6.9 Data Loading Parallelism

In minibatch training of GNNs, we usually need to cover several stages to generate a minibatch, including:

  • Iterate over item set and generate minibatch seeds in batch size.

  • Sample negative items for each seed from graph.

  • Sample neighbors for each seed from graph.

  • Exclude seed edges from the sampled subgraphs.

  • Fetch node and edge features for the sampled subgraphs.

  • Copy the MiniBatches to the target device.

datapipe = gb.ItemSampler(itemset, batch_size=1024, shuffle=True)
datapipe = datapipe.sample_uniform_negative(g, 5)
datapipe = datapipe.sample_neighbor(g, [10, 10]) # 2 layers.
datapipe = datapipe.transform(gb.exclude_seed_edges)
datapipe = datapipe.fetch_feature(feature, node_feature_keys=["feat"])
datapipe = datapipe.copy_to(device)
dataloader = gb.DataLoader(datapipe)

All these stages are implemented in separate IterableDataPipe and stacked together with PyTorch DataLoader. This design allows us to easily customize the data loading process by chaining different data pipes together. For example, if we want to sample negative items for each seed from graph, we can simply chain the NegativeSampler after the ItemSampler.

But simply chaining data pipes together incurs performance overheads as various hardware resources such as CPU, GPU, PCIe, etc. are utilized by different stages. As a result, the data loading mechanism is optimized to minimize the overheads and achieve the best performance.

In specific, GraphBolt wraps the data pipes before fetch_feature with multiprocessing which enables multiple processes to run in parallel. As for fetch_feature data pipe, we keep it running in the main process to avoid data movement overheads between processes.

What’s more, in order to overlap the data movement and model computation, we wrap data pipes before copy_to with torchdata.datapipes.iter.Perfetcher which prefetches elements from previous data pipes and puts them into a buffer. Such prefetching is totally transparent to users and requires no extra code. It brings a significant performance boost to minibatch training of GNNs.

Please refer to the source code of DataLoader for more details.