes, parity information). BEER exploits the key insight that non-intrusively inducing data-retention errors with carefully-crafted test pat-terns reveals behavior that is unique to a specific ECC functionWe use BEER to identify the ECC functions of 80 real LPDDR4 DRAM chips with on-die ECC from three major DRAM manufacturers. We evaluate BEER's correctness in simulation and performance on a real system to show that BEER is effective and practical across a wide range of on-die ECC functions. To demonstrate BEER's value, we propose and discuss several ways that third parties can use BEER to improve their design and testing practices. As a concrete example, we introduce and evaluate BEEP, the first error profiling method-ology that uses the known on-die ECC function to recover the number and bit-exact locations of unobservable raw bit errors responsible for observable post-correction errors.

Main memory, composed of DRAM, is a performance bottleneck for many applications, due to the high DRAM access latency. In-DRAM caches work to mitigate this latency by augmenting regular-latency DRAM with small-but-fast regions of DRAM that serve as a cache for the data held in the regular-latency (i.e., slow) region of DRAM. While an effective in-DRAM cache can allow a large fraction of memory requests to be served from a fast DRAM region, the latency savings are often hindered by inefficient mechanisms for migrating (i.e., relocating) copies of data into and out of the fast regions. Existing in-DRAM caches have two sources of inefficiency: (1) their data relocation granularity is an entire multi-kilobyte row of DRAM, even though much of the row may never be accessed due to poor data locality; and (2) because the relocation latency increases with the physical distance between the slow and fast regions, multiple fast regions are physically interleaved among slow regions to reduce the relocation latency, resulting in increased hardware area and manufacturing complexityWe propose a new substrate, FIGARO, that uses existing shared global buffers among subarrays within a DRAM bank to provide support for in-DRAM data relocation across subar-rays at the granularity of a single cache block. FIGARO has a distance-independent latency within a DRAM bank, and avoids complex modifications to DRAM (such as the interleaving of fast and slow regions). Using FIGARO, we design a fine-grained in-DRAM cache called FIGCache. The key idea of FIGCache is to cache only small, frequently-accessed portions of different DRAM rows in a designated region of DRAM. By caching only the parts of each row that are expected to be accessed in the near future, we can pack more of the frequently-accessed data into FIGCache, and can benefit from additional row hits in DRAM (i.e., accesses to an already-open row, which have a lower latency than accesses to an unopened row). FIGCache provides benefits for systems with both heterogeneous DRAM banks (i.e., banks with fast regions and slow regions) and conventional homogeneous DRAM banks (i.e., banks with only slow regions)Our evaluations across a wide variety of applications show that FIGCache improves the average performance of a system using DDR4 DRAM by 16.3% and reduces average DRAM energy consumption by 7.8% for 8-core workloads, over a conventional system without in-DRAM caching. We show that FIGCache outperforms state-of-the-art in-DRAM caching techniques, and that its performance gains are robust across many system and mechanism parameters.

Cloud providers are concerned that Rowhammer poses a potentially critical threat to their servers, yet today they lack a systematic way to test whether the DRAM used in their servers is vulnerable to Rowhammer attacks. This paper presents an endto-end methodology to determine if cloud servers are susceptible to these attacks. With our methodology, a cloud provider can construct worst-case testing conditions for DRAM.We apply our methodology to three classes of servers from a major cloud provider. Our findings show that none of the CPU instruction sequences used in prior work to mount Rowhammer attacks create worst-case DRAM testing conditions. To address this limitation, we develop an instruction sequence that leverages microarchitectural side-effects to "hammer" DRAM at a near-optimal rate on modern Intel Skylake and Cascade Lake platforms. We also design a DDR4 fault injector that can reverse engineer row adjacency for any DDR4 DIMM. When applied to our cloud provider's DIMMs, we find that DRAM rows do not always follow a linear map.

MOTIVATION: Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs. These long reads are used to construct an assembly (i.e. the subject's genome), which is further used in downstream genome analysis. Unfortunately, third-generation sequencing technologies have high sequencing error rates and a large proportion of base pairs in these long reads is incorrectly identified. These errors propagate to the assembly and affect the accuracy of genome analysis. Assembly polishing algorithms minimize such error propagation by polishing or fixing errors in the assembly by using information from alignments between reads and the assembly (i.e. read-to-assembly alignment information). However, current assembly polishing algorithms can only polish an assembly using reads from either a certain sequencing technology or a small assembly. Such technology-dependency and assembly-size dependency require researchers to (i) run multiple polishing algorithms and (ii) use small chunks of a large genome to use all available readsets and polish large genomes, respectively. RESULTS: We introduce Apollo, a universal assembly polishing algorithm that scales well to polish an assembly of any size (i.e. both large and small genomes) using reads from all sequencing technologies (i.e. second- and third-generation). Our goal is to provide a single algorithm that uses read sets from all available sequencing technologies to improve the accuracy of assembly polishing and that can polish large genomes. Apollo (i) models an assembly as a profile hidden Markov model (pHMM), (ii) uses read-to-assembly alignment to train the pHMM with the Forward-Backward algorithm and (iii) decodes the trained model with the Viterbi algorithm to produce a polished assembly. Our experiments with real readsets demonstrate that Apollo is the only algorithm that (i) uses reads from any sequencing technology within a single run and (ii) scales well to polish large assemblies without splitting the assembly into multiple parts. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/CMU-SAFARI/Apollo. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

This retrospective paper describes the RowHammer problem in dynamic random access memory (DRAM), which was initially introduced by Kim et al. at the ISCA 2014 Conference. RowHammer is a prime (and perhaps the first) example of how a circuit-level failure mechanism can cause a practical and widespread system security vulnerability. It is the phenomenon that repeatedly accessing a row in a modern DRAM chip causes bit flips in physically adjacent rows at consistently predictable bit locations. RowHammer is caused by a hardware failure mechanism called DRAM disturbance errors, which is a manifestation of circuit-level cell-to-cell interference in a scaled memory technology. Researchers from Google Project Zero demonstrated in 2015 that this hardware failure mechanism can be effectively exploited by user-level programs to gain kernel privileges on real systems. Many other follow-up works demonstrated other practical attacks exploiting RowHammer. In this paper, we comprehensively survey the scientific literature on RowHammer-based attacks as well as mitigation techniques to prevent RowHammer. We also discuss what other related vulnerabilities may be lurking in DRAM and other types of memories, e.g., NAND flash memory or phase change memory, that can potentially threaten the foundations of secure systems, as the memory technologies scale to higher densities. We conclude by describing and advocating a principled approach to memory reliability and security research that can enable us to better anticipate and prevent such vulnerabilities.

Experimental characterization of DRAM errors is a powerful technique for understanding DRAM behavior and provides valuable insights for improving overall system performance, energy efficiency, and reliability. Unfortunately, recent DRAM technology scaling issues are forcing manufacturers to adopt on-die error-correction codes (ECC), which pose a significant challenge for DRAM error characterization studies by obfuscating raw error distributions using undocumented, proprietary, and opaque error-correction hardware. As we show in this work, errors observed in devices with on-die ECC no longer follow expected, well-studied distributions (e.g., lognormal retention times) but rather depend on the particular ECC scheme used. In this work, we develop Error-correction INference (EIN), a new statistical inference methodology that overcomes the inability to understand the error characteristics of DRAM devices with ondie ECC. EIN uses maximum a posteriori (MAP) estimation over statistical models that we develop to represent ECC operation to: i) reverse-engineer the ECC scheme and ii) infer the pre-correction error rates given only the post-correction errors. We design and publicly release EINSim, a flexible open-source simulator that can apply EIN to a wide variety ofDRAM devices and standards. We evaluate EIN through the first experimental error-characterization study of DRAM devices with on-die ECC in open literature. Using the data-retention error rates of 232 (82) LPDDR4 devices with (without) on-die ECC across a wide range of temperatures, refresh rates, and test patterns, we show that EIN enables: i) reverse-engineering the on-die ECC scheme, which we find to be a single-error correction Hamming code with (n = 136, k = 128, d = 3), ii) inferring pre-correction error rates given only post-correction errors, and iii) recovering the well-studied pre-correction error distributions that on-die ECC obfuscates.

We propose a new DRAM-based true random number generator (TRNG) that leverages DRAM cells as an entropy source. The key idea is to intentionally violate the DRAM access timing parameters and use the resulting errors as the source of randomness. Our technique specifically decreases the DRAM row activation latency (timing parameter t R a D ) below manufacturer recommended specifications, to induce read errors, or activation failures, that exhibit true random behavior. We then aggregate the resulting data from multiple cells to obtain a TRNG capable of providing a high throughput of random numbers at low latency.

DRAM has been the dominant technology for architecting main memory for decades. Recent trends in multi-core system design and large-dataset applications have amplified the role of DRAM as a critical system bottleneck. We propose Copy-Row DRAM (CROW), a flexible substrate that enables new mechanisms for improving DRAM performance, energy efficiency, and reliability. We use the CROW substrate to implement 1) a low-cost in-DRAM caching mechanism that lowers DRAM activation latency to frequently-accessed rows by 38% and 2) a mechanism that avoids the use of short-retention-time rows to mitigate the performance and energy overhead of DRAM refresh operations. CROW's flexibility allows the implementation of both mechanisms at the same time. Our evaluations show that the two mechanisms synergistically improve system performance by 20.0% and reduce DRAM energy by 22.3% for memory-intensive four-core workloads, while incurring 0.48% extra area overhead in the DRAM chip and 11.3 KiB storage overhead in the memory controller, and consuming 1.6% of DRAM storage capacity, for one particular implementation.

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, to overcome the high error rates of the nanopore sequencing technology.

Physically Unclonable Functions (PUFs) are commonly used in cryptography to identify devices based on the uniqueness of their physical microstructures. DRAM-based PUFs have numerous advantages over PUF designs that exploit alternative substrates: DRAM is a major component of many modern systems, and a DRAM-based PUF can generate many unique identiers. However, none of the prior DRAM PUF proposals provide implementations suitable for runtime-accessible PUF evaluation on commodity DRAM devices. Prior DRAM PUFs exhibit unacceptably high latencies, especially at low temperatures (e.g., >125.8s on average for a 64KiB memory segment below 55C), and they cause high system interference by keeping part of DRAM unavailable during PUF evaluation. In this paper, we introduce the DRAM latency PUF, a new class of fast, reliable DRAM PUFs. The key idea is to reduce DRAM read access latency below the reliable datasheet specications using software-only system calls. Doing so results in error patterns that reect the compound eects of manufacturing variations in various DRAM structures (e.g., capacitors, wires, sense ampli- ers). Based on a rigorous experimental characterization of 223 modern LPDDR4 DRAM chips, we demonstrate that these error patterns 1) satisfy runtime-accessible PUF requirements, and 2) are quickly generated (i.e., at 88.2ms) irrespective of operating temperature using a real system with no additional hardware modications. We show that, for a constant DRAM capacity overhead of 64KiB, our implementation of the DRAM latency PUF enables an average (minimum, maximum) PUF evaluation time speedup of 152x (109x, 181x) at 70C and 1426x (868x, 1783x) at 55C when compared to a DRAM retention PUF and achieves greater speedups at even lower temperatures.

DRAM latency is a major bottleneck for many applications in modern computing systems. In this work, we rigorously characterize the effects of reducing DRAM access latency on 282 state-of-the-art LPDDR4 DRAM modules. As found in prior work on older DRAM generations (DDR3), we show that regions of LPDDR4 DRAM modules can be accessed with latencies that are significantly lower than manufacturer-specified values without causing failures. We present novel data that 1) further supports the viability of such latency reduction mechanisms and 2) exposes a variety of new cases in which access latencies can be effectively reduced. Using our observations, we propose a new low-cost mechanism, Solar-DRAM, that 1) identifies failure-prone regions of DRAM at reduced latency and 2) robustly reduces average DRAM access latency while maintaining data correctness, by issuing DRAM requests with reduced access latencies to non-failure-prone DRAM regions. We evaluate Solar-DRAM on a wide variety of multi-core workloads and show that for 4-core homogeneous workloads, Solar-DRAM provides an average (maximum) system performance improvement of 4.31% (10.87%) compared to using the default fixed DRAM access latency.

Modern solid-state drives (SSDs) use new host-interface protocols, such as NVMe, to provide applications with fast access to storage. These new protocols make use of a concept known as the multi-queue SSD (MQ-SSD), where the SSD has direct access to the application-level I/O request queues. This removes most of the OS software stack that was used in older protocols to control how and when the I/O requests were dispatched to storage devices. Unfortunately, while the elimination of the OS software stack leads to a significant performance improvement, we show in this paper that it introduces a new problem: unfairness. This is because the elimination of the OS software stack eliminates the mechanisms that were used to provide fairness among applications in older SSDs. To study application-level unfairness, we perform experiments using four real state-of-the-art MQ-SSDs. We demonstrate that the lack of fair scheduling mechanisms leads to high unfairness among concurrently-executing applications due to the interference among them. For instance, when one of these applications issues many more I/O requests than others, the other applications are slowed down significantly. We perform a comprehensive analysis of interference in real MQ-SSDs, and find four major interference sources: (1) the intensity of requests sent by each application, (2) differences in request access patterns, (3) the ratio of reads to writes, and (4) garbage collection. To alleviate unfairness in MQ-SSDs, we propose the Flash-Level INterference-aware scheduler (FLIN). FLIN is a lightweight I/O request scheduling mechanism that provides fairness among requests from different applications. FLIN uses a three-stage scheduling algorithm that protects against all four major sources of interference, while respecting the application-level priorities assigned by the host. FLIN is implemented fully within the SSD controller firmware, requiring no new hardware, and has negligible (<;0.06%) storage cost. Compared to a state-of-the-art I/O scheduler, FLIN improves the fairness and performance of a wide range of enterprise and datacenter storage workloads, with an average improvement of 70% and 47%, respectively.

Long DRAM access latency is a major bottleneck for system performance. In order to access data in DRAM, a memory controller (1) activates (i.e., opens) a row of DRAM cells in a cell array, (2) restores the charge in the activated cells back to their full level, (3) performs read and write operations to the activated row, and (4) precharges the cell array to prepare for the next activation. The restoration operation is responsible for a large portion (up to 43.6%) of the total DRAM access latency. We find two frequent cases where the restoration operations performed by DRAM do not need to fully restore the charge level of the activated DRAM cells, which we can exploit to reduce the restoration latency. First, DRAM rows are periodically refreshed (i.e., brought back to full charge) to avoid data loss due to charge leakage from the cell. The charge level of a DRAM row that will be refreshed soon needs to be only partially restored, providing just enough charge so that the refresh can correctly detect the cells' data values. Second, the charge level of a DRAM row that will be activated again soon can be only partially restored, providing just enough charge for the activation to correctly detect the data value. However, partial restoration needs to be done carefully: for a row that will be activated again soon, restoring to only the minimum possible charge level can undermine the benefits of complementary mechanisms that reduce the activation time of highly-charged rows. To enable effective latency reduction for both activation and restoration, we propose charge-level-aware look-ahead partial restoration (CAL). CAL consists of two key components. First, CAL accurately predicts the next access time, which is the time between the current restoration operation and the next activation of the same row. Second, CAL uses the predicted next access time and the next refresh time to reduce the restoration time, ensuring that the amount of partial charge restoration is enough to maintain the benefits of reducing the activation time of a highly-charged row. We implement CAL fully in the memory controller, without any changes to the DRAM module. Across a wide variety of applications, we find that CAL improves the average performance of an 8-core system by 14.7%, and reduces average DRAM energy consumption by 11.3%.

Modern DRAM-based systems suffer from significant energy and latency penalties due to conservative DRAM refresh standards. Volatile DRAM cells can retain information across a wide distribution of times ranging from milliseconds to many minutes, but each cell is currently refreshed every 64ms to account for the extreme tail end of the retention time distribution, leading to a high refresh overhead. Due to poor DRAM technology scaling, this problem is expected to get worse in future device generations. Hence, the current approach of refreshing all cells with the worst-case refresh rate must be replaced with a more intelligent design.

Many important applications trigger bulk bitwise operations, i.e., bitwise operations on large bit vectors. In fact, recent works design techniques that exploit fast bulk bitwise operations to accelerate databases (bitmap indices, BitWeaving) and web search (BitFunnel). Unfortunately, in existing architectures, the throughput of bulk bitwise operations is limited by the memory bandwidth available to the processing unit (e.g., CPU, GPU, FPGA, processing-in-memory).

Memory isolation is a key property of a reliable and secure computing system-an access to one memory address should not have unintended side effects on data stored in other addresses. However, as DRAM process technology scales down to smaller dimensions, it becomes more difficult to prevent DRAM cells from electrically interacting with each other. In this paper, we expose the vulnerability of commodity DRAM chips to disturbance errors. By reading from the same address in DRAM, we show that it is possible to corrupt data in nearby addresses. More specifically, activating the same row in DRAM corrupts data in nearby rows. We demonstrate this phenomenon on Intel and AMD systems using a malicious program that generates many DRAM accesses. We induce errors in most DRAM modules (110 out of 129) from three major DRAM manufacturers. From this we conclude that many deployed systems are likely to be at risk. We identify the root cause of disturbance errors as the repeated toggling of a DRAM row's wordline, which stresses inter-cell coupling effects that accelerate charge leakage from nearby rows. We provide an extensive characterization study of disturbance errors and their behavior using an FPGA-based testing platform. Among our key findings, we show that (i) it takes as few as 139K accesses to induce an error and (ii) up to one in every 1.7K cells is susceptible to errors. After examining various potential ways of addressing the problem, we propose a low-overhead solution to prevent the errors.