BGL_NSDI2023

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Open source code of BGL NSDI 2023

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# BGL NSDI 2023
This is the source code of BGL: GPU-Efficient GNN Training by Optimizing Graph Data I/O and Preprocessing,  published in NSDI 2023.

We build BGL on the top of DGL v 0.5.0.

Hence, to run BGL, you should build DGL firstly by following the DGL compilation command(https://docs.dgl.ai/install/index.html#install-from-source).

## Code for each components
We have three key components in BGL, feature cache engine, graph partition module and async training pipeline.

The source code of feature cache engine and async training pipeline is in the file src/rpc/multi_gpu_tensor_cache_engine.cc

The proximity-aware ordering is in the file src/graph/graph_traversal.cc

The graph partition module is based on the GMiner partition algorithm, which is open-sourced in https://github.com/yaobaiwei/GMiner. We provide the main codes of partition algorithm in the examples/pytorch/graphsage/experimental/partition_codes

## Example
We have testes three GNN models: GraphSAGE, GCN and GAT.

The models and running scripts are in examples/pytorch/graphsage/experimental.

## Cite

If you use our codes and want to cite our paper, use following bibtex
```
@inproceedings {285052,
author = {Tianfeng Liu and Yangrui Chen and Dan Li and Chuan Wu and Yibo Zhu and Jun He and Yanghua Peng and Hongzheng Chen and Hongzhi Chen and Chuanxiong Guo},
title = {{BGL}: {GPU-Efficient} {GNN} Training by Optimizing Graph Data {I/O} and Preprocessing},
booktitle = {20th USENIX Symposium on Networked Systems Design and Implementation (NSDI 23)},
year = {2023},
isbn = {978-1-939133-33-5},
address = {Boston, MA},
pages = {103--118},
url = {https://www.usenix.org/conference/nsdi23/presentation/liu-tianfeng},
publisher = {USENIX Association},
month = apr,
}
```

# Deep Graph Library (DGL)

[![PyPi Latest Release](https://img.shields.io/pypi/v/dgl.svg)](https://pypi.org/project/dgl/)
[![Conda Latest Release](https://anaconda.org/dglteam/dgl/badges/version.svg)](https://anaconda.org/dglteam/dgl)
[![Build Status](http://ci.dgl.ai:80/buildStatus/icon?job=DGL/master)](http://ci.dgl.ai:80/job/DGL/job/master/)
[![Benchmark by ASV](http://img.shields.io/badge/benchmarked%20by-asv-green.svg?style=flat)](https://asv.dgl.ai/)
[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://raw.githubusercontent.com/leodestiny/BGL_NSDI2023/main/LICENSE)

Documentation ([Latest](https://docs.dgl.ai/en/latest/) | [Stable](https://docs.dgl.ai)) | [DGL at a glance](https://docs.dgl.ai/tutorials/basics/1_first.html#sphx-glr-tutorials-basics-1-first-py) | [Model Tutorials](https://docs.dgl.ai/tutorials/models/index.html) | [Discussion Forum](https://discuss.dgl.ai) | [Slack Channel](https://join.slack.com/t/deep-graph-library/shared_invite/zt-eb4ict1g-xcg3PhZAFAB8p6dtKuP6xQ)

DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs. DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow.

<img src="http://data.dgl.ai/asset/image/DGL-Arch.png" alt="DGL v0.4 architecture" width="600">
 
 Figure: DGL Overall Architecture

## <img src="http://data.dgl.ai/asset/image/new.png" width="30">DGL News
**08/21/2020**: The new **v0.5.0 release** includes distributed GNN training, overhauled documentation and user guide, and several more features. We have also submitted some models to the [OGB](https://ogb.stanford.edu) leaderboard. See our [release note](https://github.com/dmlc/dgl/releases/tag/0.5.0) for more details.

**06/11/2020**: Amazon Shanghai AI Lab and AWS Deep Engine Science team working along with academic collaborators from the University of Minnesota, The Ohio State University, and Hunan University have created the **[Drug Repurposing Knowledge Graph (DRKG)](https://github.com/gnn4dr/DRKG)** and a set of machine learning tools, [DGL-KE](https://github.com/awslabs/dgl-ke), that can be used to prioritize drugs for repurposing studies. 
DRKG is a comprehensive biological knowledge graph that relates human genes, compounds, biological processes, drug side effects, diseases and symptoms. DRKG includes, curates, and normalizes information from six publicly available databases and data that were collected from recent publications related to Covid-19. It has 97,238 entities belonging to 13 types of entities, and 5,874,261 triplets belonging to 107 types of relations. 
More about the dataset is in this [blogpost](https://www.dgl.ai/news/2020/06/09/covid.html).

## Using DGL

**A data scientist** may want to apply a pre-trained model to your data right away. For this you can use DGL's [Application packages, formally *Model Zoo*](https://github.com/dmlc/dgl/tree/master/apps). Application packages are developed for domain applications, as is the case for [DGL-LifeScience](https://github.com/awslabs/dgl-lifesci). We will soon add model zoo for knowledge graph embedding learning and recommender systems. Here's how you will use a pretrained model:
```python
from dgllife.data import Tox21
from dgllife.model import load_pretrained
from dgllife.utils import smiles_to_bigraph, CanonicalAtomFeaturizer

dataset = Tox21(smiles_to_bigraph, CanonicalAtomFeaturizer())
model = load_pretrained('GCN_Tox21') # Pretrained model loaded
model.eval()

smiles, g, label, mask = dataset[0]
feats = g.ndata.pop('h')
label_pred = model(g, feats)
print(smiles)                   # CCOc1ccc2nc(S(N)(=O)=O)sc2c1
print(label_pred[:, mask != 0]) # Mask non-existing labels
# tensor([[ 1.4190, -0.1820,  1.2974,  1.4416,  0.6914,  
# 2.0957,  0.5919,  0.7715, 1.7273,  0.2070]])
```

**Further reading**: DGL is released as a managed service on AWS SageMaker, see the medium posts for an easy trip to DGL on SageMaker([part1](https://medium.com/@julsimon/a-primer-on-graph-neural-networks-with-amazon-neptune-and-the-deep-graph-library-5ce64984a276) and [part2](https://medium.com/@julsimon/deep-graph-library-part-2-training-on-amazon-sagemaker-54d318dfc814)).

**Researchers** can start from the growing list of [models implemented in DGL](https://github.com/dmlc/dgl/tree/master/examples). Developing new models does not mean that you have to start from scratch. Instead, you can reuse many [pre-built modules](https://docs.dgl.ai/api/python/nn.html). Here is how to get a standard two-layer graph convolutional model with a pre-built GraphConv module:
```python
from dgl.nn.pytorch import GraphConv
import torch.nn.functional as F

# build a two-layer GCN with ReLU as the activation in between
class GCN(nn.Module):
    def __init__(self, in_feats, h_feats, num_classes):
        super(GCN, self).__init__()
        self.gcn_layer1 = GraphConv(in_feats, h_feats)
        self.gcn_layer2 = GraphConv(h_feats, num_classes)
    
    def forward(self, graph, inputs):
        h = self.gcn_layer1(graph, inputs)
        h = F.relu(h)
        h = self.gcn_layer2(graph, h)
        return h
```

Next level down, you may want to innovate your own module. DGL offers a succinct message-passing interface (see tutorial [here](https://docs.dgl.ai/tutorials/basics/3_pagerank.html)). Here is how Graph Attention Network (GAT) is implemented ([complete codes](https://docs.dgl.ai/api/python/nn.pytorch.html#gatconv)). Of course, you can also find GAT as a module [GATConv](https://docs.dgl.ai/api/python/nn.pytorch.html#gatconv):
```python
import torch.nn as nn
import torch.nn.functional as F

# Define a GAT layer
class GATLayer(nn.Module):
    def __init__(self, in_feats, out_feats):
        super(GATLayer, self).__init__()
        self.linear_func = nn.Linear(in_feats, out_feats, bias=False)
        self.attention_func = nn.Linear(2 * out_feats, 1, bias=False)
        
    def edge_attention(self, edges):
        concat_z = torch.cat([edges.src['z'], edges.dst['z']], dim=1)
        src_e = self.attention_func(concat_z)
        src_e = F.leaky_relu(src_e)
        return {'e': src_e}
    
    def message_func(self, edges):
        return {'z': edges.src['z'], 'e':edges.data['e']}
        
    def reduce_func(self, nodes):
        a = F.softmax(nodes.mailbox['e'], dim=1)
        h = torch.sum(a * nodes.mailbox['z'], dim=1)
        return {'h': h}
                               
    def forward(self, graph, h):
        z = self.linear_func(h)
        graph.ndata['z'] = z
        graph.apply_edges(self.edge_attention)
        graph.update_all(self.message_func, self.reduce_func)
        return graph.ndata.pop('h')
```
## Performance and Scalability

**Microbenchmark on speed and memory usage**: While leaving tensor and autograd functions to backend frameworks (e.g. PyTorch, MXNet, and TensorFlow), DGL aggressively optimizes storage and computation with its own kernels. Here's a comparison to another popular package -- PyTorch Geometric (PyG). The short story is that raw speed is similar, but DGL has much better memory management.

| Dataset | Model | Accuracy | Time PyG &emsp;&emsp; DGL | Memory PyG &emsp;&emsp; DGL |
| -------- |:------------:|:--------------------------------------------:|:--------------------------------------------------------------------:|:-----------------------------------------------------:|
| Cora | GCN GAT | 81.31 &plusmn; 0.88 83.98 &plusmn; 0.52 | 0.478 &emsp;&emsp; 0.666 1.608 &emsp;&emsp; 1.399 | 1.1 &emsp;&emsp; 1.1 1.2 &emsp;&emsp; 1.1 |
| CiteSeer | GCN GAT | 70.98 &plusmn; 0.68 69.96 &plusmn; 0.53 | 0.490 &emsp;&emsp; 0.674 1.606 &emsp;&emsp; 1.399 | 1.1 &emsp;&emsp; 1.1 1.3 &emsp;&emsp; 1.1 |
| PubMed | GCN GAT | 79.00 &plusmn; 0.41 77.65 &plusmn; 0.32 | 0.491 &emsp;&emsp; 0.690 1.946 &emsp;&emsp; 1.393 | 1.1 &emsp;&emsp; 1.1 1.6 &emsp;&emsp; 1.1 |
| Reddit | GCN | 93.46 &plusmn; 0.06 | *OOM*&emsp;&emsp; 28.6 | *OOM* &emsp;&emsp; 11.7 |
| Reddit-S | GCN | N/A | 29.12 &emsp;&emsp; 9.44 | 15.7 &emsp;&emsp; 3.6 |

Table: Training time(in seconds) for 200 epochs and memory consumption(GB)

Here is another comparison of DGL on TensorFlow backend with other TF-based GNN tools (training time in seconds for one epoch):

| Dateset | Model | DGL | GraphNet | tf_geometric |
| ------- | ----- | --- | -------- | ------------ |
| Core | GCN | 0.0148 | 0.0152 | 0.0192 |
| Reddit | GCN | 0.1095 | OOM | OOM |
| PubMed | GCN | 0.0156 | 0.0553 | 0.0185 |
| PPI | GCN | 0.09 | 0.16 | 0.21 |
| Cora | GAT | 0.0442 | n/a | 0.058 |
| PPI | GAT | 0.398 | n/a | 0.752 |

High memory utilization allows DGL to push the limit of single-GPU performance, as seen in below images.
| <img src="http://data.dgl.ai/asset/image/DGLvsPyG-time1.png" width="400"> | <img src="http://data.dgl.ai/asset/image/DGLvsPyG-time2.png" width="400"> |
| -------- | -------- |

**Scalability**: DGL has fully leveraged multiple GPUs in both one machine and clusters for increasing training speed, and has better performance than alternatives, as seen in below images.

| <img src="http://data.dgl.ai/asset/image/one-four-GPUs-DGLvsGraphVite.png"> | <img src="http://data.dgl.ai/asset/image/one-fourMachines.png"> | 
| :---------------------------------------: | -- |

**Further reading**: Detailed comparison of DGL and other Graph alternatives can be found [here](https://arxiv.org/abs/1909.01315).

## DGL Models and Applications

### DGL for research
Overall there are 30+ models implemented by using DGL:
- [PyTorch](https://github.com/dmlc/dgl/tree/master/examples/pytorch)
- [MXNet](https://github.com/dmlc/dgl/tree/master/examples/mxnet)
- [TensorFlow](https://github.com/dmlc/dgl/tree/master/examples/tensorflow)

### DGL for domain applications
- [DGL-LifeSci](https://github.com/awslabs/dgl-lifesci), previously DGL-Chem
- [DGL-KE](https://github.com/awslabs/dgl-ke)
- DGL-RecSys(coming soon)

### DGL for NLP/CV problems
- [TreeLSTM](https://github.com/dmlc/dgl/tree/master/examples/pytorch/tree_lstm)
- [GraphWriter](https://github.com/dmlc/dgl/tree/master/examples/pytorch/graphwriter)
- [Capsule Network](https://github.com/dmlc/dgl/tree/master/examples/pytorch/capsule)

We are currently in Beta stage.  More features and improvements are coming.

## Installation

DGL should work on

* all Linux distributions no earlier than Ubuntu 16.04
* macOS X
* Windows 10

DGL requires Python 3.5 or later.

Right now, DGL works on [PyTorch](https://pytorch.org) 1.2.0+, [MXNet](https://mxnet.apache.org) 1.5.1+, and [TensorFlow](https://tensorflow.org) 2.1.0+.

### Using anaconda

```
conda install -c dglteam dgl           # cpu version
conda install -c dglteam dgl-cuda9.0   # CUDA 9.0
conda install -c dglteam dgl-cuda9.2   # CUDA 9.2
conda install -c dglteam dgl-cuda10.0  # CUDA 10.0
conda install -c dglteam dgl-cuda10.1  # CUDA 10.1
conda install -c dglteam dgl-cuda10.2  # CUDA 10.2
```

### Using pip

|           | Latest Nightly Build Version  | Stable Version          |
|-----------|-------------------------------|-------------------------|
| CPU       | `pip install --pre dgl`       | `pip install dgl`       |
| CUDA 9.0  | `pip install --pre dgl-cu90`  | `pip install dgl-cu90`  |
| CUDA 9.2  | `pip install --pre dgl-cu92`  | `pip install dgl-cu92`  |
| CUDA 10.0 | `pip install --pre dgl-cu100` | `pip install dgl-cu100` |
| CUDA 10.1 | `pip install --pre dgl-cu101` | `pip install dgl-cu101` |
| CUDA 10.2 | `pip install --pre dgl-cu102` | `pip install dgl-cu102` |

### Built from source code

Refer to the guide [here](https://docs.dgl.ai/install/index.html#install-from-source).

## DGL Major Releases

| Releases | Date | Features |
|-----------|--------|-------------------------|
| v0.4.3 | 03/31/2020 | - TensorFlow support - DGL-KE - DGL-LifeSci - Heterograph sampling APIs (experimental) |
| v0.4.2 | 01/24/2020 | - Heterograph support - TensorFlow support (experimental) - MXNet GNN modules | 
| v0.3.1 | 08/23/2019 | - APIs for GNN modules - Model zoo (DGL-Chem) - New installation |
| v0.2 | 03/09/2019 | - Graph sampling APIs - Speed improvement |
| v0.1 | 12/07/2018 | - Basic DGL APIs - PyTorch and MXNet support - GNN model examples and tutorials |

## New to Deep Learning and Graph Deep Learning?

Check out the open source book [*Dive into Deep Learning*](https://d2l.ai/).

For those who are new to graph neural network, please see the [basic of DGL](https://docs.dgl.ai/tutorials/basics/index.html).

For audience who are looking for more advanced, realistic, and end-to-end examples, please see [model tutorials](https://docs.dgl.ai/tutorials/models/index.html).

## Contributing

Please let us know if you encounter a bug or have any suggestions by [filing an issue](https://github.com/dmlc/dgl/issues).

We welcome all contributions from bug fixes to new features and extensions.

We expect all contributions discussed in the issue tracker and going through PRs.  Please refer to our [contribution guide](https://docs.dgl.ai/contribute.html).

## Cite

If you use DGL in a scientific publication, we would appreciate citations to the following paper:
```
@article{wang2019dgl,
    title={Deep Graph Library: Towards Efficient and Scalable Deep Learning on Graphs},
    url={https://arxiv.org/abs/1909.01315},
    author={Wang, Minjie and Yu, Lingfan and Zheng, Da and Gan, Quan and Gai, Yu and Ye, Zihao and Li, Mufei and Zhou, Jinjing and Huang, Qi and Ma, Chao and Huang, Ziyue and Guo, Qipeng and Zhang, Hao and Lin, Haibin and Zhao, Junbo and Li, Jinyang and Smola, Alexander J and Zhang, Zheng},
    journal={ICLR Workshop on Representation Learning on Graphs and Manifolds},
    year={2019}
}
```

## The Team

DGL is developed and maintained by [NYU, NYU Shanghai, AWS Shanghai AI Lab, and AWS MXNet Science Team](https://www.dgl.ai/pages/about.html).

## License

DGL uses Apache License 2.0.

BGL_NSDI2023

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