461 research outputs found

    An In-Memory Architecture for High-Performance Long-Read Pre-Alignment Filtering

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    With the recent move towards sequencing of accurate long reads, finding solutions that support efficient analysis of these reads becomes more necessary. The long execution time required for sequence alignment of long reads negatively affects genomic studies relying on sequence alignment. Although pre-alignment filtering as an extra step before alignment was recently introduced to mitigate sequence alignment for short reads, these filters do not work as efficiently for long reads. Moreover, even with efficient pre-alignment filters, the overall end-to-end (i.e., filtering + original alignment) execution time of alignment for long reads remains high, while the filtering step is now a major portion of the end-to-end execution time. Our paper makes three contributions. First, it identifies data movement of sequences between memory units and computing units as the main source of inefficiency for pre-alignment filters of long reads. This is because although filters reject many of these long sequencing pairs before they get to the alignment stage, they still require a huge cost regarding time and energy consumption for the large data transferred between memory and processor. Second, this paper introduces an adaptation of a short-read pre-alignment filtering algorithm suitable for long reads. We call this LongGeneGuardian. Finally, it presents Filter-Fuse as an architecture that supports LongGeneGuardian inside the memory. FilterFuse exploits the Computation-In-Memory computing paradigm, eliminating the cost of data movement in LongGeneGuardian. Our evaluations show that FilterFuse improves the execution time of filtering by 120.47x for long reads compared to State-of-the-Art (SoTA) filter, SneakySnake. FilterFuse also improves the end-to-end execution time of sequence alignment by up to 49.14x and 5207.63x compared to SneakySnake with SoTA aligner and only SoTA aligner, respectively

    Pathfinding Future PIM Architectures by Demystifying a Commercial PIM Technology

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    Processing-in-memory (PIM) has been explored for decades by computer architects, yet it has never seen the light of day in real-world products due to their high design overheads and lack of a killer application. With the advent of critical memory-intensive workloads, several commercial PIM technologies have been introduced to the market ranging from domain-specific PIM architectures to more general-purpose PIM architectures. In this work, we deepdive into UPMEM's commercial PIM technology, a general-purpose PIM-enabled parallel architecture that is highly programmable. Our first key contribution is the development of a flexible simulation framework for PIM. The simulator we developed (aka PIMulator) enables the compilation of UPMEM-PIM source codes into its compiled machine-level instructions, which are subsequently consumed by our cycle-level performance simulator. Using PIMulator, we demystify UPMEM's PIM design through a detailed characterization study. Building on top of our characterization, we conduct a series of case studies to pathfind important architectural features that we deem will be critical for future PIM architectures to suppor

    DRAM Bender: An Extensible and Versatile FPGA-based Infrastructure to Easily Test State-of-the-art DRAM Chips

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    To understand and improve DRAM performance, reliability, security and energy efficiency, prior works study characteristics of commodity DRAM chips. Unfortunately, state-of-the-art open source infrastructures capable of conducting such studies are obsolete, poorly supported, or difficult to use, or their inflexibility limit the types of studies they can conduct. We propose DRAM Bender, a new FPGA-based infrastructure that enables experimental studies on state-of-the-art DRAM chips. DRAM Bender offers three key features at the same time. First, DRAM Bender enables directly interfacing with a DRAM chip through its low-level interface. This allows users to issue DRAM commands in arbitrary order and with finer-grained time intervals compared to other open source infrastructures. Second, DRAM Bender exposes easy-to-use C++ and Python programming interfaces, allowing users to quickly and easily develop different types of DRAM experiments. Third, DRAM Bender is easily extensible. The modular design of DRAM Bender allows extending it to (i) support existing and emerging DRAM interfaces, and (ii) run on new commercial or custom FPGA boards with little effort. To demonstrate that DRAM Bender is a versatile infrastructure, we conduct three case studies, two of which lead to new observations about the DRAM RowHammer vulnerability. In particular, we show that data patterns supported by DRAM Bender uncovers a larger set of bit-flips on a victim row compared to the data patterns commonly used by prior work. We demonstrate the extensibility of DRAM Bender by implementing it on five different FPGAs with DDR4 and DDR3 support. DRAM Bender is freely and openly available at https://github.com/CMU-SAFARI/DRAM-Bender.Comment: To appear in TCAD 202

    LIPIcs, Volume 274, ESA 2023, Complete Volume

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    LIPIcs, Volume 274, ESA 2023, Complete Volum

    Fundamentals

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    Volume 1 establishes the foundations of this new field. It goes through all the steps from data collection, their summary and clustering, to different aspects of resource-aware learning, i.e., hardware, memory, energy, and communication awareness. Machine learning methods are inspected with respect to resource requirements and how to enhance scalability on diverse computing architectures ranging from embedded systems to large computing clusters

    Boustrophedonic Frames: Quasi-Optimal L2 Caching for Textures in GPUs

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    © 2023 Copyright held by the owner/author(s). This document is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ This document is the Accepted version of a Published Work that appeared in final form in 32nd International Conference on Parallel Architectures and Compilation Techniques (PACT), Viena, Austria, October 2023. To access the final edited and published work see https://doi.org/10.1109/PACT58117.2023.00019Literature is plentiful in works exploiting cache locality for GPUs. A majority of them explore replacement or bypassing policies. In this paper, however, we surpass this exploration by fabricating a formal proof for a no-overhead quasi-optimal caching technique for caching textures in graphics workloads. Textures make up a significant part of main memory traffic in mobile GPUs, which contributes to the total GPU energy consumption. Since texture accesses use a shared L2 cache, improving the L2 texture caching efficiency would decrease main memory traffic, thus improving energy efficiency, which is crucial for mobile GPUs. Our proposal reaches quasi-optimality by exploiting the frame-to-frame reuse of textures in graphics. We do this by traversing frames in a boustrophedonic1 manner w.r.t. the frame-to-frame tile order. We first approximate the texture access trace to a circular trace and then forge a formal proof for our proposal being optimal for such traces. We also complement the proof with empirical data that demonstrates the quasi-optimality of our no-cost proposal

    Design and Code Optimization for Systems with Next-generation Racetrack Memories

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    With the rise of computationally expensive application domains such as machine learning, genomics, and fluids simulation, the quest for performance and energy-efficient computing has gained unprecedented momentum. The significant increase in computing and memory devices in modern systems has resulted in an unsustainable surge in energy consumption, a substantial portion of which is attributed to the memory system. The scaling of conventional memory technologies and their suitability for the next-generation system is also questionable. This has led to the emergence and rise of nonvolatile memory ( NVM ) technologies. Today, in different development stages, several NVM technologies are competing for their rapid access to the market. Racetrack memory ( RTM ) is one such nonvolatile memory technology that promises SRAM -comparable latency, reduced energy consumption, and unprecedented density compared to other technologies. However, racetrack memory ( RTM ) is sequential in nature, i.e., data in an RTM cell needs to be shifted to an access port before it can be accessed. These shift operations incur performance and energy penalties. An ideal RTM , requiring at most one shift per access, can easily outperform SRAM . However, in the worst-cast shifting scenario, RTM can be an order of magnitude slower than SRAM . This thesis presents an overview of the RTM device physics, its evolution, strengths and challenges, and its application in the memory subsystem. We develop tools that allow the programmability and modeling of RTM -based systems. For shifts minimization, we propose a set of techniques including optimal, near-optimal, and evolutionary algorithms for efficient scalar and instruction placement in RTMs . For array accesses, we explore schedule and layout transformations that eliminate the longer overhead shifts in RTMs . We present an automatic compilation framework that analyzes static control flow programs and transforms the loop traversal order and memory layout to maximize accesses to consecutive RTM locations and minimize shifts. We develop a simulation framework called RTSim that models various RTM parameters and enables accurate architectural level simulation. Finally, to demonstrate the RTM potential in non-Von-Neumann in-memory computing paradigms, we exploit its device attributes to implement logic and arithmetic operations. As a concrete use-case, we implement an entire hyperdimensional computing framework in RTM to accelerate the language recognition problem. Our evaluation shows considerable performance and energy improvements compared to conventional Von-Neumann models and state-of-the-art accelerators

    Side-Channel Analysis and Cryptography Engineering : Getting OpenSSL Closer to Constant-Time

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    As side-channel attacks reached general purpose PCs and started to be more practical for attackers to exploit, OpenSSL adopted in 2005 a flagging mechanism to protect against SCA. The opt-in mechanism allows to flag secret values, such as keys, with the BN_FLG_CONSTTIME flag. Whenever a flag is checked and detected, the library changes its execution flow to SCA-secure functions that are slower but safer, protecting these secret values from being leaked. This mechanism favors performance over security, it is error-prone, and is obscure for most library developers, increasing the potential for side-channel vulnerabilities. This dissertation presents an extensive side-channel analysis of OpenSSL and criticizes its fragile flagging mechanism. This analysis reveals several flaws affecting the library resulting in multiple side-channel attacks, improved cache-timing attack techniques, and a new side channel vector. The first part of this dissertation introduces the main topic and the necessary related work, including the microarchitecture, the cache hierarchy, and attack techniques; then it presents a brief troubled history of side-channel attacks and defenses in OpenSSL, setting the stage for the related publications. This dissertation includes seven original publications contributing to the area of side-channel analysis, microarchitecture timing attacks, and applied cryptography. From an SCA perspective, the results identify several vulnerabilities and flaws enabling protocol-level attacks on RSA, DSA, and ECDSA, in addition to full SCA of the SM2 cryptosystem. With respect to microarchitecture timing attacks, the dissertation presents a new side-channel vector due to port contention in the CPU execution units. And finally, on the applied cryptography front, OpenSSL now enjoys a revamped code base securing several cryptosystems against SCA, favoring a secure-by-default protection against side-channel attacks, instead of the insecure opt-in flagging mechanism provided by the fragile BN_FLG_CONSTTIME flag

    Optimización del rendimiento y la eficiencia energética en sistemas masivamente paralelos

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    RESUMEN Los sistemas heterogéneos son cada vez más relevantes, debido a sus capacidades de rendimiento y eficiencia energética, estando presentes en todo tipo de plataformas de cómputo, desde dispositivos embebidos y servidores, hasta nodos HPC de grandes centros de datos. Su complejidad hace que sean habitualmente usados bajo el paradigma de tareas y el modelo de programación host-device. Esto penaliza fuertemente el aprovechamiento de los aceleradores y el consumo energético del sistema, además de dificultar la adaptación de las aplicaciones. La co-ejecución permite que todos los dispositivos cooperen para computar el mismo problema, consumiendo menos tiempo y energía. No obstante, los programadores deben encargarse de toda la gestión de los dispositivos, la distribución de la carga y la portabilidad del código entre sistemas, complicando notablemente su programación. Esta tesis ofrece contribuciones para mejorar el rendimiento y la eficiencia energética en estos sistemas masivamente paralelos. Se realizan propuestas que abordan objetivos generalmente contrapuestos: se mejora la usabilidad y la programabilidad, a la vez que se garantiza una mayor abstracción y extensibilidad del sistema, y al mismo tiempo se aumenta el rendimiento, la escalabilidad y la eficiencia energética. Para ello, se proponen dos motores de ejecución con enfoques completamente distintos. EngineCL, centrado en OpenCL y con una API de alto nivel, favorece la máxima compatibilidad entre todo tipo de dispositivos y proporciona un sistema modular extensible. Su versatilidad permite adaptarlo a entornos para los que no fue concebido, como aplicaciones con ejecuciones restringidas por tiempo o simuladores HPC de dinámica molecular, como el utilizado en un centro de investigación internacional. Considerando las tendencias industriales y enfatizando la aplicabilidad profesional, CoexecutorRuntime proporciona un sistema flexible centrado en C++/SYCL que dota de soporte a la co-ejecución a la tecnología oneAPI. Este runtime acerca a los programadores al dominio del problema, posibilitando la explotación de estrategias dinámicas adaptativas que mejoran la eficiencia en todo tipo de aplicaciones.ABSTRACT Heterogeneous systems are becoming increasingly relevant, due to their performance and energy efficiency capabilities, being present in all types of computing platforms, from embedded devices and servers to HPC nodes in large data centers. Their complexity implies that they are usually used under the task paradigm and the host-device programming model. This strongly penalizes accelerator utilization and system energy consumption, as well as making it difficult to adapt applications. Co-execution allows all devices to simultaneously compute the same problem, cooperating to consume less time and energy. However, programmers must handle all device management, workload distribution and code portability between systems, significantly complicating their programming. This thesis offers contributions to improve performance and energy efficiency in these massively parallel systems. The proposals address the following generally conflicting objectives: usability and programmability are improved, while ensuring enhanced system abstraction and extensibility, and at the same time performance, scalability and energy efficiency are increased. To achieve this, two runtime systems with completely different approaches are proposed. EngineCL, focused on OpenCL and with a high-level API, provides an extensible modular system and favors maximum compatibility between all types of devices. Its versatility allows it to be adapted to environments for which it was not originally designed, including applications with time-constrained executions or molecular dynamics HPC simulators, such as the one used in an international research center. Considering industrial trends and emphasizing professional applicability, CoexecutorRuntime provides a flexible C++/SYCL-based system that provides co-execution support for oneAPI technology. This runtime brings programmers closer to the problem domain, enabling the exploitation of dynamic adaptive strategies that improve efficiency in all types of applications.Funding: This PhD has been supported by the Spanish Ministry of Education (FPU16/03299 grant), the Spanish Science and Technology Commission under contracts TIN2016-76635-C2-2-R and PID2019-105660RB-C22. This work has also been partially supported by the Mont-Blanc 3: European Scalable and Power Efficient HPC Platform based on Low-Power Embedded Technology project (G.A. No. 671697) from the European Union’s Horizon 2020 Research and Innovation Programme (H2020 Programme). Some activities have also been funded by the Spanish Science and Technology Commission under contract TIN2016-81840-REDT (CAPAP-H6 network). The Integration II: Hybrid programming models of Chapter 4 has been partially performed under the Project HPC-EUROPA3 (INFRAIA-2016-1-730897), with the support of the EC Research Innovation Action under the H2020 Programme. In particular, the author gratefully acknowledges the support of the SPMT Department of the High Performance Computing Center Stuttgart (HLRS)
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