2,906 research outputs found

    Faster inference from state space models via GPU computing

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    Funding: C.F.-J. is funded via a doctoral scholarship from the University of St Andrews, School of Mathematics and Statistics.Inexpensive Graphics Processing Units (GPUs) offer the potential to greatly speed up computation by employing their massively parallel architecture to perform arithmetic operations more efficiently. Population dynamics models are important tools in ecology and conservation. Modern Bayesian approaches allow biologically realistic models to be constructed and fitted to multiple data sources in an integrated modelling framework based on a class of statistical models called state space models. However, model fitting is often slow, requiring hours to weeks of computation. We demonstrate the benefits of GPU computing using a model for the population dynamics of British grey seals, fitted with a particle Markov chain Monte Carlo algorithm. Speed-ups of two orders of magnitude were obtained for estimations of the log-likelihood, compared to a traditional ‘CPU-only’ implementation, allowing for an accurate method of inference to be used where this was previously too computationally expensive to be viable. GPU computing has enormous potential, but one barrier to further adoption is a steep learning curve, due to GPUs' unique hardware architecture. We provide a detailed description of hardware and software setup, and our case study provides a template for other similar applications. We also provide a detailed tutorial-style description of GPU hardware architectures, and examples of important GPU-specific programming practices.Publisher PDFPeer reviewe

    GPU-optimized approaches to molecular docking-based virtual screening in drug discovery: A comparative analysis

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    Finding a novel drug is a very long and complex procedure. Using computer simulations, it is possible to accelerate the preliminary phases by performing a virtual screening that filters a large set of drug candidates to a manageable number. This paper presents the implementations and comparative analysis of two GPU-optimized implementations of a virtual screening algorithm targeting novel GPU architectures. This work focuses on the analysis of parallel computation patterns and their mapping onto the target architecture. The first method adopts a traditional approach that spreads the computation for a single molecule across the entire GPU. The second uses a novel batched approach that exploits the parallel architecture of the GPU to evaluate more molecules in parallel. Experimental results showed a different behavior depending on the size of the database to be screened, either reaching a performance plateau sooner or having a more extended initial transient period to achieve a higher throughput (up to 5x), which is more suitable for extreme-scale virtual screening campaigns

    Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs

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    Virtual screening is an early stage in the drug discovery process that selects the most promising candidates. In the urgent computing scenario, finding a solution in the shortest time frame is critical. Any improvement in the performance of a virtual screening application translates into an increase in the number of candidates evaluated, thereby raising the probability of finding a drug. In this paper, we show how we can improve application throughput using Out-of-kernel optimizations. They use input features, kernel requirements, and architectural features to rearrange the kernel inputs, executing them out of order, to improve the computation efficiency. These optimizations’ implementations are designed on an extreme-scale virtual screening application, named LiGen, that can hinge on CUDA and SYCL kernels to carry out the computation on modern supercomputer nodes. Even if they are tailored to a single application, they might also be of interest for applications that share a similar design pattern. The experimental results show how these optimizations can increase kernel performance by 2 X, respectively, up to 2.2X in CUDA and up to 1.9X, in SYCL. Moreover, the reported speedup can be achieved with the best-proposed parameterization, as shown by the data we collected and reported in this manuscript

    Resource-aware scheduling for 2D/3D multi-/many-core processor-memory systems

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    This dissertation addresses the complexities of 2D/3D multi-/many-core processor-memory systems, focusing on two key areas: enhancing timing predictability in real-time multi-core processors and optimizing performance within thermal constraints. The integration of an increasing number of transistors into compact chip designs, while boosting computational capacity, presents challenges in resource contention and thermal management. The first part of the thesis improves timing predictability. We enhance shared cache interference analysis for set-associative caches, advancing the calculation of Worst-Case Execution Time (WCET). This development enables accurate assessment of cache interference and the effectiveness of partitioned schedulers in real-world scenarios. We introduce TCPS, a novel task and cache-aware partitioned scheduler that optimizes cache partitioning based on task-specific WCET sensitivity, leading to improved schedulability and predictability. Our research explores various cache and scheduling configurations, providing insights into their performance trade-offs. The second part focuses on thermal management in 2D/3D many-core systems. Recognizing the limitations of Dynamic Voltage and Frequency Scaling (DVFS) in S-NUCA many-core processors, we propose synchronous thread migrations as a thermal management strategy. This approach culminates in the HotPotato scheduler, which balances performance and thermal safety. We also introduce 3D-TTP, a transient temperature-aware power budgeting strategy for 3D-stacked systems, reducing the need for Dynamic Thermal Management (DTM) activation. Finally, we present 3QUTM, a novel method for 3D-stacked systems that combines core DVFS and memory bank Low Power Modes with a learning algorithm, optimizing response times within thermal limits. This research contributes significantly to enhancing performance and thermal management in advanced processor-memory systems

    Towards a centralized multicore automotive system

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    Today’s automotive systems are inundated with embedded electronics to host chassis, powertrain, infotainment, advanced driver assistance systems, and other modern vehicle functions. As many as 100 embedded microcontrollers execute hundreds of millions of lines of code in a single vehicle. To control the increasing complexity in vehicle electronics and services, automakers are planning to consolidate different on-board automotive functions as software tasks on centralized multicore hardware platforms. However, these vehicle software services have different and contrasting timing, safety, and security requirements. Existing vehicle operating systems are ill-equipped to provide all the required service guarantees on a single machine. A centralized automotive system aims to tackle this by assigning software tasks to multiple criticality domains or levels according to their consequences of failures, or international safety standards like ISO 26262. This research investigates several emerging challenges in time-critical systems for a centralized multicore automotive platform and proposes a novel vehicle operating system framework to address them. This thesis first introduces an integrated vehicle management system (VMS), called DriveOSℱ, for a PC-class multicore hardware platform. Its separation kernel design enables temporal and spatial isolation among critical and non-critical vehicle services in different domains on the same machine. Time- and safety-critical vehicle functions are implemented in a sandboxed Real-time Operating System (OS) domain, and non-critical software is developed in a sandboxed general-purpose OS (e.g., Linux, Android) domain. To leverage the advantages of model-driven vehicle function development, DriveOS provides a multi-domain application framework in Simulink. This thesis also presents a real-time task pipeline scheduling algorithm in multiprocessors for communication between connected vehicle services with end-to-end guarantees. The benefits and performance of the overall automotive system framework are demonstrated with hardware-in-the-loop testing using real-world applications, car datasets and simulated benchmarks, and with an early-stage deployment in a production-grade luxury electric vehicle

    Efficient GPU Offloading with OpenMP for a Hyperbolic Finite Volume Solver on Dynamically Adaptive Meshes

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    We identify and show how to overcome an OpenMP bottleneck in the administration of GPU memory. It arises for a wave equation solver on dynamically adaptive block-structured Cartesian meshes, which keeps all CPU threads busy and allows all of them to offload sets of patches to the GPU. Our studies show that multithreaded, concurrent, non-deterministic access to the GPU leads to performance breakdowns, since the GPU memory bookkeeping as offered through OpenMP’s map clause, i.e., the allocation and freeing, becomes another runtime challenge besides expensive data transfer and actual computation. We, therefore, propose to retain the memory management responsibility on the host: A caching mechanism acquires memory on the accelerator for all CPU threads, keeps hold of this memory and hands it out to the offloading threads upon demand. We show that this user-managed, CPU-based memory administration helps us to overcome the GPU memory bookkeeping bottleneck and speeds up the time-to-solution of Finite Volume kernels by more than an order of magnitude

    ACiS: smart switches with application-level acceleration

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    Network performance has contributed fundamentally to the growth of supercomputing over the past decades. In parallel, High Performance Computing (HPC) peak performance has depended, first, on ever faster/denser CPUs, and then, just on increasing density alone. As operating frequency, and now feature size, have levelled off, two new approaches are becoming central to achieving higher net performance: configurability and integration. Configurability enables hardware to map to the application, as well as vice versa. Integration enables system components that have generally been single function-e.g., a network to transport data—to have additional functionality, e.g., also to operate on that data. More generally, integration enables compute-everywhere: not just in CPU and accelerator, but also in network and, more specifically, the communication switches. In this thesis, we propose four novel methods of enhancing HPC performance through Advanced Computing in the Switch (ACiS). More specifically, we propose various flexible and application-aware accelerators that can be embedded into or attached to existing communication switches to improve the performance and scalability of HPC and Machine Learning (ML) applications. We follow a modular design discipline through introducing composable plugins to successively add ACiS capabilities. In the first work, we propose an inline accelerator to communication switches for user-definable collective operations. MPI collective operations can often be performance killers in HPC applications; we seek to solve this bottleneck by offloading them to reconfigurable hardware within the switch itself. We also introduce a novel mechanism that enables the hardware to support MPI communicators of arbitrary shape and that is scalable to very large systems. In the second work, we propose a look-aside accelerator for communication switches that is capable of processing packets at line-rate. Functions requiring loops and states are addressed in this method. The proposed in-switch accelerator is based on a RISC-V compatible Coarse Grained Reconfigurable Arrays (CGRAs). To facilitate usability, we have developed a framework to compile user-provided C/C++ codes to appropriate back-end instructions for configuring the accelerator. In the third work, we extend ACiS to support fused collectives and the combining of collectives with map operations. We observe that there is an opportunity of fusing communication (collectives) with computation. Since the computation can vary for different applications, ACiS support should be programmable in this method. In the fourth work, we propose that switches with ACiS support can control and manage the execution of applications, i.e., that the switch be an active device with decision-making capabilities. Switches have a central view of the network; they can collect telemetry information and monitor application behavior and then use this information for control, decision-making, and coordination of nodes. We evaluate the feasibility of ACiS through extensive RTL-based simulation as well as deployment in an open-access cloud infrastructure. Using this simulation framework, when considering a Graph Convolutional Network (GCN) application as a case study, a speedup of on average 3.4x across five real-world datasets is achieved on 24 nodes compared to a CPU cluster without ACiS capabilities

    Enabling HW-based task scheduling in large multicore architectures

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    Dynamic Task Scheduling is an enticing programming model aiming to ease the development of parallel programs with intrinsically irregular or data-dependent parallelism. The performance of such solutions relies on the ability of the Task Scheduling HW/SW stack to efficiently evaluate dependencies at runtime and schedule work to available cores. Traditional SW-only systems implicate scheduling overheads of around 30K processor cycles per task, which severely limit the ( core count , task granularity ) combinations that they might adequately handle. Previous work on HW-accelerated Task Scheduling has shown that such systems might support high performance scheduling on processors with up to eight cores, but questions remained regarding the viability of such solutions to support the greater number of cores now frequently found in high-end SMP systems. The present work presents an FPGA-proven, tightly-integrated, Linux-capable, 30-core RISC-V system with hardware accelerated Task Scheduling. We use this implementation to show that HW Task Scheduling can still offer competitive performance at such high core count, and describe how this organization includes hardware and software optimizations that make it even more scalable than previous solutions. Finally, we outline ways in which this architecture could be augmented to overcome inter-core communication bottlenecks, mitigating the cache-degradation effects usually involved in the parallelization of highly optimized serial code.This work is supported by the TEXTAROSSA project G.A. n.956831, as part of the EuroHPC initiative, by the Spanish Government (grants PCI2021-121964, TEXTAROSSA; PDC2022-133323-I00, Multi-Ka; PID2019-107255GB-C21 MCIN/AEI/10.13039/501100011033; and CEX2021-001148-S), by Generalitat de Catalunya (2021 SGR 01007), and FAPESP (grant 2019/26702-8).Peer ReviewedPostprint (published version

    Efficient Intra-Rack Resource Disaggregation for HPC Using Co-Packaged DWDM Photonics

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    The diversity of workload requirements and increasing hardware heterogeneity in emerging high performance computing (HPC) systems motivate resource disaggregation. Resource disaggregation allows compute and memory resources to be allocated individually as required to each workload. However, it is unclear how to efficiently realize this capability and cost-effectively meet the stringent bandwidth and latency requirements of HPC applications. To that end, we describe how modern photonics can be co-designed with modern HPC racks to implement flexible intra-rack resource disaggregation and fully meet the bit error rate (BER) and high escape bandwidth of all chip types in modern HPC racks. Our photonic-based disaggregated rack provides an average application speedup of 11% (46% maximum) for 25 CPU and 61% for 24 GPU benchmarks compared to a similar system that instead uses modern electronic switches for disaggregation. Using observed resource usage from a production system, we estimate that an iso-performance intra-rack disaggregated HPC system using photonics would require 4x fewer memory modules and 2x fewer NICs than a non-disaggregated baseline.Comment: 15 pages, 12 figures, 4 tables. Published in IEEE Cluster 202

    Miriam: Exploiting Elastic Kernels for Real-time Multi-DNN Inference on Edge GPU

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    Many applications such as autonomous driving and augmented reality, require the concurrent running of multiple deep neural networks (DNN) that poses different levels of real-time performance requirements. However, coordinating multiple DNN tasks with varying levels of criticality on edge GPUs remains an area of limited study. Unlike server-level GPUs, edge GPUs are resource-limited and lack hardware-level resource management mechanisms for avoiding resource contention. Therefore, we propose Miriam, a contention-aware task coordination framework for multi-DNN inference on edge GPU. Miriam consolidates two main components, an elastic-kernel generator, and a runtime dynamic kernel coordinator, to support mixed critical DNN inference. To evaluate Miriam, we build a new DNN inference benchmark based on CUDA with diverse representative DNN workloads. Experiments on two edge GPU platforms show that Miriam can increase system throughput by 92% while only incurring less than 10\% latency overhead for critical tasks, compared to state of art baselines
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