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At least 19 records

Frog: Asynchronous Graph Processing on GPU with Hybrid Coloring Model

GPUs have been increasingly used to accelerate graph processing for complicated computational problems regarding graph theory. Many parallel graph algorithms adopt the asynchronous computing model to accelerate the iterative convergence. Unfortunately, the consistent asynchronous computing requires locking or atomic operations, leading to significant penalties/overheads when implemented on GPUs. As such, coloring algorithm is adopted to separate the vertices with potential updating conflicts, guaranteeing the consistency/correctness of the parallel processing. Common coloring algorithms, however, may suffer from low parallelism because of a large number of colors generally required for processing a large-scale graph with billions of vertices. We propose a light-weight asynchronous processing framework called Frog with a preprocessing/hybrid coloring model. The fundamental idea is based on Pareto principle (or 80-20 rule) about coloring algorithms as we observed through masses of realworld graph coloring cases. We find that a majority of vertices (about 80%) are colored with only a few colors, such that they can be read and updated in a very high degree of parallelism without violating the sequential consistency. Accordingly, our solution separates the processing of the vertices based on the distribution of colors. In this work, we mainly answer three questions: (1) how to partition the vertices in a sparse graph with maximized parallelism, (2) how to process large-scale graphs that cannot fit into GPU memory, and (3) how to reduce the overhead of data transfers on PCIe while processing each partition. Here, we conduct experiments on real-world data (Amazon, DBLP, YouTube, RoadNet-CA, WikiTalk and Twitter) to evaluate our approach and make comparisons with well-known non-preprocessed (such as Totem, Medusa, MapGraph and Gunrock) and preprocessed (Cusha) approaches, by testing four classical algorithms (BFS, PageRank, SSSP and CC). On all the tested applications and datasets, Frog is able to significantly outperform existing GPU-based graph processing systems except Gunrock and MapGraph. MapGraph gets better performance than Frog when running BFS on RoadNet-CA. The comparison between Gunrock and Frog is inconclusive. Frog can outperform Gunrock more than 1.04X when running PageRank and SSSP, while the advantage of Frog is not obvious when running BFS and CC on some datasets especially for RoadNet-CA.

97 MATHEMATICS AND COMPUTING↗

Left ventricular diastolic filling with an implantable ventricular assist device: beat to beat variability with overall improvement

OBJECTIVES: We studied the effects of left ventricular (LV) unloading by an implantable ventricular assist device on LV diastolic filling. BACKGROUND: Although many investigators have reported reliable systemic and peripheral circulatory support with implantable LV assist devices, little is known about their effect on cardiac performance. METHODS: Peak velocities of early diastolic filling, late diastolic filling, late to early filling ratio, deceleration time of early filling, diastolic filling period and atrial filling fraction were measured by intraoperative transesophageal Doppler echocardiography before and after insertion of an LV assist device in eight patients. A numerical model was developed to simulate this situation. RESULTS: Before device insertion, all patients showed either a restrictive or a monophasic transmitral flow pattern. After device insertion, transmitral flow showed rapid beat to beat variation in each patient, from abnormal relaxation to restrictive patterns. However, when the average values obtained from 10 consecutive beats were considered, overall filling was significantly normalized from baseline, with early filling velocity falling from 87 +/- 31 to 64 +/- 26 cm/s (p < 0.01) and late filling velocity rising from 8 +/- 11 to 32 +/- 23 cm/s (p < 0.05), resulting in an increase in the late to early filling ratio from 0.13 +/- 0.18 to 0.59 +/- 0.38 (p < 0.01) and a rise in the atrial filling fraction from 8 +/- 10% to 26 +/- 17% (p < 0.01). The deceleration time (from 112 +/- 40 to 160 +/- 44 ms, p < 0.05) and the filling period corrected by the RR interval (from 39 +/- 8% to 54 +/- 10%, p < 0.005) were also significantly prolonged. In the computer model, asynchronous LV assistance produced significant beat to beat variation in filling indexes, but overall a normalization of deceleration time as well as other variables. CONCLUSIONS: With LV assistance, transmitral flow showed rapidly varying patterns beat by beat in each patient, but overall diastolic filling tended to normalize with an increase of atrial contribution to the filling. Because of the variable nature of the transmitral flow pattern with the assist device, the timing of the device cycle must be considered when inferring diastolic function from transmitral flow pattern.

Non-NASA Center↗

A mathematical model of asynchronous data flow in parallel computers *

Abstract We present a simplified model of data flow on processors in a high-performance computing framework involving computations necessitating inter-processor communications. From this ordinary differential model, we take its asymptotic limit, resulting in a model which treats the computer as a continuum of processors and data flow as an Eulerian fluid governed by a conservation law. We derive a Hamilton–Jacobi equation associated with this conservation law for which the existence and uniqueness of solutions can be proven. We then present the results of numerical experiments for both discrete and continuum models; these show a qualitative agreement between the two and the effect of variations in the computing environment’s processing capabilities on the progress of the modelled computation.

Barnard, Richard C.↗

Asynchronous Ballistic Reversible Fluxon Logic

In a previous study, we described a new abstract circuit model for reversible computation called Asynchronous Ballistic Reversible Computing (ABRC), in which localized information bearing pulses propagate ballistically along signal paths between stateful abstract devices, and elastically scatter off those devices serially, while updating the device state in a logically-reversible and deterministic fashion. The ABRC model has been shown to be capable of universal computation. In the research reported here, we begin exploring how the ABRC model might be realized in practice using single flux quantum (SFQ) solitons (fluxons) in superconducting Josephson junction (JJ) circuits. One natural family of realizations could utilize fluxon polarity to represent binary data in individual pulses propagating near-ballistically along discrete or continuous long Josephson junctions (LJJs) or microstrip passive transmission lines (PTLs), and utilize the flux charge (-1, 0, +1) of a JJ-containing superconducting loop with Φ 0 < I c L < 2Φ 0 to encode a ternary state variable internal to a device. A natural question then arises as to which of the definable abstract ABRC device functionalities using this data representation might be implementable using a JJ circuit that dissipates only a small fraction of the input fluxon energy. We discuss conservation rules and symmetries considered as constraints to be obeyed in these circuits, and begin the process of classifying the possible ABRC devices in this family having up to 3 bidirectional I/O terminals, and up to 3 internal states.

97 MATHEMATICS AND COMPUTING↗

BARC Element Classifier (barc)

SAND2024-02120O This program enumerates and classifies all possible functional elements in several different categories within the Ballistic Asynchronous Reversible Computing (barc) model of computation. barc software is a research tool that is being used to help document the possible digital behaviors of primitive functional elements in the ABRC a.k.a. BARC model of computation. The method of operation of this software leverages elementary concepts and methods from discrete mathematics: combinatorics (permutations), partitions and equivalence classes, symmetry transformations, and the theory of finite groups. Implementation is in Python programming language. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Frank, Michael↗

ARENA: Asynchronous Reconfigurable Accelerator Ring to Enable Data-Centric Parallel Computing

The next generation HPC and data centers are likely to be reconfigurable and data-centric due to the trend of hardware specialization and the emergence of data-driven applications. In this work, we propose ARENA – an asynchronous reconfigurable accelerator ring architecture as a potential scenario on how the future HPC and data centers will be like. Despite using the coarse-grained reconfigurable arrays (CGRAs) as the substrate platform, our key contribution is not only the CGRA-cluster design itself, but also the ensemble of a new architecture and programming model that enables asynchronous tasking across a cluster of reconfigurable nodes, so as to bring specialized computation to the data rather than the reverse. We presume distributed data storage without asserting any prior knowledge on the data distribution. Hardware specialization occurs at runtime when a task finds the majority of data it requires are available at the present node. In other words, we dynamically generate specialized CGRA accelerators where the data reside. The asynchronous tasking for bringing computation to data is achieved by circulating the task token, which describes the dataflow graphs to be executed for a task, among the CGRA cluster connected by a fast ring network. Evaluations on a set of HPC and data-driven applications across different domains show that ARENA can provide better parallel scalability with reduced data movement (53.9 percent). Compared with contemporary compute-centric parallel models, ARENA can bring on average 4.37× speedup. The synthesized CGRAs and their task-dispatchers only occupy 2.93mm 2 chip area under 45nm process technology and can run at 800MHz with on average 759.8mW power consumption. ARENA also supports the concurrent execution of multi-applications, offering ideal architectural support for future high-performance parallel computing and data analytics systems.

97 MATHEMATICS AND COMPUTING↗

A model of asynchronous iterative algorithms for solving large, sparse, linear systems

Solving large, sparse, linear systems of equations is one of the fundamental problems in large scale scientific and engineering computation. A model of a general class of asynchronous, iterative solution methods for linear systems is developed. In the model, the system is solved by creating several cooperating tasks that each compute a portion of the solution vector. This model is then analyzed to determine the expected intertask data transfer and task computational complexity as functions of the number of tasks. Based on the analysis, recommendations for task partitioning are made. These recommendations are a function of the sparseness of the linear system, its structure (i.e., randomly sparse or banded), and dimension.

Reed, D. A.↗

Reliability models for dataflow computer systems

The demands for concurrent operation within a computer system and the representation of parallelism in programming languages have yielded a new form of program representation known as data flow (DENN 74, DENN 75, TREL 82a). A new model based on data flow principles for parallel computations and parallel computer systems is presented. Necessary conditions for liveness and deadlock freeness in data flow graphs are derived. The data flow graph is used as a model to represent asynchronous concurrent computer architectures including data flow computers.

Kavi, K. M.↗

Dynamic Adaptable Asynchronous Progress Model for MPI RMA Multiphase Applications

Casper is a process-based asynchronous progress model for MPI one-sided communication on multi-and many-core architectures. The one-sided communication is not truly one-sided in most MPI implementations: the target process still relies on software progress to complete incoming operations. Casper allows the user to specify an arbitrary number of cores dedicated to background ghost processes and transparently redirects the RMA operations to ghost processes by utilizing the PMPI redirection and MPI-3 shared-memory technologies. Although Casper benefits applications that suffer from lack of asynchronous progress, the operation redirection design might not support complex multiphase applications effectively, which often involve dynamically changing communication density and computing workloads. In this paper, we present an adaptive mechanism in Casper to address the limitation of static asynchronous progress in multiphase applications. For this we exploit two adaptive strategies, a user-guided strategy and a fully transparent and automatic strategy based on self-profiling and prediction, to dynamically reconfigure the asynchronous progress in Casper according to real-time performance characteristics during multiphase execution. We evaluate the adaptive approaches in both microbenchmarks and a real quantum chemistry application suite, NWChem, on the Cray XC30 supercomputer and an Intel Omni-Path cluster.

97 MATHEMATICS AND COMPUTING↗

Asynchronous Execution of Heterogeneous Tasks in ML-Driven HPC Workflows

Heterogeneous scientific workflows consist of numerous types of tasks that require execution on heterogeneous resources. Asynchronous execution of those tasks is crucial to improve resource utilization, task throughput and reduce workflows' makespan. Therefore, middleware capable of scheduling and executing different task types across heterogeneous resources must enable asynchronous execution of tasks. In this paper, we investigate the requirements and properties of the asynchronous task execution of machine learning (ML)-driven high-performance computing (HPC) workflows. We model the degree of asynchronicity permitted for arbitrary workflows and propose key metrics that can be used to determine qualitative benefits when employing asynchronous execution. Our experiments represent relevant scientific drivers, we perform them at scale on Summit, and we show that the performance enhancements due to asynchronous execution are consistent with our model.

97 MATHEMATICS AND COMPUTING↗

¬¬Integration of Quantification of Margins and Uncertainties Methodology into Parallel Discrete Event Simulator Framework

Parallel Discrete Events Simulation (PDES) is becoming increasingly important to lab efforts in security and intelligence. It is used to model complex asynchronous systems such as computer networks, satellite systems, vehicular traffic, and human performance. Uncertainty Quantification (UQ) techniques have become a mainstay of Verification and Validation (V&V) efforts on physics simulations. However, PDES models are very different from traditional physics simulations, and research into UQ techniques for PDES is in its infancy. It is not clear which traditional UQ techniques can be applied to PDES, or what new techniques will need to be developed. The goal of this project was to identify existing UQ techniques that can be applied to PDES, and to develop new techniques as necessary. The project implemented or developed techniques to handle issues that do not appear in traditional physics simulations, but are common among PDES, including sampling techniques for high-dimensional homogenous inputs, response surfaces for high-variance heteroskedastic output, and characterization of skewed output distributions. These are foundational UQ techniques that must be used in any complete UQ analysis (Tong 2018).

97 MATHEMATICS AND COMPUTING↗

Parallel, iterative solution of sparse linear systems - Models and architectures

Solving large, sparse, linear systems of equations is a fundamental problem in large scale scientific and engineering computation. A model of a general class of asynchronous, iterative solution methods for linear systems is developed. In the model, the system is solved by creating several cooperating tasks that each compute a portion of the solution vector. A data transfer model predicting both the probability that data must be transferred between two tasks and the amount of data to be transferred is presented. This model is used to derive an execution time model for predicting parallel execution time and an optimal number of tasks given the dimension and sparsity of the coefficient matrix and the costs of computation, synchronization, and communication. The suitability of different parallel architectures for solving randomly sparse linear systems is discussed. Based on the complexity of task scheduling, one parallel architecture, based on a broadcast bus, is presented and analyzed.

Reed, D. A.↗

A Hartree-Fock Application Using UPC++ and the New DArray Library

The Hartree-Fock (HF) method is the fundamental first step for incorporating quantum mechanics into many-electron simulations of atoms and molecules, and it is an important component of computational chemistry toolkits like NWChem. The GTFock code is an HF implementation that, while it does not have all the features in NWChem, represents crucial algorithmic advances that reduce communication and improve load balance by doing an up-front static partitioning of tasks, followed by work stealing whenever necessary. To enable innovations in algorithms and exploit next generation exascale systems, it is crucial to support quantum chemistry codes using expressive and convenient programming models and runtime systems that are also efficient and scalable. Here, this paper presents an HF implementation similar to GTFock using UPC++, a partitioned global address space model that includes flexible communication, asynchronous remote computation, and a powerful multidimensional array library. UPC++ offers runtime features that are useful for HF such as active messages, a rich calculus for array operations, hardware-supported fetch-and-add, and functions for ensuring asynchronous runtime progress. We present a new distributed array abstraction, DArray, that is convenient for the kinds of random-access array updates and linear algebra operations on block-distributed arrays with irregular data ownership. Finally, we analyze the performance of atomic fetch-and-add operations (relevant for load balancing) and runtime attentiveness, then compare various techniques and optimizations for each. Our optimized implementation of HF using UPC++ and the DArrays library shows up to 20% improvement over GTFock with Global Arrays at scales up to 24,000 cores.

97 MATHEMATICS AND COMPUTING↗

IRIS-MASH: Efficient Multi-device Asynchronous Multi-Stream Heterogeneous Computing

In the rapidly evolving field of high-performance computing (HPC), effectively leveraging heterogeneous devices through asynchronous task programming is paramount. This paper presents a robust asynchronous task programming model tailored for a multi-device, multi-stream execution environment that incorporates a diverse array of heterogeneous computing units, including GPUs from various vendors and other accelerators. Current state-of-the-art task programming models provide methodologies to support asynchronous task executions, but they typically handle homogeneous devices using native programming languages, while support for heterogeneous devices is limited to frameworks like OpenCL. This gap presents significant challenges in abstracting heterogeneous devices to harness their true asynchronous capabilities effectively using their native programming languages. By implementing asynchronous task execution, our model significantly boosts the performance of tiled algorithm task graphs through overlapping data transfers with computation and enabling the simultaneous execution of multiple kernels. We integrate this approach into a heterogeneous Intelligent Runtime System (IRIS) and assess its performance using a suite of tiled algorithm benchmarks from the heterogeneous math kernels library (MatRIS) based on IRIS. Experimental results demonstrate a performance improvement ranging from 1.6 × to 2 × over IRIS without asynchronous support, and a notable 22% performance enhancement compared to established runtime systems such as StarPU and PaRSEC. This approach significantly improves computation efficiency of HPC workflows and provides a solid base for future exploration and development in the area of asynchronous task programming in heterogeneous systems.

Miniskar, Narasinga Rao [ORNL] (ORCID:000000018259↗

DeepHyper: Asynchronous Hyperparameter Search for Deep Neural Networks

Hyperparameters employed by deep learning (DL) methods play a substantial role in the performance and reliability of these methods in practice. Unfortunately, finding performance-optimizing hyperparameter settings is a notoriously difficult task. Hyperparameter search methods typically have limited production-strength implementations or do not target scalability within a highly parallel machine, portability across different machines, experimental comparison between different methods, and tighter integration with workflow systems. In this paper, we present DeepHyper, a Python package that provides a common interface for the implementation and study of scalable hyperparameter search methods. It adopts the Balsam workflow system to hide the complexities of running large numbers of hyperparameter configurations in parallel on high-performance computing (HPC) systems. We implement and study asynchronous model-based search methods that consist of sampling a small number of input hyperparameter configurations and progressively fitting surrogate models over the input-output space until exhausting a user-defined budget of evaluations. We evaluate the efficacy of these methods relative to approaches such as random search, genetic algorithms, Bayesian optimization, and hyperband on DL benchmarks on CPU- and GPU-based HPC systems.

Balaprakash, Prasanna↗

2016 High Performance Computing Annual Report

Sandia National Laboratories’ California site is celebrating its 60th anniversary (1956 to 2016), and high performance computing has been a key enabler for its scientists and engineers throughout much of its history. Since its founding, Sandia California has helped pioneer the use of HPC platforms including hosting Sandia’s first Cray-1 supercomputer in the 1970s and supporting development of scalable cluster computing platforms to create a new paradigm for cost-effective supercomputing in the 1990s. Recent decades of investment in creation of scalable application frameworks for scientific computing have also enabled new generations of modeling and simulation codes. These resources have facilitated computational analysis of complex phenomena in diverse applications spanning national defense, energy, and homeland security. Today, Sandia California researchers work with partners in academia, industry, and national labs to evolve the state-of-the-art in HPC, modeling, and data analysis (including foundational capabilities for exascale computing platforms) and apply them in transformational ways. Research efforts include mitigating the effects of silent hardware failures that can jeopardize the results of large-scale computations, developing exascale-capable asynchronous task-parallel programming models and runtime systems, formulating new techniques to better explore and analyze extreme-scale data sets, and increasing our understanding of materials and chemical sciences which has applications spanning nuclear weapons stockpile stewardship to more efficient automobile engines. The following section highlights some of these research and applications projects and further illustrates the breadth of our HPC capabilities.

97 MATHEMATICS AND COMPUTING↗