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At least 19 records

SpectralFly: Ramanujan Graphs as Flexible and Efficient Interconnection Networks

In recent years, graph theoretic considerations have become increasingly important in the design of HPC interconnection topologies. One approach is to seek optimal or near-optimal families of graphs with respect to a particular graph theoretic property, such as diameter. For example, the SlimFly topology is based on a construction of McKay, Miller, and \v{S}ir\'{a}\v{n} which produces a diameter two graph on a number of nodes approaching the Moore bound, i.e. the largest possible diameter two graph with a fixed radix. Motivated by recent work of Aksoy, Bruillard, Young, and Raugas, we consider topologies which optimize the spectral gap rather than the diameter. In particular, we introduce a novel HPC topology, SpectralFly, designed around the Ramanujan graph construction of Lubotzky, Phillips, and Sarnak (LPS). In this work, we show that the combinatorial properties, such as diameter, bisection bandwidth, average path length, and resilience to link failure, of SpectralFly topologies are better than, or comparable to, similarly constrained DragonFly, SlimFly, and BundleFly topologies. Additionally, we simulate the performance of SpectralFly topologies on a representative sample of physics-inspired HPC workloads using the Structure Simulation Toolkit Macroscale Element Library simulator and demonstrate considerable benefit to using LPS construction as the basis of the SpectralFly topology.

graphs and networks, network topology, interconnec↗

Harnessing Data Movement in Virtual Clusters for In-Situ Execution

As a result of increasing data volume and velocity, Big Data science at exascale has shifted towards the in-situ paradigm, where large scale simulations run concurrently alongside data analytics. With in-situ, data generated from simulations can be processed while still in memory, thereby avoiding the slow storage bottleneck. However, running simulations and analytics together on shared resources will likely result in substantial contention if left unmanaged, as demonstrated in this work, leading to much reduced efficiency of simulations and analytics. Recently, virtualization technologies such as Linux containers have been widely applied to data centers and physical clusters to provide highly efficient and elastic resource provisioning for consolidated workloads including scientific simulations and data analytics. In this paper, we investigate to facilitate network traffic manipulation and reduce mutual interference on the network for in-situ applications in virtual clusters. In order to dynamically allocate the network bandwidth when it is needed, we adopt SARIMA-based techniques to analyze and predict MPI traffic issued from simulations. Although this can be an effective technique, the naïve usage of network virtualization can lead to performance degradation for bursty asynchronous transmissions within an MPI job. Here, we analyze and resolve this performance degradation in virtual clusters.

97 MATHEMATICS AND COMPUTING↗

Neck Muscle Coactivation Response to Varied Levels of Mental Workload During Simulated Flight Tasks

Objective To evaluate neck muscle coactivation across different levels of mental workload during simulated flight tasks. Background Neck pain (NP) is highly prevalent among military aviators. Given the complex nature within the flight environment, mental workload may be a risk factor for NP. This may induce higher levels of neck muscle coactivity, which over time may accelerate fatigue, increase neck discomfort, and affect flight task performance. Method Three counterbalanced mental workload conditions represented by simulated flight tasks modulated by interstimulus frequency and complexity were investigated using the Modifiable Multitasking Environment (ModME). The primary measure was a neck coactivation index to describe the neuromuscular effort of the neck muscles as a system. Additional measures included perceived workload (NASA TLX), subjective discomfort, and task performance. Participants ( n = 60; 30M, 30F) performed three test conditions over 1 hr each while seated in a simulated seating environment. Results Neck coactivation indices (CoA) and subjective neck discomfort corresponded with increasing level of mental workload. Average CoAs for low, medium, and high workloads were: .0278(SD = .0232), .0286(SD = .0231), and .0295(SD = .0228), respectively. NASA TLX mental, temporal, effort, and overall scores also increased with the level of mental workload assigned. For ModME task performance, the overall performance score, monitoring accuracy, and resource management accuracy decreased while reaction times increased with the increasing level of mental workload. Communication accuracy was lowest with the low mental workload but had higher reaction times relative to increasing workload. Conclusion Mental workload affects neck muscle coactivation during combinations of simulated flight tasks within a simulated helicopter seating environment. Application The results of this study provide insights into the physical response to mental workload. With increasing multisensory modalities within the work environment, these insights may assist the consideration of physical effects from cognitive factors.

Behavioral Sciences↗

ATHENA: Analytical Tool for Heterogeneous Neuromorphic Architectures

The ASC program seeks to use machine learning to improve efficiencies in its stockpile stewardship mission. Moreover, there is a growing market for technologies dedicated to accelerating AI workloads. Many of these emerging architectures promise to provide savings in energy efficiency, area, and latency when compared to traditional CPUs for these types of applications — neuromorphic analog and digital technologies provide both low-power and configurable acceleration of challenging artificial intelligence (AI) algorithms. If designed into a heterogeneous system with other accelerators and conventional compute nodes, these technologies have the potential to augment the capabilities of traditional High Performance Computing (HPC) platforms [5]. This expanded computation space requires not only a new approach to physics simulation, but the ability to evaluate and analyze next-generation architectures specialized for AI/ML workloads in both traditional HPC and embedded ND applications. Developing this capability will enable ASC to understand how this hardware performs in both HPC and ND environments, improve our ability to port our applications, guide the development of computing hardware, and inform vendor interactions, leading them toward solutions that address ASC’s unique requirements.

97 MATHEMATICS AND COMPUTING↗

Enabling Scalable and Extensible Memory-mapped Datastores in Userspace

Exascale workloads are expected to incorporate data-intensive processing in close coordination with traditional physics simulations. These emerging scientific, data-analytics and machine learning applications need to access a wide variety of datastores in flat files and structured databases. Programmer productivity is greatly enhanced by mapping datastores into the application process's virtual memory space to provide a unified “in-memory” interface. Currently, memory mapping is provided by system software primarily designed for generality and reliability. However, scalability at high concurrency is a formidable challenge on exascale systems. Also, there is a need for extensibility to support new datastores potentially requiring HPC data transfer services. In this article, we present UMap , a scalable and extensible userspace service for memory-mapping datastores. Furthermore, through decoupled queue management, concurrency aware adaptation, and dynamic load balancing, UMap enables application performance to scale even at high concurrency. We evaluate UMap in data-intensive applications, including sorting, graph traversal, database operations, and metagenomic analytics. Our results show that UMap as a userspace service outperforms an optimized kernel-based service across a wide range of intra-node concurrency by 1.22-1.9 × . We performed two case studies to demonstrate UMap 's extensibility. First, a new datastore residing in remote memory is incorporated into UMap as an application-specific plugin. Second, we present a persistent memory allocator Metall built atop UMap for unified storage/memory.

97 MATHEMATICS AND COMPUTING↗

Exploring the Interaction Between Head-Supported Mass, Posture, and Visual Stress on Neck Muscle Activation

Objective Assess neck muscle activity for varying interactions between helmet, posture, and visual stress in a simulated “helo-hunch” posture. Background Military aviators frequently report neck pain (NP). Risk factors for NP include head-supported mass, awkward postures, and mental workload. Interactions between these factors could induce constant low-level muscle activation during helicopter flight and better explain instances of NP. Method Interactions between physical loading (helmet doffed/donned), posture (symmetric/asymmetric), and visual stress (low/high contrast) were studied through neck muscle electromyography (EMG), head kinematics, subjective discomfort, perceived workload, and task performance. Subjects ( n = 16) performed eight 30-min test conditions (varied physical loading, posture, and visual stress) while performing a simple task in a simulated “helo-hunch” seating environment. Results Conditions with a helmet donned had fewer EMG median frequency cycles (which infer motor unit rotation for rest/recovery, where more cycles are better) in the left cervical extensor and left sternocleidomastoid. Asymmetric posture (to the right) resulted in higher normalized EMG activity in the right cervical extensor and left sternocleidomastoid and resulted in less lateral bending compared with neutral across all conditions. Conditions with high visual stress also resulted in fewer EMG cycles in the right cervical extensor. Conclusion A complex interaction exists between the physical load of the helmet, postural stress from awkward postures, and visual stress within a simulated “helo-hunch” seating environment. Application These results provide insight into how visual factors influence biomechanical loading. Such insights may assist future studies in designing short-term administrative controls and long-term engineering controls.

Behavioral Sciences↗

Early Performance Results on 4th Gen Intel(R) Xeon (R) Scalable Processors with DDR and Intel(R) Xeon(R) processors, codenamed Sapphire Rapids with HBM

The Crossroads supercomputer was designed to simulate some of the most complex physical devices in the world. These simulations routinely require 1/2 petabyte or more of system memory running on thousands of compute nodes for months at a time on the most powerful supercomputers. Improvements in time to solutions for these workloads can have major impact on our mission capabilities. In this paper we present early results of representative application workloads on 4th Gen Intel Xeon and Intel Xeon Processors codenamed Sapphire Rapids with HBM. These results demonstrate an extremely promising 8.57x improvement (node to node) over our prior generation Intel Broadwell (BDW) based HPC systems. No code modifications were required to achieve this speedup, providing a compelling path forward toward major reductions in time to solution and the complexity of physical systems that can be simulated in the future.

97 MATHEMATICS AND COMPUTING↗

Finding Your Niche: An Evolutionary Approach to HPC Topologies

Traditional interconnection network design approaches focus on building general network topologies by optimizing the bisection bandwidth or minimizing the network’s diameter to reduce the maximum distance between any two nodes, thus amortizing the overall execution time of the HPC workloads. While such network topologies may accommodate a wide variety of applications in general, this may result in sub-optimal performance for many frequently-executed or dynamic workloads. In this paper, instead of focusing on designing an all-encompassing, general-purpose network topology, we develop a methodology to design customized network interconnects, evolved by “finding” the optimal topologies for a particular target workload given by its communication and contention profiles. To this end, we implement a Genetic Algorithm (GA)-based approach for network topology design tailored to improve the overall execution time of a particular workload of interest. We conducted extensive experiments with well-known motifs in physics-based workloads (Sweep3D and FFT), as well as with a representative graph application (MiniVite), using the well-known Structural Simulation Toolkit (SST) Macroscale Element Library (SST/macro) simulator for network interconnect evaluation. We demonstrate that our genetic algorithm-based approach is robust enough to find the underlying optimal topology of a particular workload.

network interconnects, graph search, meta-heuristi↗

Fit Fly: A Case Study of Interconnect Innovation through Parallel Simulation

To meet the demand for exascale-level performance from high-performance computing (HPC) interconnects, many system architects are turning to simulation results for accurate and reliable predictions of the performance of prospective technologies. Testing full-scale networks with a variety of benchmarking tools, including synthetic workloads and application traces, can give crucial insight into what ideas are most promising without needing to physically construct a test network. While flexible, however, this approach is extremely compute time intensive. We address this time complexity challenge through the use of large-scale, optimistic parallel simulation that ultimately leads to faster HPC network architecture innovations. In this paper we demonstrate this innovation capability through a real-world network design case study. Specifically, we have simulated and compared four extreme-scale interconnects: Dragonfly, Megafly, Slim Fly, and a new dual-rail-dual-plane variation of the Slim Fly network topology. We present this new variant of Slim Fly, dubbed Fit Fly, to show how interconnect innovation and evaluation-beyond what is possible through analytic methods-can be achieved through parallel simulation. We validate and compare the model with various network designs using the CODES interconnect simulation framework. By running large-scale simulations in a parallel environment, we are able to quickly generate reliable performance results that can help network designers break ground on the next generation of high-performance network designs.

High Performance Computing↗

Rapid Simulation of Unconventional Reservoirs by Multidomain Multiresolution Modeling Based on the Diffusive Time of Flight

Summary The fast marching method (FMM)-based rapid flow simulation has been shown to accelerate simulation efficiency by orders of magnitude by transforming 3D simulation to equivalent 1D simulation using the concept of the “diffusive time of flight” (DTOF). However, the 1D transformation does not directly apply to multiwell problems. In this paper, we propose a novel DTOF-based multidomain multiresolution discretization scheme to accelerate multiwell simulation of unconventional reservoirs. Our method formulates multiwell simulation problems based on the DTOF which displays the pressure front propagation in unconventional reservoirs. The DTOF contours are used to partition the reservoir into local and shared domains. A local domain is where the flow is dominated by a single well, and the shared domain is where the fluid flow is influenced by multiple wells. The DTOF contours expand independently in local domains and interfere in the shared domain. After the partitioning, each domain is discretized using a multiresolution scheme whereby the original 3D fine mesh is preserved near the wells to account for detailed physics including gravity, and the rest of the domain is discretized into 1D mesh based on the DTOF contours to alleviate the simulation workload. The power and efficacy of our approach are demonstrated using synthetic and field-scale simulation models with different degrees of geologic and well-completion complexity. The simulation results, number of active cells, and computation time for the proposed discretization scheme are compared with the original high-fidelity 3D model for each case. The results show that the proposed method is suitable for multiwell simulation problems in unconventional reservoirs and can accelerate flow simulations by orders of magnitude with minimal loss of accuracy. The novelty of this work is the creation of DTOF-derived multiresolution discretization with local and shared domains to simplify and accelerate the calculation of subsurface flow problems, especially in unconventional reservoirs. Our workflow can be easily interfaced with commercial simulators, making it suitable for large-scale field applications.

Engineering↗

PRISTINE: An Emulation Platform for PCB-Level Hardware Trojans

Printed circuit Boards (PCBs) are becoming increasingly vulnerable to malicious design alteration, also known as Trojan attacks, due to a distributed business model that often involves various untrusted parties. Such attacks can be mounted at various stages in the PCB life cycle. The relative ease of alteration of PCB hardware even after fabrication (due to physical access to surface-mounted critical components and traces) makes them attractive for an adversary to manipulate their functional/physical behavior for malicious intent. There is a growing need to explore viable Trojan attacks in a PCB, analyze their functional and physical characteristics (e.g., impact on power or delay), and study the effectiveness of countermeasures against these attacks. While simulation-based approaches for PCB Trojan insertion are effective at creating a large population of possible Trojans, they fail to provide functional feasibility analysis with a realistic workload for a trigger circuit. Also, they cannot estimate a Trojan’s side-channel footprint due to the unavailability of physical models of diverse PCB components. To address these deficiencies, in this paper, we present PRISTINE, a PCB-level emulation system for any integrity or physical tampering issues, specifically, hardware Trojan insertion. The need for building such an emulation platform to resolve PCB trust issues in the supply chain is also surveyed and discussed. Both custom Hardware Hacking (HaHa) boards and multiple commercial PCBs are then used to test the ability of the proposed system to emulate various hardware Trojans specially designed to exploit board-specific hardware characteristics. Experimental results on emulated board-level Trojans show that a wide range of Trojans can be successfully activated, thus enabling the expected payload effects on both types of boards to be studied and quantified. The resulting data are further analyzed to create PCB-level Trojan benchmarks. In particular, a comparative evaluation of the experimental results is used to propose a risk level metric that quantifies the probability of detection and degree of payload impact of each Trojan on a given commercial PCB.

47 OTHER INSTRUMENTATION↗

Characterizing Machine Learning I/O Workloads on Leadership Scale HPC Systems

High performance computing (HPC) is no longer solely limited to traditional workloads such as simulation and modeling. With the increase in the popularity of machine learning (ML) and deep learning (DL) technologies, we are observing that an increasing number of HPC users are incorporating ML methods into their workflow and scientific discovery processes, across a wide spectrum of science domains such as biology, earth science, and physics. This gives rise to a diverse set of I/O patterns than the traditional checkpoint/restart-based HPC I/O behavior. The details of the I/O characteristics of such ML I/O workloads have not been studied extensively for large-scale leadership HPC systems. This paper aims to fill that gap by providing an in-depth analysis to gain an understanding of the I/O behavior of ML I/O workloads using darshan - an I/O characterization tool designed for lightweight tracing and profiling. We study the darshan logs of more than 23, 000 HPC ML I/O jobs over a time period of one year running on Summit - the second-fastest supercomputer in the world. This paper provides a systematic I/O characterization of ML I/O jobs running on a leadership scale supercomputer to understand how the I/O behavior differs across science domains and the scale of workloads, and analyze the usage of parallel file system and burst buffer by ML I/O workloads.

Paul, Arnab↗

Telerobotic Control of Dexterous Dual-Arm Robots for D and D Operations - 18622

Robotic systems hold the potential to significantly reduce exposure of workers to hazardous environments such as in the deactivation and decommissioning (D and D) of nuclear facilities. Our goal is to enable an operator with minimal training to easily control a remote dual-arm robot to perform demolition tasks with hand tools. We propose a system that combines semi-autonomous coordination of the robot's arms with an intuitive operator interface based on virtual reality (VR) technology. A limb coordination system enables independent control of the robot arms, as well as coupled motion required to hold and manipulate rigid bodies such as reciprocating saws, angle grinders and crow bars. Using a VR head mounted display and stereo video from the robot for situational awareness and tracked VR hand controllers to command robot arm movement, an operator will be able to walk up to the control console, pick up the controllers, engage the manipulators, fly the grippers, grasp a tool with one or both robot arms and easily move them in unison to perform tasks. We present preliminary results using simulation and a physical dual-arm platform based on the Johns Hopkins University Applied Physics Laboratory's Modular Prosthetic Limb, an anthropomorphic device that provides hyper-dexterous human-like manipulation capabilities. Anticipated benefits of the robotic system for D and D operations include improved situational awareness, increased mission complexity, and reduced operator training time, workload, and task execution times. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Accelerating science: The usage of commercial clouds in ATLAS Distributed Computing

The ATLAS experiment at CERN is one of the largest scientific machines built to date and will have ever growing computing needs as the Large Hadron Collider collects an increasingly larger volume of data over the next 20 years. ATLAS is conducting R&D projects on Amazon Web Services and Google Cloud as complementary resources for distributed computing, focusing on some of the key features of commercial clouds: lightweight operation, elasticity and availability of multiple chip architectures. The proof of concept phases have concluded with the cloud-native, vendoragnostic integration with the experiment’s data and workload management frameworks. Google Cloud has been used to evaluate elastic batch computing, ramping up ephemeral clusters of up to O(100k) cores to process tasks requiring quick turnaround. Amazon Web Services has been exploited for the successful physics validation of the Athena simulation software on ARM processors. We have also set up an interactive facility for physics analysis allowing endusers to spin up private, on-demand clusters for parallel computing with up to 4 000 cores, or run GPU enabled notebooks and jobs for machine learning applications. The success of the proof of concept phases has led to the extension of the Google Cloud project, where ATLAS will study the total cost of ownership of a production cloud site during 15 months with 10k cores on average, fully integrated with distributed grid computing resources and continue the R&D projects.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A GPU-accelerated package for simulation of flow in nanoporous source rocks with many-body dissipative particle dynamics

Mesoscopic simulations of hydrocarbon flow in source shales are concerning, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid–fluid and fluid–solid interactions in nano- to micro-scale shale pores, which are physically and chemically sophisticated, must be captured. To address those challenges, we present a GPU-accelerated package for simulation of flow in nano- to micro-pore networks with a many-body dissipative particle dynamics (mDPD) mesoscale model. Based on a fully distributed parallel paradigm, the code offloads all intensive workloads on GPUs. Other advancements, such as smart particle packing and no-slip boundary condition in complex pore geometries, are also implemented for the construction and the simulation of the realistic shale pores from 3D nanometer-resolution stack images. Our code is validated for accuracy and compared against the CPU counterpart for speedup. In our benchmark tests, the code delivers nearly perfect strong scaling and weak scaling (with up to 512 million particles) on up to 512 K20X GPUs on Oak Ridge National Laboratory’s (ORNL) Titan supercomputer. Moreover, a single-GPU benchmark on ORNL’s SummitDev and IBM’s AC922 suggests that the host-to-device NVLink can boost performance over PCIe by a remarkable 40%. Lastly, we demonstrate, through a flow simulation in realistic shale pores, that the CPU counterpart requires 840 Power9 cores to rival the performance delivered by our package with four V100 GPUs on ORNL’s Summit architecture. This simulation package enables quick-turnaround and high-throughput mesoscopic numerical simulations for exploring complex flow phenomena in nano- to micro-porous rocks with realistic pore geometries.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Efficient Parallelization of Irregular Applications on GPU Architectures

With the enlarging computation capacity of general Graphics Processing Units (GPUs), leveraging GPUs to accelerate parallel applications has become a critical topic in academia and industry. However, a wide range of irregular applications with the computation-/memory-intensive nature cannot easily achieve high GPU utilization. The challenges mainly involve the following aspects: first, data dependence leads to coarse-grained kernel and inefficient parallelism; second, heavy GPU memory usage may cause frequent memory evictions and extra overhead of I/O; third, specific computation patterns produce memory redundancies; last, workload balance and data reusability conjunctly benefit the overall performance, but there may exist a dynamic trade-off between them. Targeting these challenges, this dissertation proposes multiple optimizations to accelerate two real-world applications: many-body correlation functions to simulate nuclear physics in a large-scale scientific system; the other is the eALS-based matrix factorization recommendation system. To accelerate the calculations of many-body correlation functions, this dissertation presents three frameworks in GPU memory management and multi-GPU scheduling. Firstly, an optimized systematic GPU memory management framework, MemHC, utilizes a series of new memory reduction designs in GPU memory allocation, CPU/GPU communications, and GPU memory oversubscription. Secondly, an enhanced multi-GPU scheduling framework, MICCO, particularly by taking both data dimension (e.g., data reuse and data eviction) and computation dimension into account. MICCO designs a heuristic scheduling algorithm and a machine learning-based regression model to generate the optimal settings of a proposed new concept to manage the trade-off. Thirdly, a locality-aware multi-GPU scheduling framework. This scheduler leverages pipeline batch generation with a looking-ahead strategy by building local dependency graphs for memory transfer reduction and better data reuse, achieving up to 79.92% memory cost reduction and 1.67x speedup. To parallelize the eALS-based recommendation system, this dissertation proposes an efficient CPU/GPU heterogeneous recommendation system, HEALS. HEALS employs newly designed architecture-adaptive data formats to achieve load balance and good data locality on CPU and GPU. To mitigate the data dependence, HEALS presents a CPU/GPU collaboration model for both task parallelism and data parallelism with multiple kernel computation optimizations. In summary, this dissertation efficiently accelerates two typical irregular applications on GPUs by building four frameworks, including CPU/GPU collaboration, GPU memory management, and multi-GPU scheduling.

Wang, Qihan↗

TrioSim: A Lightweight Simulator for Large-Scale DNN Workloads on Multi-GPU Systems

Deep Neural Networks (DNNs) have become increasingly capable of performing tasks ranging from image recognition to content generation. The training and inference of DNNs heavily rely on GPUs, as GPUs' massively parallel architecture delivers extremely high computing capability. With the growing complexity of DNNs and the size of training datasets, training DNNs with a large number of GPUs is becoming a prevalent strategy. Researchers have been exploring how to design software and hardware systems for GPU farms to achieve the best utilization, efficiency, and DNN accuracy during training or inference. However, when designing and deploying such systems, designers usually rely on testing on physical hardware platforms equipped with many GPUs, incurring high costs that are almost prohibitive for system designers to test different configurations and designs, even for highly resourceful companies. While an alternative solution is to test on GPU simulators, they are often too slow for these l

Li, Ying [William & Mary, Williamsburg, VA, USA] (↗

Modeling Distributed Computing Infrastructures for HEP Applications

Predicting the performance of various infrastructure design options in complex federated infrastructures with computing sites distributed over a wide area network that support a plethora of users and workflows, such as the Worldwide LHC Computing Grid (WLCG), is not trivial. Due to the complexity and size of these infrastructures, it is not feasible to deploy experimental test-beds at large scales merely for the purpose of comparing and evaluating alternate designs. An alternative is to study the behaviours of these systems using simulation. This approach has been used successfully in the past to identify efficient and practical infrastructure designs for High Energy Physics (HEP). A prominent example is the Monarc simulation framework, which was used to study the initial structure of the WLCG. New simulation capabilities are needed to simulate large-scale heterogeneous computing systems with complex networks, data access and caching patterns. A modern tool to simulate HEP workloads that execute on distributed computing infrastructures based on the SimGrid and WRENCH simulation frameworks is outlined. Studies of its accuracy and scalability are presented using HEP as a case-study. Hypothetical adjustments to prevailing computing architectures in HEP are studied providing insights into the dynamics of a part of the WLCG and candidates for improvements.

Horzela, Maximilian↗