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Genomics-GPU: A Benchmark Suite for GPU-accelerated Genome Analysis

Genomics-GPU: A Benchmark Suite for GPU-accelerated Genome A...

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ieee international symposium on performance Analysis of Systems and Software (ISPASS)

作者： Liu, Zhuren Zhang, Shouzhe Garrigus, Justin Zhao, Hui Univ North Texas Dept Comp Sci & Engn Denton TX 76203 USA

ISBN: (纸本)9798350397390

Genomic analysis is the study of genes which includes the identification, measurement, or comparison of genomic features. Genomics research is of great importance to our society because it can be used to detect diseases, create vaccines, and develop drugs and treatments. As a type of general-purpose accelerators with massive parallel processing capability, GPUs have been recently used for genomics analysis. Developing GPU-based hardware and software frameworks for genome analysis is becoming a promising research area. To support this type of research, benchmarks are needed that can feature representative, concurrent, and diverse applications running on GPUs. In this work, we created a benchmark suite called Genomics-GPU, which contains 10 widely-used genomic analysis applications. It covers genome comparison, matching, and clustering for DNAs and RNAs. We also adapted these applications to exploit the CUDA Dynamic Parallelism (CDP), a recent advanced feature supporting dynamic GPU programming, to further improve the performance. Our benchmark suite can serve as a basis for algorithm optimization and also facilitate GPU architecture development for genomics analysis.

关键词： genomics bioinformatics benchmarking GPU accelerated computing genome analysis computer architecture

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Mapping quantum algorithms to multi-core quantum computing architectures 56

Mapping quantum algorithms to multi-core quantum computing a...

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56th ieee international symposium on Circuits and Systems (ISCAS)

作者： Ovide, Anabel Rodrigo, Santiago Bandic, Medina Van Someren, Hans Feld, Sebastian Abadal, Sergi Alarcon, Eduard Almudever, Carmen G. Univ Politecn Valencia Valencia Spain Tech Univ Catalonia BarcelonaTech Barcelona Spain Delft Univ Technol Delft Netherlands

ISBN: (纸本)9781665451093

Current monolithic quantum computer architectures have limited scalability. One promising approach for scaling them up is to use a modular or multi-core architecture, in which different quantum processors (cores) are connected via quantum and classical links. This new architectural design poses new challenges such as the expensive inter-core communication. To reduce these movements when executing a quantum algorithm, an efficient mapping technique is required. In this paper, a detailed critical discussion of the quantum circuit mapping problem for multi-core quantum computing architectures is provided. In addition, we further explore the performance of a mapping method, which is formulated as a partitioning over time graph problem, by performing an architectural scalability analysis.

关键词： scalability quantum computing systems multicore quantum computers mapping of quantum algorithms

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Geo-Distributed Analytical Streaming architecture for IoT Platforms

Geo-Distributed Analytical Streaming Architecture for IoT Pl...

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2024 ieee international Conference on Cluster computing, CLUSTER 2024

作者： Hoseiny Farahabady, M. Reza Zomaya, Albert Y. The University of Sydney School of Computer Science Center for Distributed and High Performance Computing SydneyNSW2006 Australia

ISBN: (纸本)9798350358711

The surge in real-time IoT data introduces scalability and computational challenges, necessitating advanced architectural and technological solutions. Streamed data processing is increasingly adopted across industries to enhance operational efficiency by extracting insights from vast, unstructured datasets. However, complex analytical tasks, such as multi-join queries, often require stateful iterative calculations on high-volume, high-velocity data, which challenges conventional programming models like MapReduce. This paper introduces an architectural model enabling application developers to create intricate streaming computational logic within an IoT platform. Our architecture supports scalable applications across distributed edge-tier nodes, particularly for iterative analytical operations on streamed data. We discuss core concepts and a timestamp model (borrowed from the timely data-flow concept) attached to data items circulating between computational blocks, which can execute concurrently on different edge-tier nodes. Additionally, we detail a buffer management mechanism that dynamically adjusts memory size in each computational block on nodes with limited capacity. This mechanism considers application performance requirements and runtime conditions to optimize buffer sizes. performance evaluation against cloud-tier alternatives confirms the effectiveness of our solution. Experimental results show a significant reduction in p-99 delay compared to cloud-tier deployment with a database engine for analytical applications involving multi-join operations. © 2024 ieee.

关键词： MapReduce

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Implementation of Radio Wave Propagation using RT Cores and Consideration of Programming Models

Implementation of Radio Wave Propagation using RT Cores and ...

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37th ieee international Parallel and Distributed Processing symposium (IPDPS)

作者： Hashinoki, Shinya Ohshima, Satoshi Katagiri, Takahiro Nagai, Torn Hoshino, Tetsuya Nagoya Univ Grad Sch Informat Nagoya Aichi Japan Nagoya Univ Informat Technol Ctr Nagoya Aichi Japan

ISBN: (纸本)9798350311990

With the NVIDIA Turing architecture generation, several NVIDIA graphics processing units (GPUs) have introduced ray tracing acceleration hardware (RT cores). Ray tracing processing can be regarded as a simulation of wave and particle propagation, collision, and reflection. Therefore, it is expected to be applied to computational science and highperformance computing. However, few studies have been conducted using RT cores. The purpose of this research is to demonstrate the use of RT cores in the scientific and technical computing fields. We implemented a radio wave propagation loss calculation with the programmable ray tracing application framework OptiX and evaluated its performance. Furthermore, we investigated the challenges of reducing the description of framework-specific settings and the needs of hardware allocation. In the simple two spheres experiment, the RT core implementation showed the highest performance. Moreover, the acceleration was super linear scaling, between (10000, 5000) and (20000, 10000). In the experiment with a sphere and planes, the performance achieved by the RT cores was up to approximately 390 times higher than the parallel execution of the BVH search algorithm. We also proved that a large number of RT cores yielded higher performance. In the open data problem space experiment, we evaluated various GPUs and revealed that a larger number of RT cores is effective. These results show that RT cores are sufficiently effective for radio propagation calculations with an adequate number of ray projections. Through this research, we contributed to the RT core use in computational science by proposing an implementation method for ray tracing applications and revealing the effects of RT cores in radio wave propagation loss calculations.

关键词： high-performance computing ray tracing RT core radio wave propagation

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high performance Optimized and Unified Bus Monitor for Distributed Avionics architecture Validation under Hardware-in-Loop Simulation Framework 12

High Performance Optimized and Unified Bus Monitor for Distr...

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12th international Conference on Current Trends in Advanced computing, ICCTAC 2024

作者： Karvande, Rajesh Shankar Madhavi, Tatineni 'f' RCI DRDO TS Hyderabad India EECE GITAM TS Hyderabad India

ISBN: (纸本)9798350395808

The Avionics system of the aerospace and defense industry designed with complex distributed architecture. Every system is intelligent and processing data on it's own. The subsystems communicate with the onboard computer which is the main unit of avionics system. This data exchange is based mostly on serial communication with a maximum rate of 1 Mbps. Many data communication protocols are available;among them most popular is the MIL-STD-1553 because of dual redundant and simple architecture. The data traffic on the MIL-STD 1553 bus is monitored and recorded on the Bus Monitor. The configuration was one Bus Monitor for one communication node. In the case of multi-mode avionics configuration more than one Bus-Monitor is essential to integrate. These Bus Monitor configured separately with no synchronization among them. The development of a single computer-based multi-node optimized Bus Monitor for distributed architecture is designed and developed. The new design and development process of optimized multi-mode Bus Monitor under the real time Linux platform is explained in this paper. Further, the unified Bus-Monitor for number of aerospace project's configuration is developed and deployed on high performance processor architecture with optimized embedded computer. The development has been done for Hardware-In-Loop Simulation facility that is used for validation of avionics software © 2024 ieee.

关键词： Buses

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PIMCloud: QoS-Aware Resource Management of Latency-Critical Applications in Clouds with Processing-in-Memory 28

PIMCloud: QoS-Aware Resource Management of Latency-Critical ...

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28th Annual ieee international symposium on high-performance computer architecture (HPCA)

作者： Chen, Shuang Jiang, Yi Delimitrou, Christina Martinez, Jose F. Cornell Univ Comp Syst Lab Ithaca NY 14850 USA

ISBN: (纸本)9781665420273

The slowdown of Moore's Law, combined with advances in 3D stacking of logic and memory, have pushed architects to revisit the concept of processing-in-memory (PIM) to overcome the memory wall bottleneck. This PIM renaissance finds itself in a very different computing landscape from the one twenty years ago, as more and more computation shifts to the cloud. Most PIM architecture papers still focus on best-effort applications, while PIM's impact on latency-critical cloud applications is not well understood. This paper explores how datacenters can exploit PIM architectures in the context of latency-critical applications. We adopt a general-purpose cloud server with HBM-based, 3D stacked logic+memory modules, and study the impact of PIM on six diverse interactive cloud applications. We reveal the previously neglected opportunity that PIM presents to these services, and show the importance of properly managing PIM-related resources to meet the QoS targets of interactive services and maximize resource efficiency. Then, we present PIMCloud, a QoS-aware resource manager designed for cloud systems with PIM allowing colocation of multiple latency-critical and best-effort applications. We show that PIMCloud efficiently manages PIM resources: it (1) improves effective machine utilization by up to 70% and 85% (average 24% and 33%) under 2-app and 3-app mixes, compared to the best state-of-the-art manager;(2) helps latency-critical applications meet QoS;and (3) adapts to varying load patterns.

关键词： Three-dimensional displays Stacking Quality of service computer architecture Resource management Servers

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Application Defined On-chip Networks for Heterogeneous Chiplets: An Implementation Perspective 28

Application Defined On-chip Networks for Heterogeneous Chipl...

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28th Annual ieee international symposium on high-performance computer architecture (HPCA)

作者： Wang, Tianqi Feng, Fan Xiang, Shaolin Li, Qi Xia, Jing Huawei Shenzhen Peoples R China

ISBN: (纸本)9781665420273

With the help of advanced packaging technologies to integrate multiple chips (e.g., CPU, AI, IO), a chiplet-based SoC design process can enable fast system construction. However, the design of network-on-chip used within the individual chiplets and across chiplets is an extremly challenge. We introduce the design process and methodology of a bufferless multi-ring NoC for heterogeneous chiplet-based SoC. Our design is portable and can be used in diverse scenarios, like Server-CPU, AI-Processor, and Baseband-Processor. The co-design of the application, architecture, and implementation is the key to make the system power efficient and high performance. We determined many architectural design choices by reflecting an analysis of a set of target applications by application teams and several physical implementation constraints provided by development teams. In this paper, we present the pragmatic practice of our co-design effort for the NoC. As a result, the system has been proven to achieve 16TB/s bandwidth in an AI processor and low latency, in a server CPU with nearly one hundred cores.

关键词： Design methodology computer architecture Bandwidth Network-on-chip Packaging Energy efficiency Servers

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AFS: Accurate, Fast, and Scalable Error-Decoding for Fault-Tolerant Quantum computers 28

AFS: Accurate, Fast, and Scalable Error-Decoding for Fault-T...

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28th Annual ieee international symposium on high-performance computer architecture (HPCA)

作者： Das, Poulami Pattison, Christopher A. Manne, Srilatha Carmean, Douglas M. Svore, Krysta M. Qureshi, Moinuddin Delfosse, Nicolas Georgia Inst Technol Atlanta GA 30332 USA CALTECH Pasadena CA 91125 USA Microsoft Quantum Redmond WA USA Microsoft Res Redmond WA USA

ISBN: (纸本)9781665420273

Quantum computers promise computational advantages for many important problems across various application domains. Unfortunately, physical quantum devices are highly susceptible to errors that limit us from running most of these quantum applications. Quantum Error Correction (QEC) codes are required to implement Fault-Tolerant Quantum computers (FTQC) on which computations can be performed without encountering errors. Error decoding is a critical component of quantum error correction and is responsible for transforming a set of qubit measurements generated by the QEC code, called the syndrome, into error locations and error types. For the feasibility of implementation, error decoders must not only identify errors with high accuracy, but also be fast and scalable to a large number of qubits. Unfortunately, most of the prior works on error decoding have focused primarily only on the accuracy and have relied on software implementations that are too slow to be of practical use. Furthermore, these studies only look at designing a single decoder and do not analyze the challenges involved in scaling the storage and bandwidth requirements when performing error correction in large systems with thousands of qubits. In this paper, we present AFS, an accurate, fast, and scalable decoder architecture that is designed to operate in the context of systems with hundreds of logical qubits. We present the hardware implementation of AFS, which is based on the Union Find decoding algorithm and employs a three-stage pipelined design. AFS provides orders of magnitude higher accuracy compared to recent SFQ-based hardware decoders (logical error rate of 6 x 10(-10) for physical error rate of 10(-3)) and low decoding latency (42ns on average), while being robust to measurement errors introduced while extracting syndromes during the QEC cycles. We also reduce the amount of decoding hardware required to perform QEC simultaneously on all the logical qubits by co-designing the micro-architectur

关键词： Quantum computing Quantum error correction Fault-tolerant quantum computing Decoding Union-Find decoding Surface codes

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performance Analysis and Optimization of Nvidia H100 Confidential computing for AI Workloads 22

Performance Analysis and Optimization of Nvidia H100 Confide...

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22nd ieee international symposium on Parallel and Distributed Processing with Applications, ISPA 2024

作者： Tan, Yifan Mi, Zeyu Institute of Parallel and Distributed Systems Seiee Shanghai Jiao Tong University China

ISBN: (纸本)9798331509712

NVIDIA's H100 Confidential computing (CC) counters the security hazards inherent in cloud AI workloads. It enforces data encryption to achieve data confidentiality, which leads to substantial throughput reductions as high as 93% in various AI workloads (such as TensorRT, PEFT and vLLM). Confronting this substantial overhead issue, we first delve into the underlying causes through meticulous analysis. This groundwork enables us to devise an innovative runtime system that operates seamlessly in the background, completely transparent to end-users. The cornerstone of our system lies in leveraging multiple encryption workers. Experiments demonstrate that our solution effectively reduces throughput drop to less than 28.1%. © 2024 ieee.

关键词： Confidential computing GPU H100 LLM

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Meta360: Exploring User-Specific and Robust Viewport Prediction in 360-Degree Videos through Bi-Directional LSTM and Meta-Adaptation 22

Meta360: Exploring User-Specific and Robust Viewport Predict...

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22nd ieee international symposium on Mixed and Augmented Reality (ISMAR)

作者： Li, Junjie Wang, Yumei Liu, Yu Beijing Univ Posts & Telecommun Beijing Peoples R China

ISBN: (纸本)9798350328387

Viewport prediction is a critical aspect of virtual reality (VR) video streaming, directly impacting user experience in adaptive streaming. However, most existing algorithms treat users as homogeneous entities and overlook the variations in user behaviors and video content. Additionally, they often struggle with long-term predictions and intense movement. Our research sheds light on the importance of considering user behavior variations and leveraging advanced techniques to optimize robust viewport prediction in VR video streaming. First, we address these limitations by conducting a comprehensive feature analysis on existing datasets to uncover distinctive user behaviors. Building upon these findings, we propose a novel approach that utilizes the power of Bidirectional Long Short-Term Memory (BiLSTM) networks and meta-learning. The BiLSTM architecture effectively captures long-term dependencies, which can strengthen the robustness of viewport prediction especially in long-term prediction and intense movement. Additionally, meta-learning enables personalized adaptation to individual users' viewing behaviors. Through extensive evaluations on diverse datasets, our algorithm Meta360 demonstrates superior performance in terms of accuracy and robustness compared to state-of-the-art methods.

关键词： Human-centered computing Human computer interaction (HCI) Interaction paradigms Virtual reality computing methodologies Artificial intelligence computer vision computer vision problems

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