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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Exploring MPI Communication Models for Graph Applications Using Graph Matching as a Case Study

Traditional implementations of parallel graph operations on distributed memory platforms are written using Message Passing Interface (MPI) point to point communication primitives such as Send-Recv (blocking and nonblocking). Apart from this classical model, the MPI community has over the years added other communication models; however, their suitability for handling the irregular traffic workloads typical of graph operations remain comparatively less explored. Our aim in this paper is to study these relatively underutilized communication models of MPI for graph applications. More specifically, we evaluate MPI’s one-sided programming, or Remote Memory Access (RMA), and nearest neighborhood collectives using a process graph topology. There are features in these newer models that are intended to better map to irregular communication patterns, as exemplified in graph algorithms. As a concrete application for our case study, we use distributed memory implementations of a weighted graph matching algorithm to investigate performances of MPI-3 RMA and neighborhood collective operations compared to nonblocking Send- Recv. A matching in a graph is a subset of edges such that no two matched edges are incident on the same vertex. A maximum weight matching is a matching of maximum weight computed as the sum of the weights of matched edges. Algorithms for optimal matching have quadratic complexity and are difficult to parallelize. More importantly, execution of graph matching is dominated by high volume of irregular memory accesses, making it an ideal candidate for studying the effects of various MPI communication models on graph applications at scale. Our neighborhood collectives and RMA implementations yields up to 6× speedup over traditional optimized nonblocking Send-Recv implementations, on thousands of cores of the NERSC Cori supercomputer. We believe the lessons learned from this case study can be adopted to benefit a wider range of graph application codes.

Ghosh, Sayan↗
DOE OSTI2019

Properties of the Graph Modularity Matrix and its Applications

We study the popular modularity matrix and respective functional used in connection with graph clustering and derive some properties useful when performing vertex aggregation of the associated graph. These properties are employed in the derivation of a multilevel parallel pairwise aggregation algorithm. Some illustrative examples which include algebraic multigrid (AMG) coarsening that follows strong direction of anisotropy in finite element problems as well as comparative performance results of the studied algorithm are presented.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A Block-Based Triangle Counting Algorithm on Heterogeneous Environments

Triangle counting is a fundamental building block in graph algorithms. In this article, we propose a block-based triangle counting algorithm to reduce data movement during both sequential and parallel execution. Our block-based formulation makes the algorithm naturally suitable for heterogeneous architectures. The problem of partitioning the adjacency matrix of a graph is well-studied. Our task decomposition goes one step further: it partitions the set of triangles in the graph. By streaming these small tasks to compute resources, we can solve problems that do not fit on a device. We demonstrate the effectiveness of our approach by providing an implementation on a compute node with multiple sockets, cores and GPUs. The current state-of-the-art in triangle enumeration processes the Friendster graph in 2.1 seconds, not including data copy time between CPU and GPU. Using that metric, our approach is 20 percent faster. When copy times are included, our algorithm takes 3.2 seconds. This is 5.6 times faster than the fastest published CPU-only time.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A Block-Based Triangle Counting Algorithm on Heterogeneous Environments

Triangle counting is a fundamental building block in graph algorithms. In this paper, we propose a block-based triangle counting algorithm to reduce data movement during both sequential and parallel execution. Our block-based formulation makes the algorithm naturally suitable for heterogeneous architectures. The problem of partitioning the adjacency matrix of a graph is well-studied. Our task decomposition goes one step further: it partitions the set of triangles in the graph. By streaming these small tasks to compute resources, we can solve problems that do not fit on a device. We demonstrate the effectiveness of our approach by providing an implementation on a compute node with multiple sockets, cores and GPUs. The current state-of-the-art in triangle enumeration processes the Friendster graph in 2.1 seconds, not including data copy time between CPU and GPU. Using that metric, our approach is 20 percent faster. When copy times are included, our algorithm takes 3.2 seconds. This is 5.6 times faster than the fastest published CPU-only time.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Neuromorphic Graph Algorithms: Cycle Detection, Odd Cycle Detection, and Max Flow

Neuromorphic computing is poised to become a promising computing paradigm in the post Moore’s law era due to its extremely low power usage and inherent parallelism. Spiking neural networks are the traditional use case for neuromorphic systems, and have proven to be highly effective at machine learning tasks such as control problems. More recently, neuromorphic systems have been applied outside of the arena of machine learning, primarily in the field of graph algorithms. Neuromorphic systems have been shown to perform graph algorithms faster and with lower power consumption than their traditional (GPU/CPU) counterparts, and are hence an attractive option for a co-processing unit in future high performance computing systems, where graph algorithms play a critical role. In this paper, we present a neuromorphic implementation of cycle detection, odd cycle detection, and the Ford-Fulkerson max-flow algorithm. We further evaluate the performance of these implementations using the NEST neuromorphic simulator by using spike counts and simulation time as proxies for energy consumption and run time. In addition to gains inherent in neuromorphic systems, we show that within the neuromorphic implementations early stopping criteria can be implemented to further improve performance.

Kay, Bill↗
DOE OSTI2020

Evaluation of Graph Analytics Frameworks Using the GAP Benchmark Suite

The analysis of connected data is an increasingly important application in high-performance computing. Such analyses can reveal fraudulent patterns in financial transactions, optimize telecommunications networks, predict information flow in social networks, etc. However, the landscape of graph analytics is highly diverse. Graph algorithms stress processor architectures differently, and no one graph can represent all topologies. Consequently, no single approach or framework is expected to be optimal for all graph analytics problems. To help make sense of this diverse landscape, we evaluated four approaches to graph analytics: GraphBLAS, Galois, BGL17, GraphIt; and compare them against hand-tuned implementations that take advantage of hardware features on our test platform. Graph- BLAS formulates graph analytics as sparse linear algebra. Galois provides syntactic constructs for data parallelism over irregular data structures. BGL17 is a generic C++ template library for implementing graph algorithms. GraphIt provides a domain- specific language to describe and optimize graph algorithms. We use the GAP Benchmark Suite to establish baseline performance and guide the side-by-side evaluation of each framework. GAP consists of 30 tests: six graph analytics algorithms (breadth- first search, single-source shortest path, PageRank, betweenness centrality, connected components, and triangle counting) run on five graphs, each with different topological characteristics (e.g., high diameter, skewed degree distribution, high average degree). High-performance reference implementations are included for each benchmark algorithm. Because a graph can be loaded into memory a number of ways (e.g., flat file on disk, compressed sparse format, data frames, retrieved from SQL or NoSQL databases), our evaluation focused on computational performance rather than I/O. Our results show the relative strengths of each framework.

Graph algorithms, Benchmarking, shared-memory prog↗
DOE OSTI2024

Data-flow parallelism for high-energy and nuclear physics frameworks

The processing tasks of an event-processing workflow in high-energy and nuclear physics (HENP) can typically be represented as a directed acyclic graph formed according to the data flow—i.e. the data dependencies among algorithms executed as part of the workflow. With this representation, an HENP framework can optimally execute a workflow, exploiting the parallelism inherent among independent tasks. Despite such a natural description of a workflow, most HENP frameworks do not make use of technologies that provide concurrent execution of graph-based tasking structures. In this talk, we describe Fermilab efforts to adopt a graph-based technology (specifically Intel’s oneTBB flow graph) for meeting the framework needs of its experiments, notably DUNE. Building on the Meld project as presented at CHEP2023, we demonstrate that all common processing idioms supported by current frameworks can naturally be supported by oneTBB’s data-flow technology, optimally leveraging the concurrent capabilities of the machine. In addition, we discuss collaborative efforts between Fermilab and the Intel oneTBB development team, who is considering improvements to the flow-graph technology to better support HENP use cases.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Data-flow parallelism for high-energy and nuclear physics computing frameworks

The processing tasks of a scientific workflow in high-energy and nuclear physics (HENP) can typically be represented as a directed acyclic graph formed according to the data flow—i.e. the data dependencies among algorithms executed as part of the workflow. With this representation, an HENP computing framework can optimally execute a workflow, exploiting the parallelism inherent among independent tasks. Despite such a natural description of a workflow, most HENP frameworks do not make use of technologies that provide concurrent execution of graph-based tasking structures. In this session, we describe Fermilab efforts to adopt a graph-based technology (specifically Intel’s oneTBB flow graph) for meeting the framework needs of its experiments, notably DUNE. After introducing the physics DUNE intends to explore, we will show that all common processing idioms supported by current HENP frameworks can naturally be supported by oneTBB’s data-flow technology, optimally leveraging the concurrent capabilities of the machine. In addition, we discuss collaborative efforts between Fermilab and the Intel oneTBB development team, who is considering improvements to the flow-graph technology to better support HENP use cases.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Neuromorphic Graph Algorithms: Extracting Longest Shortest Paths and Minimum Spanning Trees

Neuromorphic computing is poised to become a promising computing paradigm in the post Moore's law era due to its extremely low power usage and inherent parallelism. Traditionally speaking, a majority of the use cases for neuromorphic systems have been in the field of machine learning. In order to expand their usability, it is imperative that neuromorphic systems be used for non-machine learning tasks as well. The structural aspects of neuromorphic systems (i.e., neurons and synapses) are similar to those of graphs (i.e., nodes and edges), However, it is not obvious how graph algorithms would translate to their neuromorphic counterparts. In this work, we propose a preprocessing technique that introduces fractional offsets on the synaptic delays of neuromorphic graphs in order to break ties. This technique, in turn, enables two graph algorithms: longest shortest path extraction and minimum spanning trees.

Kay, Bill↗
DOE OSTI2021

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

C-SAW: a framework for graph sampling and random walk on GPUs

Many applications require to learn, mine, analyze and visualize large-scale graphs. These graphs are often too large to be addressed efficiently using conventional graph processing technologies. Fortunately, recent research efforts find out graph sampling and random walk, which significantly reduce the size of original graphs, can benefit the tasks of learning, mining, analyzing and visualizing large graphs by capturing the desirable graph properties. This paper introduces C-SAW, the first framework that accelerates Sampling and Random Walk framework on GPUs. Particularly, C-SAW makes three contributions: First, our framework provides a generic API which allows users to implement a wide range of sampling and random walk algorithms with ease. Second, offloading this framework on GPU, we introduce warp-centric parallel selection, and two novel optimizations for collision migration. Third, towards supporting graphs that exceed the GPU memory capacity, we introduce efficient data transfer optimizations for out-of-memory and multi-GPU sampling, such as workload-aware scheduling and batched multi-instance sampling. Taken together, our framework constantly outperforms the state of the art projects in addition to the capability of supporting a wide range of sampling and random walk algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Parallelization techniques for quantum simulation of fermionic systems

Mapping fermionic operators to qubit operators is an essential step for simulating fermionic systems on a quantum computer. We investigate how the choice of such a mapping interacts with the underlying qubit connectivity of the quantum processor to enable (or impede) parallelization of the resulting Hamiltonian-simulation algorithm. It is shown that this problem can be mapped to a path coloring problem on a graph constructed from the particular choice of encoding fermions onto qubits and the fermionic interactions onto paths. The basic version of this problem is called the weak coloring problem. Taking into account the fine-grained details of the mapping yields what is called the strong coloring problem, which leads to improved parallelization performance. A variety of illustrative analytical and numerical examples are presented to demonstrate the amount of improvement for both weak and strong coloring-based parallelizations. Our results are particularly important for implementation on near-term quantum processors where minimizing circuit depth is necessary for algorithmic feasibility.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Extreme Scale De Novo Metagenome Assembly

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big shared memory machines and cannot handle contemporary metagenome datasets that exceed Terabytes in size. In this paper, we introduce the MetaHipMer pipeline, a high-quality and high-performance metagenome assembler that employs an iterative de Bruijn graph approach. MetaHipMer leverages a specialized scaffolding algorithm that produces long scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is end-to-end parallelized using the Unified Parallel C language and therefore can run seamlessly on shared and distributed-memory systems. Experimental results show that MetaHipMer matches or outperforms the state-of-the-art tools in terms of accuracy. Ultimately, MetaHipMer scales efficiently to large concurrencies and is able to assemble previously intractable grand challenge metagenomes. We demonstrate the unprecedented capability of MetaHipMer by computing the first full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion reads - size 2.6 TBytes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

OpenSn: A massively parallel, open-source simulation environment for discrete ordinates radiation transport

OpenSn is an open-source, massively parallel deterministic radiation transport code for solving the discrete-ordinates ( S N ) form of the Boltzmann transport equation on unstructured, arbitrary polyhedral meshes. It supports high-fidelity simulations involving steady-state, eigenvalue, and adjoint problems for neutral particles (e.g., neutrons, photons, multi-particles), using the multigroup approximation in energy. OpenSn combines angular discretization via discrete ordinates with a discontinuous Galerkin finite element method (DGFEM) in space, enabling accurate resolution of transport physics on arbitrary polyhedral cells, included locally refined spatial grids. It includes multiple angular quadrature types, including locally refined angular quadratures. Written in modern C++ with a Python API, OpenSn runs efficiently on platforms ranging from laptops to supercomputers. The transport sweep algorithm is implemented using a task-based, directed-acyclic-graph (DAG) approach for each angle and supports asynchronous parallelism across thousands of MPI ranks. Group-set aggregation improves compute intensity, and synthetic acceleration techniques (e.g., diffusion synthetic acceleration, second-moment method) enhance solver convergence. OpenSn has been verified on reactor physics problems and demonstrated excellent weak and strong scaling performance on more than 32,768 processes, making it a versatile and robust platform for large-scale transport simulations in complex geometries.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Reducing Communication in Graph Neural Network Training

Graph Neural Networks (GNNs) are powerful and flexible neural networks that use the naturally sparse connectivity information of the data. GNNs represent this connectivity as sparse matrices, which have lower arithmetic intensity and thus higher communication costs compared to dense matrices, making GNNs harder to scale to high concurrencies than convolutional or fully-connected neural networks. Here, we introduce a family of parallel algorithms for training GNNs and show that they can asymptotically reduce communication compared to previous parallel GNN training methods. We implement these algorithms, which are based on 1D, 1. 5D, 2D, and 3D sparse-dense matrix multiplication, using torch.distributed on GPU-equipped clusters. Our algorithms optimize communication across the full GNN training pipeline. We train GNNs on over a hundred GPUs on multiple datasets, including a protein network with over a billion edges.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Scalable Pattern Matching in Metadata Graphs via Constraint Checking

Pattern matching is a fundamental tool for answering complex graph queries. Unfortunately, existing solutions have limited capabilities: They do not scale to process large graphs and/or support only a restricted set of search templates or usage scenarios. Moreover, the algorithms at the core of the existing techniques are not suitable for today’s graph processing infrastructures relying on horizontal scalability and shared-nothing clusters, as most of these algorithms are inherently sequential and difficult to parallelize. In this article we present an algorithmic pipeline that bases pattern matching on constraint checking. The key intuition is that each vertex and edge participating in a match has to meet a set of constraints implicitly specified by the search template. These constraints can be verified independently and typically are less expensive to compute than searching the full template. The pipeline we propose generates these constraints and iterates over them to eliminate all the vertices and edges that do not participate in any match, thus reducing the background graph to a subgraph that is the union of all template matches—the complete set of all vertices and edges that participate in at least one match. Additional analysis can be performed on this annotated, reduced graph, such as full match enumeration, match counting, or computing vertex/edge centrality. Furthermore, a vertex-centric formulation for constraint checking algorithms exists, and this makes it possible to harness existing high-performance, vertex-centric graph processing frameworks. This technique (i) enables highly scalable pattern matching in metadata (labeled) graphs; (ii) supports arbitrary patterns with 100% precision; (iii) enables tradeoffs between precision and time-to-solution, while always selects all vertices and edges that participate in matches, thus offering 100% recall; and (iv) supports a set of popular data analytics scenarios. We implement our approach on top of HavoqGT, an open-source asynchronous graph processing framework, and demonstrate its advantages through strong and weak scaling experiments on massive scale real-world (up to 257 billion edges) and synthetic (up to 4.4 trillion edges) labeled graphs, respectively, and at scales (1,024 nodes / 36,864 cores), orders of magnitude larger than used in the past for similar problems. This article serves two purposes: First, it synthesises the knowledge accumulated during a long-term project. Second, it presents new system features, usage scenarios, optimizations, and comparisons with related work that strengthen the confidence that pattern matching based on iterative pruning via constraint checking is an effective and scalable approach in practice. The new contributions include the following: (i) We demonstrate the ability of the constraint checking approach to efficiently support two additional search scenarios that often emerge in practice, interactive incremental search and exploratory search. (ii) We empirically compare our solution with two additional state-of-the-art systems, Arabsque and TriAD. (iii) We show the ability of our solution to accommodate a more diverse range of datasets with varying properties, e.g., scale, skewness, label distribution, and match frequency. (iv) We introduce or extend a number of system features (e.g., work aggregation, load balancing, and the ability to cap the generated traffic) and design optimizations and demonstrate their advantages with respect to improving performance and scalability. (v) We present bottleneck analysis and insights into artifacts that influence performance. (vi) We present a theoretical complexity argument that motivates the performance gains we observe.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Direction-optimizing Label Propagation Framework for Structure Detection in Graphs: Design, Implementation, and Experimental Analysis

Label Propagation is not only a well-known machine learning algorithm for classification but also an effective method for discovering communities and connected components in networks. We propose a new Direction-optimizing Label Propagation Algorithm (DOLPA) framework that enhances the performance of the standard Label Propagation Algorithm (LPA), increases its scalability, and extends its versatility and application scope. As a central feature, the DOLPA framework relies on the use of frontiers and alternates between label push and label pull operations to attain high performance. It is formulated in such a way that the same basic algorithm can be used for finding communities or connected components in graphs by only changing the objective function used. Additionally, DOLPA has parameters for tuning the processing order of vertices in a graph to reduce the number of edges visited and improve the quality of solution obtained. We present the design and implementation of the enhanced algorithm as well as our shared-memory parallelization of it using OpenMP. We also present an extensive experimental evaluation of our implementations using the LFR benchmark and real-world networks drawn from various domains. Compared with an implementation of LPA for community detection available in a widely used network analysis software, we achieve at most five times the F-Score while maintaining similar runtime for graphs with overlapping communities. We also compare DOLPA against an implementation of the Louvain method for community detection using the same LFR-graphs and show that DOLPA achieves about three times the F-Score at just 10% of the runtime. For connected component decomposition, our algorithm achieves orders of magnitude speedups over the basic LP-based algorithm on large-diameter graphs, up to 13.2× speedup over the Shiloach-Vishkin algorithm, and up to 1.6× speedup over Afforest on an Intel Xeon processor using 40 threads.

97 MATHEMATICS AND COMPUTING↗