4 research outputs found

    GenArchBench: Porting and Optimizing a Genomics Benchmark Suite to Arm-based HPC Processors

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    Arm usage has substantially grown in the High-Performance Computing (HPC) community. Japanese supercomputer Fugaku, powered by Arm-based A64FX processors, held the top position on the Top500 list between June 2020 and June 2022, currently sitting in the second position. The recently released 7th generation of Amazon EC2 instances for compute-intensive workloads (C7g) is also powered by Arm Graviton3 processors. Projects like European Mont-Blanc and U.S. DOE/NNSA Astra are further examples of Arm irruption in HPC. In parallel, over the last decade, the rapid improvement of genomic sequencing technologies and the exponential growth of sequencing data has placed a significant bottleneck on the computational side. While the majority of genomics applications have been thoroughly tested and optimized for x86 systems, just a few are prepared to perform efficiently on Arm machines, let alone exploit the advantages of the newly introduced Scalable Vector Extensions (SVE). This thesis presents GenArchBench, the first genome analysis benchmark suite targeting Arm architectures. We have selected a set of computationally demanding kernels from the most widely used tools in genome data analysis and ported them to Arm-based A64FX and Graviton3 processors. The porting features the usage of the novel Arm SVE instructions, algorithmic and code optimizations, and the exploitation of Arm-optimized libraries. All in all, the GenArch benchmark suite comprises 13 multi-core kernels from critical stages of widely-used genome analysis pipelines, including base-calling, read mapping, variant calling, and genome assembly. Moreover, our benchmark suite includes different input data sets per kernel (small and large), each with a corresponding regression test to verify the correctness of each execution automatically. In this work, we present the optimizations implemented in each kernel and a detailed performance evaluation and comparison of their performance on four different architectures (i.e., A64FX, Graviton3, Intel Xeon Platinum, and AMD EPYC). Additionally, as proof of the impact of this work, we study the performance improvement in a production-ready genomics pipeline using the GenArchBench optimized kernels

    Dependable Embedded Systems

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    This Open Access book introduces readers to many new techniques for enhancing and optimizing reliability in embedded systems, which have emerged particularly within the last five years. This book introduces the most prominent reliability concerns from today’s points of view and roughly recapitulates the progress in the community so far. Unlike other books that focus on a single abstraction level such circuit level or system level alone, the focus of this book is to deal with the different reliability challenges across different levels starting from the physical level all the way to the system level (cross-layer approaches). The book aims at demonstrating how new hardware/software co-design solution can be proposed to ef-fectively mitigate reliability degradation such as transistor aging, processor variation, temperature effects, soft errors, etc. Provides readers with latest insights into novel, cross-layer methods and models with respect to dependability of embedded systems; Describes cross-layer approaches that can leverage reliability through techniques that are pro-actively designed with respect to techniques at other layers; Explains run-time adaptation and concepts/means of self-organization, in order to achieve error resiliency in complex, future many core systems

    Design and Experimental Evaluation of a Hybrid Wheeled-Leg Exploration Rover in the Context of Multi-Robot Systems

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    With this dissertation, the electromechanic design, implementation, locomotion control, and experimental evaluation of a novel type of hybrid wheeled-leg exploration rover are presented. The actively articulated suspension system of the rover is the basis for advanced locomotive capabilities of a mobile exploration robot. The developed locomotion control system abstracts the complex kinematics of the suspension system and provides platform control inputs usable by autonomous behaviors or human remote control. Design and control of the suspension system as well as experimentation with the resulting rover are in the focus of this thesis. The rover is part of a heterogeneous modular multi-robot exploration system with an aspired sample return mission to the lunar south pole or currently hard-to-access regions on Mars. The multi-robot system pursues a modular and reconfigurable design methodology. It combines heterogeneous robots with different locomotion capabilities for enhanced overall performance. Consequently, the design of the multi-robot system is presented as the frame of the rover developments. The requirements for the rover design originating from the deployment in a modular multi-robot system are accentuated and summarized in this thesis
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