Search NASA⌕ Search

SEARCH · Search NASA

Results for “distributed memory parallel”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

550 records · Page 31

Communication-Avoiding and Memory-Constrained Sparse Matrix-Matrix Multiplication at Extreme Scale

Sparse matrix-matrix multiplication (SpGEMM) is a widely used kernel in various graph, scientific computing and machine learning algorithms. In this paper, we consider SpGEMMs performed on hundreds of thousands of processors generating trillions of nonzeros in the output matrix. Distributed SpGEMM at this extreme scale faces two key challenges: (1) high communication cost and (2) inadequate memory to generate the output. Furthermore, we address these challenges with an integrated communication-avoiding and memory-constrained SpGEMM algorithm that scales to 262,144 cores (more than 1 million hardware threads) and can multiply sparse matrices of any size as long as inputs and a fraction of output fit in the aggregated memory. As we go from 16,384 cores to 262,144 cores on a Cray XC40 supercomputer, the new SpGEMM algorithm runs 10x faster when multiplying large-scale protein-similarity matrices.

97 MATHEMATICS AND COMPUTING↗

Scaling Resolution of Gigapixel Whole Slide Images Using Spatial Decomposition on Convolutional Neural Networks

Gigapixel images are prevalent in scientific domains ranging from remote sensing, and satellite imagery to microscopy, etc. However, training a deep learning model at the natural resolution of those images has been a challenge in terms of both, overcoming the resource limit (e.g. HBM memory constraints), as well as scaling up to a large number of GPUs. In this paper, we trained Residual neural Networks (ResNet) on 22,528 x 22,528-pixel size images using a distributed spatial decomposition method on 2,304 GPUs on the Summit Supercomputer. We applied our method on a Whole Slide Imaging (WSI) dataset from The Cancer Genome Atlas (TCGA) database. WSI images can be in the size of 100,000 x 100,000 pixels or even larger, and in this work we studied the effect of image resolution on a classification task, while achieving state-of-the-art AUC scores. Moreover, our approach doesn't need pixel-level labels, since we're avoiding patching from the WSI images completely, while adding the capability of training arbitrary large-size images. This is achieved through a distributed spatial decomposition method, by leveraging the non-block fat-tree interconnect network of the Summit architecture, which enabled GPU-to-GPU direct communication. Finally, detailed performance analysis results are shown, as well as a comparison with a data-parallel approach when possible.

Tsaris, Aristeidis (aris)↗

NSTX-U advances in real-time deterministic PCIe-based internode communication

Distributing control mechanisms across modern commercial off the shelf (COTS) GNU/Linux systems often introduces difficult to mitigate non-deterministic behavior. Existing methods to address this problem involve non-real-time technologies such as Remote Direct Memory Access (RDMA) over Infiniband or custom Ethernet solutions, such as RDMA over Converged Ethernet (RoCE) or userspace Ethernet drivers, that trade determinism for ease of use or lower cost. The National Spherical Torus Experiment Upgrade (NSTX-U) is pursuing a new design that allows direct communication between heterogeneous systems with scalable, microsecond latency with 1 μs of jitter on that latency, outside of the constant transmission delay at the physical layer. The future design of the NSTX-U Real-time Communication System will utilize direct PCIe-to-PCIe communication with kernel support tuned for low overhead, allowing two (or more, through a switch) real-time (RT) systems to communicate and share resources as one larger entity. As a result, this greatly increases the processing capability of the primary Plasma Control System (PCS), turning previously insurmountable computational challenges into a more manageable divide and conquer parallel task.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A Scalable Online Monitoring System Based on Elasticsearch for Distributed Data Acquisition in Cms

The part of the CMS Data Acquisition (DAQ) system responsible for data readout and event building is a complex network of interdependent distributed applications. To ensure successful data taking, these programs have to be constantly monitored in order to facilitate the timeliness of necessary corrections in case of any deviation from specified behaviour. A large number of diverse monitoring data samples are periodically collected from multiple sources across the network. Monitoring data are kept in memory for online operations and optionally stored on disk for post-mortem analysis. We present a generic, reusable solution based on an open source NoSQL database, Elasticsearch, which is fully compatible and non-intrusive with respect to the existing system. The motivation is to benefit from an off the-shelf software to facilitate the development, maintenance and support efforts. Elasticsearch provides failover and data redundancy capabilities as well as a programming language independent JSON-over-HTTP interface. The possibility of horizontal scaling matches the requirements of a DAQ monitoring system. The data load from all sources is balanced by redistribution over an Elasticsearch cluster that can be hosted on a computer cloud. In order to achieve the necessary robustness and to validate the scalability of the approach the above monitoring solution currently runs in parallel with an existing in-house developed DAQ monitoring system.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Ad Hoc File Systems for High-Performance Computing

Storage backends of parallel compute clusters are still based mostly on magnetic disks, while newer and faster storage technologies such as flash-based SSDs or non-volatile random access memory (NVRAM) are deployed within compute nodes. Including these new storage technologies into scientific workflows is unfortunately today a mostly manual task, and most scientists therefore do not take advantage of the faster storage media. One approach to systematically include nodelocal SSDs or NVRAMs into scientific workflows is to deploy ad hoc file systems over a set of compute nodes, which serve as temporary storage systems for single applications or longer-running campaigns. This paper presents results from the Dagstuhl Seminar 17202 “Challenges and Opportunities of User-Level File Systems for HPC” and discusses application scenarios as well as design strategies for ad hoc file systems using node-local storage media. The discussion includes open research questions, such as how to couple ad hoc file systems with the batch scheduling environment and how to schedule stage-in and stage-out processes of data between the storage backend and the ad hoc file systems. Also presented are strategies to build ad hoc file systems by using reusable components for networking and how to improve storage device compatibility. Various interfaces and semantics are presented, for example those used by the three ad hoc file systems BeeOND, GekkoFS, and BurstFS. Their presentation covers a range from file systems running in production to cutting-edge research focusing on reaching the performance limits of the underlying devices.

97 MATHEMATICS AND COMPUTING↗

Dynamic Load Balancing Based on Constrained K-D Tree Decomposition for Parallel Particle Tracing

Particle tracing is a fundamental technique in flow field data visualization. In this work, we present a novel dynamic load balancing method for parallel particle tracing. Specifically, we employ a constrained k-d tree decomposition approach to dynamically redistribute tasks among processes. Each process is initially assigned a regularly partitioned block along with duplicated ghost layer under the memory limit. During particle tracing, the k-d tree decomposition is dynamically performed by constraining the cutting planes in the overlap range of duplicated data. This ensures that each process is reassigned particles as even as possible, and on the other hand the new assigned particles for a process always locate in its block. Result shows good load balance and high efficiency of our method.

Zhang, Jiang↗

Proximity Portability and in Transit , M-to-N Data Partitioning and Movement in SENSEI [Book Chapter]

In high-performance parallel in situ processing, the term in transit processing refers to those configurations where data must move from a producer to a consumer that runs on separate resources. In the context of parallel and distributed computing on an HPC platform one of the central challenges is to determine a mapping of data from producer ranks to consumer ranks. This problem is complicated by the heterogeneity that arises in producer-consumer pairs, such as when producer and consumer codes have different levels of concurrency, different scaling characteristics, or different data models. The resulting mapping and movement of data from M producer to N consumer ranks can have a significant impact on aggregate application performance, particularly when the data consumer requires only a subset of the overall data for its task. This chapter focuses on the design considerations that underlie SENSEI’s implementation to this challenging problem. These design considerations extend the core SENSEI architecture and include ideas like the need to accommodate flexibility in the choice of different partitioning methods, the ability for a data consumer to request and receive only the subset of data needed for its particular operation, and the ability to leverage any of several different data transport tools. The idea of proximity portability, being able to use different data transport methods as part of an in transit workflow, is illustrated through the use of three different transport layers where switching from one transport tool to another is accomplished with only a configuration file change. Here, the chapter also includes a performance analysis summary showing the performance gains that are possible in terms of multiple metrics, such as memory footprint, time to solution, and amount of data moved, when using optimized partitioners in an in transit setting, gains that are made possible by the implementation shaped by specific design considerations.

Bethel, E. Wes↗

Parallelization of the Physical-Space Statistical Analysis System (PSAS)

Atmospheric data assimilation is a method of combining observations with model forecasts to produce a more accurate description of the atmosphere than the observations or forecast alone can provide. Data assimilation plays an increasingly important role in the study of climate and atmospheric chemistry. The NASA Data Assimilation Office (DAO) has developed the Goddard Earth Observing System Data Assimilation System (GEOS DAS) to create assimilated datasets. The core computational components of the GEOS DAS include the GEOS General Circulation Model (GCM) and the Physical-space Statistical Analysis System (PSAS). The need for timely validation of scientific enhancements to the data assimilation system poses computational demands that are best met by distributed parallel software. PSAS is implemented in Fortran 90 using object-based design principles. The analysis portions of the code solve two equations. The first of these is the "innovation" equation, which is solved on the unstructured observation grid using a preconditioned conjugate gradient (CG) method. The "analysis" equation is a transformation from the observation grid back to a structured grid, and is solved by a direct matrix-vector multiplication. Use of a factored-operator formulation reduces the computational complexity of both the CG solver and the matrix-vector multiplication, rendering the matrix-vector multiplications as a successive product of operators on a vector. Sparsity is introduced to these operators by partitioning the observations using an icosahedral decomposition scheme. PSAS builds a large (approx. 128MB) run-time database of parameters used in the calculation of these operators. Implementing a message passing parallel computing paradigm into an existing yet developing computational system as complex as PSAS is nontrivial. One of the technical challenges is balancing the requirements for computational reproducibility with the need for high performance. The problem of computational reproducibility is well known in the parallel computing community. It is a requirement that the parallel code perform calculations in a fashion that will yield identical results on different configurations of processing elements on the same platform. In some cases this problem can be solved by sacrificing performance. Meeting this requirement and still achieving high performance is very difficult. Topics to be discussed include: current PSAS design and parallelization strategy; reproducibility issues; load balance vs. database memory demands, possible solutions to these problems.

Larson, J. W.↗

HARMONY: Large-Scale Architecture Search for Efficient Hybrid Language Models

As large language models scale to trillions of parameters, their computational and memory requirements present critical challenges for efficient training and deployment. While Mixture of Experts (MoE) architectures enable efficient scaling through sparse parameter activation, and state-space models like Mamba offer linear-time complexity, principled methods for combining these paradigms remain undeveloped. We introduce HARMONY (Hybrid Architecture Research for Mamba, Optimized with Neural efficiencY), a multi-objective evolutionary neural architecture search framework for discovering efficient hybrid language models that integrate Transformer attention mechanisms, Mixture-of-Experts routing, and Mamba state-space components. Through large-scale distributed search using 16,384 MI250X GPUs on the Frontier supercomputer, HARMONY explores a comprehensive design space encompassing six attention variants (MHA, MQA, GQA, MLA, SWA, and Mamba-2), variable MoE configurations with both routed and shared experts, and extensive Mamba hyperparameters. Our framework discovers heterogeneous architectures that balance training performance with computational efficiency through multi-objective optimization incorporating latency penalties and fitness-based selection. Analysis of discovered architectures reveals that optimal hybrid designs favor heterogeneous component mixing rather than homogeneous patterns, with Mamba-2 and Multi-Head Latent Attention (MLA) emerging as preferred mechanisms. Discovered architectures demonstrate superior training efficiency: our best configuration achieves a final perplexity of 1.0874 with 2.38B parameters while processing 4,320 tokens/second, outperforming significantly larger manually designed models. Full-scale evaluation shows HARMONY's top architectures achieve better loss trajectories than equivalently-sized models using state-of-the-art configurations including Mixtral, Jamba, and Samba. Additionally, we demonstrate 91% weak scaling efficiency when training discovered 36B-parameter models across 1,024 GPUs. HARMONY is released as an open framework with comprehensive tools for building and training hybrid models using expert-data-pipeline parallelism, democratizing access to automated architecture design for next-generation language models.

Herron, Emily [ORNL] (ORCID:0000000273008172)↗

Parallel algorithms for finding connected components using linear algebra

Finding connected components is one of the most widely used operations on a graph. Optimal serial algorithms for the problem have been known for half a century, and many competing parallel algorithms have been proposed over the last several decades under various different models of parallel computation. This paper presents a class of parallel connected-component algorithms designed using linear-algebraic primitives. These algorithms are based on a PRAM algorithm by Shiloach and Vishkin and can be designed using standard GraphBLAS operations. Here, we demonstrate two algorithms of this class, one named LACC for Linear Algebraic Connected Components, and the other named FastSV which can be regarded as LACC’s simplification. With the support of the highly-scalable Combinatorial BLAS library, LACC and FastSV outperform the previous state-of-the-art algorithm by a factor of up to 12x for small to medium scale graphs. For large graphs with more than 50B edges, LACC and FastSV scale to 4K nodes (262K cores) of a Cray XC40 supercomputer and outperform previous algorithms by a significant margin. This remarkable performance is accomplished by (1) exploiting sparsity that was not present in the original PRAM algorithm formulation, (2) using high-performance primitives of Combinatorial BLAS, and (3) identifying hot spots and optimizing them away by exploiting algorithmic insights.

97 MATHEMATICS AND COMPUTING↗