Renjie Liu

Graph neural networks (GNNs) are models specialized for graph data and widely used in applications. To train GNNs on large graphs that exceed CPU memory, several systems have been designed to store data on disk and conduct out-of-core processing. However, these systems suffer from either read amplification when conducting random reads for node features that are smaller than a disk page, or degraded model accuracy by treating the graph as disconnected partitions. To close this gap, we build DiskGNN for high I/O efficiency and fast training without model accuracy degradation. The key technique is offline sampling, which decouples graph sampling from model computation. In particular, by conducting graph sampling beforehand for multiple mini-batches, DiskGNN acquires the node features that will be accessed during model computation and conducts pre-processing to pack the node features of each mini-batch contiguously on disk to avoid read amplification for computation. Given the feature access information acquired by offline sampling, DiskGNN also adopts designs including four-level feature store to fully utilize the memory hierarchy of GPU and CPU to cache hot node features and reduce disk access, batched packing to accelerate feature packing during pre-processing, and pipelined training to overlap disk access with other operations. We compare DiskGNN with state-of-the-art out-of-core GNN training systems. The results show that DiskGNN has more than 8x speedup over existing systems while matching their best model accuracy. DiskGNN is open-source at https://github.com/Liu-rj/DiskGNN.

There are several strategies to parallelize graph neural network (GNN) training over multiple GPUs. We observe that there is no consistent winner (i.e., with the shortest running time), and the optimal strategy depends on the graph dataset, GNN model, training algorithm, and hardware configurations. As such, we design the APT system to automatically select efficient parallelization strategies for GNN training tasks. To this end, we analyze the trade-offs of the strategies and design simple yet effective cost models to compare their execution time and facilitate strategy selection. Moreover, we also propose a general abstraction of the strategies, which allows to implement a unified execution engine that can be configured to run different strategies. Our experiments show that APT usually chooses the optimal or a close to optimal strategy, and the training time can be reduced by over 2x compared with always using a single strategy. APT is open-source at https://github.com/kaihaoma/APT.

Graph sampling prepares training samples for graph learning and can dominate the training time. Due to the increasing algorithm diversity and complexity, existing sampling frameworks are insufficient in the generality of expression and the efficiency of execution. To close this gap, we conduct a comprehensive study on 15 popular graph sampling algorithms to motivate the design of gSampler, a general and efficient GPU-based graph sampling framework. gSampler models graph sampling using a general 4-step Extract-Compute-Select-Finalize (ECSF) programming model, proposes a set of matrix-centric APIs that allow to easily express complex graph sampling algorithms, and incorporates a data-flow intermediate representation (IR) that translates high-level API codes for efficient GPU execution. We demonstrate that implementing graph sampling algorithms with gSampler is easy and intuitive. We also conduct extensive experiments with 7 algorithms, 4 graph datasets, and 2 hardware configurations. The results show that gSampler introduces sampling speedups of 1.14–32.7\texttimes and an average speedup of 6.54\texttimes, compared to state-of-the-art GPU-based graph sampling systems such as DGL, which translates into an overall time reduction of over 40% for graph learning. gSampler is open-source at https://tinyurl.com/29twthd4.