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1. Marius: Learning Massive Graph Embeddings on a Single Machine

   Mohoney, Jason; Waleffe, Roger; Xu, Henry; Rekatsinas, Theodoros; Venkataraman, Shivaram (January 2021, 15th USENIX Symposium on Operating Systems Design and Implementation (OSDI) 21)

   null (Ed.)

   We propose a new framework for computing the embeddings of large-scale graphs on a single machine. A graph embedding is a fixed length vector representation for each node (and/or edge-type) in a graph and has emerged as the de-facto approach to apply modern machine learning on graphs. We identify that current systems for learning the embeddings of large-scale graphs are bottlenecked by data movement, which results in poor resource utilization and inefficient training. These limitations require state-of-the-art systems to distribute training across multiple machines. We propose Marius, a system for efficient training of graph embeddings that leverages partition caching and buffer-aware data orderings to minimize disk access and interleaves data movement with computation to maximize utilization. We compare Marius against two state-of-the-art industrial systems on a diverse array of benchmarks. We demonstrate that Marius achieves the same level of accuracy but is up to one order of magnitude faster. We also show that Marius can scale training to datasets an order of magnitude beyond a single machine's GPU and CPU memory capacity, enabling training of configurations with more than a billion edges and 550 GB of total parameters on a single machine with 16 GB of GPU memory and 64 GB of CPU memory. Marius is open-sourced at www.marius-project.org. 

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2. Addressing GPU memory limitations for Graph Neural Networks in High-Energy Physics applications

   https://doi.org/10.3389/fhpcp.2024.1458674  

   Lee, Claire Songhyun; Hewes, V; Cerati, Giuseppe; Wang, Kewei; Aurisano, Adam; Agrawal, Ankit; Choudhary, Alok; Liao, Wei-Keng (September 2024, Frontiers in High Performance Computing)

   IntroductionReconstructing low-level particle tracks in neutrino physics can address some of the most fundamental questions about the universe. However, processing petabytes of raw data using deep learning techniques poses a challenging problem in the field of High Energy Physics (HEP). In the Exa.TrkX Project, an illustrative HEP application, preprocessed simulation data is fed into a state-of-art Graph Neural Network (GNN) model, accelerated by GPUs. However, limited GPU memory often leads to Out-of-Memory (OOM) exceptions during training, due to the large size of models and datasets. This problem is exacerbated when deploying models on High-Performance Computing (HPC) systems designed for large-scale applications. MethodsWe observe a high workload imbalance issue during GNN model training caused by the irregular sizes of input graph samples in HEP datasets, contributing to OOM exceptions. We aim to scale GNNs on HPC systems, by prioritizing workload balance in graph inputs while maintaining model accuracy. Our paper introduces diverse balancing strategies aimed at decreasing the maximum GPU memory footprint and avoiding the OOM exception, across various datasets. ResultsOur experiments showcase memory reduction of up to 32.14% compared to the baseline. We also demonstrate the proposed strategies can avoid OOM in application. Additionally, we create a distributed multi-GPU implementation using these samplers to demonstrate the scalability of these techniques on the HEP dataset. DiscussionBy assessing the performance of these strategies as data loading samplers across multiple datasets, we can gauge their effectiveness in both single-GPU and distributed environments. Our experiments, conducted on datasets of varying sizes and across multiple GPUs, broaden the applicability of our work to various GNN applications that handle input datasets with irregular graph sizes. 

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3. {MGG}: Accelerating Graph Neural Networks with {Fine-Grained} {Intra-Kernel} {Communication-Computation} Pipelining on {Multi-GPU} Platforms

   Wang, Yuke; Feng, Boyuan; Wang, Zheng; Barker, Kevin; Li, Ang; Ding, Yufei. (July 2023, USENIX Association)

   The increasing size of input graphs for graph neural networks (GNNs) highlights the demand for using multi-GPU platforms. However, existing multi-GPU GNN systems optimize the computation and communication individually based on the conventional practice of scaling dense DNNs. For irregularly sparse and fine-grained GNN workloads, such solutions miss the opportunity to jointly schedule/optimize the computation and communication operations for high-performance delivery. To this end, we propose MGG , a novel system design to accelerate full-graph GNNs on multi-GPU platforms. The core of MGG is its novel dynamic software pipeline to facilitate fine-grained computation-communication overlapping within a GPU kernel. Specifically, MGG introduces GNN-tailored pipeline construction and GPU-aware pipeline mapping to facilitate workload balancing and operation overlapping. MGG also incorporates an intelligent runtime design with analytical modeling and optimization heuristics to dynamically improve the execution performance. Extensive evaluation reveals that MGG outperforms state-of-the-art full-graph GNN systems across various settings: on average 4.41×, 4.81×, and 10.83× faster than DGL, MGG-UVM, and ROC, respectively. 

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4. GIST: distributed training for large-scale graph convolutional networks

   https://doi.org/10.1007/s41468-023-00127-8  

   Wolfe, Cameron_R; Yang, Jingkang; Liao, Fangshuo; Chowdhury, Arindam; Dun, Chen; Bayer, Artun; Segarra, Santiago; Kyrillidis, Anastasios (August 2023, Journal of Applied and Computational Topology)

   Abstract The graph convolutional network (GCN) is a go-to solution for machine learning on graphs, but its training is notoriously difficult to scale both in terms of graph size and the number of model parameters. Although some work has explored training on large-scale graphs, we pioneer efficient training of large-scale GCN models with the proposal of a novel, distributed training framework, called . disjointly partitions the parameters of a GCN model into several, smaller sub-GCNs that are trained independently and in parallel. Compatible with all GCN architectures and existing sampling techniques, (i) improves model performance, (ii) scales to training on arbitrarily large graphs, (iii) decreases wall-clock training time, and (iv) enables the training of markedly overparameterized GCN models. Remarkably, with , we train an astonishgly-wide 32–768-dimensional GraphSAGE model, which exceeds the capacity of a single GPU by a factor of$$8\times $$ $8\times$, to SOTA performance on the Amazon2M dataset. 

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5. Redundancy-Free Computation for Graph Neural Networks

   https://doi.org/10.1145/3394486.3403142  

   Jia, Z.; Lin, S.; Ying, R.; You, J.; Leskovec, J.; Aiken, A. (October 2020, Knowledge discovery and data mining letters)

   Graph Neural Networks (GNNs) are based on repeated aggregations of information from nodes’ neighbors in a graph. However, because nodes share many neighbors, a naive implementation leads to repeated and inefficient aggregations and represents significant computational overhead. Here we propose Hierarchically Aggregated computation Graphs (HAGs), a new GNN representation technique that explicitly avoids redundancy by managing intermediate aggregation results hierarchically and eliminates repeated computations and unnecessary data transfers in GNN training and inference. HAGs perform the same computations and give the same models/accuracy as traditional GNNs, but in a much shorter time due to optimized computations. To identify redundant computations, we introduce an accurate cost function and use a novel search algorithm to find optimized HAGs. Experiments show that the HAG representation significantly outperforms the standard GNN by increasing the end-to-end training throughput by up to 2.8× and reducing the aggregations and data transfers in GNN training by up to 6.3× and 5.6×, with only 0.1% memory overhead. Overall, our results represent an important advancement in speeding-up and scaling-up GNNs without any loss in model predictive performance. 

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