[Tutorial] Distributed node classification. (#2969)

* add init version.

* fix build.

* fix format.

* fix.

* fix.

* fix format.

* update README.

* avoid running CI on distributed training tutorials.

* Update tutorials/dist/1_node_classification.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* fix.
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

docs/README.md

@@ -30,3 +30,7 @@ Render locally
 cd build/html
 python3 -m http.server 8000
 ```
+
+Add new folders
+---------------
+Add the path of the new folder in the two lists `examples_dirs` and `gallery_dirs` in docs/source/conf.py.

docs/source/conf.py

@@ -197,9 +197,11 @@ from sphinx_gallery.sorting import FileNameSortKey
 
 examples_dirs = ['../../tutorials/blitz',
                  '../../tutorials/large',
+                 '../../tutorials/dist',
                  '../../tutorials/models']  # path to find sources
 gallery_dirs = ['tutorials/blitz/',
                 'tutorials/large/',
+                'tutorials/dist/',
                 'tutorials/models/']  # path to generate docs
 reference_url = {
     'dgl' : None,

docs/source/index.rst

@@ -26,6 +26,7 @@ Welcome to Deep Graph Library Tutorials and Documentation
    guide_cn/index
    tutorials/large/index
    tutorials/multi/index
+   tutorials/dist/index
    tutorials/models/index
 
 .. toctree::

tests/scripts/task_pytorch_tutorial_test.sh

@@ -21,7 +21,7 @@ pushd ${TUTORIAL_ROOT} > /dev/null
 pip install -r requirements.txt || fail "installing requirements"
 
 # Test
-for f in $(find . -name "*.py" ! -name "*_mx.py")
+for f in $(find . -path ./dist -prune -false -o -name "*.py" ! -name "*_mx.py")
 do
     echo "Running tutorial ${f} ..."
     python3 $f || fail "run ${f}"

tutorials/dist/1_node_classification.py

+'''
+Distributed Node Classification
+===============================
+
+In this tutorial, we will walk through the steps of performing distributed GNN training
+for a node classification task. To understand distributed GNN training, you need to
+read the tutorial of multi-GPU training first. This tutorial is developed on top of
+multi-GPU training by providing extra steps for partitioning a graph, modifying the training script
+and setting up the environment for distributed training.
+
+'''
+
+######################################################
+#Partition a graph
+#-----------------
+#
+#In this tutorial, we will use `OGBN products graph <https://ogb.stanford.edu/docs/nodeprop/#ogbn-products>`_
+#as an example to illustrate the graph partitioning. Let's first load the graph into a DGL graph.
+#Here we store the node labels as node data in the DGL Graph.
+#
+
+import dgl
+import torch as th
+from ogb.nodeproppred import DglNodePropPredDataset
+data = DglNodePropPredDataset(name='ogbn-products')
+graph, labels = data[0]
+labels = labels[:, 0]
+graph.ndata['labels'] = labels
+
+######################################################
+#We need to split the data into training/validation/test set during the graph partitioning.
+#Because this is a node classification task, the training/validation/test sets contain node IDs.
+#We recommend users to convert them as boolean arrays, in which True indicates the existence
+#of the node ID in the set. In this way, we can store them as node data. After the partitioning,
+#the boolean arrays will be stored with the graph partitions.
+#
+
+splitted_idx = data.get_idx_split()
+train_nid, val_nid, test_nid = splitted_idx['train'], splitted_idx['valid'], splitted_idx['test']
+train_mask = th.zeros((graph.number_of_nodes(),), dtype=th.bool)
+train_mask[train_nid] = True
+val_mask = th.zeros((graph.number_of_nodes(),), dtype=th.bool)
+val_mask[val_nid] = True
+test_mask = th.zeros((graph.number_of_nodes(),), dtype=th.bool)
+test_mask[test_nid] = True
+graph.ndata['train_mask'] = train_mask
+graph.ndata['val_mask'] = val_mask
+graph.ndata['test_mask'] = test_mask
+
+#####################################################
+#Then we call the `partition_graph` function to partition the graph with
+#`METIS <http://glaros.dtc.umn.edu/gkhome/metis/metis/overview>`_ and save the partitioned results
+#in the specified folder. **Note**: `partition_graph` runs on a single machine with a single thread.
+#You can go to `our user guide <https://docs.dgl.ai/en/latest/guide/distributed-preprocessing.html#distributed-partitioning>`_
+#to see more information on distributed graph partitioning.
+#
+#The code below shows an example of invoking the partitioning algorithm and generate four partitions.
+#The partitioned results are stored in a folder called `4part_data`. While partitioning a graph,
+#we allow users to specify how to balance the partitions. By default, the algorithm balances the number
+#of nodes in each partition as much as possible. However, this balancing strategy is not sufficient
+#for distributed GNN training because some partitions may have many more training nodes than other partitions
+#or some partitions may have more edges than others. As such, `partition_graph` provides two additional arguments
+#`balance_ntypes` and `balance_edges` to enforce more balancing criteria. For example, we can use the training mask
+#to balance the number of training nodes in each partition, as shown in the example below. We can also turn on
+#the `balance_edges` flag to ensure that all partitions have roughly the same number of edges.
+#
+
+dgl.distributed.partition_graph(graph, graph_name='ogbn-products', num_parts=4,
+                                out_path='4part_data',
+                                balance_ntypes=graph.ndata['train_mask'],
+                                balance_edges=True)
+
+###################################################
+#When partitioning a graph, DGL shuffles node IDs and edge IDs so that nodes/edges assigned to
+#a partition have contiguous IDs. This is necessary for DGL to maintain the mappings of global
+#node/edge IDs and partition IDs. If a user needs to map the shuffled node/edge IDs to their original IDs,
+#they can turn on the `return_mapping` flag of `partition_graph`, which returns a vector for the node ID mapping
+#and edge ID mapping. Below shows an example of using the ID mapping to save the node embeddings after
+#distributed training. This is a common use case when users want to use the trained node embeddings
+#in their downstream task. Below let's assume that the trained node embeddings are stored in the `node_emb` tensor,
+#which is indexed by the shuffled node IDs. We shuffle the embeddings again and store them in
+#the `orig_node_emb` tensor, which is indexed by the original node IDs.
+#
+
+nmap, emap = dgl.distributed.partition_graph(graph, graph_name='ogbn-products',
+                                             num_parts=4,
+                                             out_path='4part_data',
+                                             balance_ntypes=graph.ndata['train_mask'],
+                                             balance_edges=True,
+                                             return_mapping=True)
+orig_node_emb = th.zeros(node_emb.shape, dtype=node_emb.dtype)
+orig_node_emb[nmap] = node_emb
+
+#####################################################
+#Distributed training script
+#---------------------------
+#
+#The distributed training script is very similar to multi-GPU training script with just a few modifications.
+#It also relies on the Pytorch distributed component to exchange gradients and update model parameters.
+#The distributed training script only contains the code of the trainers.
+#
+#Initialize network communication
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+#Distributed GNN training requires to access the partitioned graph structure and node/edge features
+#as well as aggregating the gradients of model parameters from multiple trainers. DGL's distributed
+#component is responsible for accessing the distributed graph structure and distributed node features
+#and edge features while Pytorch distributed is responsible for exchanging the gradients of model parameters.
+#As such, we need to initialize both DGL and Pytorch distributed components at the beginning of the training script.
+#
+#We need to call DGL's initialize function to initialize the trainers' network communication and
+#connect with DGL's servers at the very beginning of the distributed training script. This function
+#has an argument that accepts the path to the cluster configuration file.
+#
+import dgl
+import torch as th
+dgl.distributed.initialize(ip_config='ip_config.txt')
+
+#####################################################################
+#The configuration file `ip_config.txt` has the following format:
+#
+#.. code-block:: shell
+#
+#  ip_addr1 [port1]
+#  ip_addr2 [port2]
+#
+#Each row is a machine. The first column is the IP address and the second column is the port for
+#connecting to the DGL server on the machine. The port is optional and the default port is 30050.
+#
+#After initializing DGL's network communication, a user can initialize Pytorch's distributed communication.
+#
+th.distributed.init_process_group(backend='gloo')
+
+#######################################################################
+#Reference to the distributed graph
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+#DGL's servers load the graph partitions automatically. After the servers load the partitions,
+#trainers connect to the servers and can start to reference to the distributed graph in the cluster as below.
+#
+g = dgl.distributed.DistGraph('ogbn-products')
+
+#######################################################################
+#As shown in the code, we refer to a distributed graph by its name. This name is basically the one passed
+#to the `partition_graph` function as shown in the section above.
+#
+#Get training and validation node IDs
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+#For distributed training, each trainer can run its own set of training nodes.
+#The training nodes of the entire graph are stored in a distributed tensor as the `train_mask` node data,
+#which was constructed before we partitioned the graph. Each trainer can invoke `node_split` to its set
+#of training nodes. The `node_split` function splits the full training set evenly and returns
+#the training nodes, majority of which are stored in the local partition, to ensure good data locality.
+#
+train_nid = dgl.distributed.node_split(g.ndata['train_mask'])
+
+######################################################################
+#We can split the validation nodes in the same way as above. In this case, each trainer gets
+#a different set of validation nodes.
+#
+valid_nid = dgl.distributed.node_split(g.ndata['val_mask'])
+
+#####################################################################
+#Define a GNN model
+#^^^^^^^^^^^^^^^^^^
+#
+#For distributed training, we define a GNN model exactly in the same way as
+#`mini-batch training <https://doc.dgl.ai/guide/minibatch.html#>`_ or
+#`full-graph training <https://doc.dgl.ai/guide/training-node.html#guide-training-node-classification>`_.
+#The code below defines the GraphSage model.
+#
+import torch.nn as nn
+import torch.nn.functional as F
+import dgl.nn as dglnn
+import torch.optim as optim
+
+class SAGE(nn.Module):
+    def __init__(self, in_feats, n_hidden, n_classes, n_layers):
+        super().__init__()
+        self.n_layers = n_layers
+        self.n_hidden = n_hidden
+        self.n_classes = n_classes
+        self.layers = nn.ModuleList()
+        self.layers.append(dglnn.SAGEConv(in_feats, n_hidden, 'mean'))
+        for i in range(1, n_layers - 1):
+            self.layers.append(dglnn.SAGEConv(n_hidden, n_hidden, 'mean'))
+        self.layers.append(dglnn.SAGEConv(n_hidden, n_classes, 'mean'))
+
+    def forward(self, blocks, x):
+        for l, (layer, block) in enumerate(zip(self.layers, blocks)):
+            x = layer(block, x)
+            if l != self.n_layers - 1:
+                x = F.relu(x)
+        return x
+
+num_hidden = 256
+num_labels = len(th.unique(g.ndata['labels'][0:g.number_of_nodes()]))
+num_layers = 2
+lr = 0.001
+model = SAGE(g.ndata['feat'].shape[1], num_hidden, num_labels, num_layers)
+loss_fcn = nn.CrossEntropyLoss()
+optimizer = optim.Adam(model.parameters(), lr=lr)
+
+###################################################################
+#For distributed training, we need to convert the model into a distributed model with
+#Pytorch's `DistributedDataParallel`.
+#
+model = th.nn.parallel.DistributedDataParallel(model)
+
+####################################################################
+#Distributed mini-batch sampler
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+#We can use the same `NodeDataLoader` to create a distributed mini-batch sampler for
+#node classification.
+#
+sampler = dgl.dataloading.MultiLayerNeighborSampler([25,10])
+train_dataloader = dgl.dataloading.NodeDataLoader(
+                             g, train_nid, sampler, batch_size=1024,
+                             shuffle=True, drop_last=False)
+valid_dataloader = dgl.dataloading.NodeDataLoader(
+                             g, valid_nid, sampler, batch_size=1024,
+                             shuffle=False, drop_last=False)
+
+###################################################################
+#Training loop
+#^^^^^^^^^^^^^
+#
+#The training loop for distributed training is also exactly the same as the single-process training.
+#
+import sklearn.metrics
+import numpy as np
+
+for epoch in range(10):
+    # Loop over the dataloader to sample mini-batches.
+    losses = []
+    for step, (input_nodes, seeds, blocks) in enumerate(train_dataloader):
+        # Load the input features as well as output labels
+        batch_inputs = g.ndata['feat'][input_nodes]
+        batch_labels = g.ndata['labels'][seeds]
+
+        # Compute loss and prediction
+        batch_pred = model(blocks, batch_inputs)
+        loss = loss_fcn(batch_pred, batch_labels)
+        optimizer.zero_grad()
+        loss.backward()
+        losses.append(loss.detach().cpu().numpy())
+        optimizer.step()
+
+    # validation
+    predictions = []
+    labels = []
+    with th.no_grad():
+        for step, (input_nodes, seeds, blocks) in enumerate(valid_dataloader):
+            inputs = g.ndata['feat'][input_nodes]
+            labels.append(g.ndata['labels'][seeds].numpy())
+            predictions.append(model(blocks, inputs).argmax(1).numpy())
+        predictions = np.concatenate(predictions)
+        labels = np.concatenate(labels)
+        accuracy = sklearn.metrics.accuracy_score(labels, predictions)
+        print('Epoch {}: Validation Accuracy {}'.format(epoch, accuracy))
+
+######################################################################
+#Set up distributed training environment
+#---------------------------------------
+#
+#After partitioning a graph and preparing the training script, we now need to set up
+#the distributed training environment and launch the training job. Basically, we need to
+#create a cluster of machines and upload both the training script and the partitioned data
+#to each machine in the cluster. A recommended solution of sharing the training script and
+#the partitioned data in the cluster is to use NFS (Network File System).
+#
+#For any users who are not familiar with NFS, below is a small tutorial of setting up NFS
+#in an existing cluster.
+#
+#NFS server side setup (ubuntu only)
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+#First, install essential libs on the storage server
+#
+#.. code-block:: shell
+#
+#  sudo apt-get install nfs-kernel-server
+#
+#Below we assume the user account is ubuntu and we create a directory of workspace in the home directory.
+#
+#.. code-block:: shell
+#
+#  mkdir -p /home/ubuntu/workspace
+#
+#We assume that the all servers are under a subnet with ip range 192.168.0.0 to 192.168.255.255.
+#We need to add the following line to `/etc/exports`
+#
+#.. code-block:: shell
+#
+#  /home/ubuntu/workspace  192.168.0.0/16(rw,sync,no_subtree_check)
+#
+#Then restart NFS, the setup on server side is finished.
+#
+#.. code-block:: shell
+#
+#  sudo systemctl restart nfs-kernel-server
+#
+#For configuration details, please refer to NFS ArchWiki (https://wiki.archlinux.org/index.php/NFS).
+#
+#NFS client side setup (ubuntu only)
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+#To use NFS, clients also require to install essential packages
+#
+#.. code-block:: shell
+#
+#  sudo apt-get install nfs-common
+#
+#You can either mount the NFS manually
+#
+#.. code-block:: shell
+#
+#  mkdir -p /home/ubuntu/workspace
+#  sudo mount -t nfs <nfs-server-ip>:/home/ubuntu/workspace /home/ubuntu/workspace
+#
+#or add the following line to `/etc/fstab` so the folder will be mounted automatically
+#
+#.. code-block:: shell
+#
+#  <nfs-server-ip>:/home/ubuntu/workspace   /home/ubuntu/workspace   nfs   defaults    0 0
+#
+#Then run
+#
+#.. code-block:: shell
+#
+#  mount -a
+#
+#Now go to `/home/ubuntu/workspace` and save the training script and the partitioned data in the folder.
+#
+#SSH Access
+#^^^^^^^^^^
+#
+#The launch script accesses the machines in the cluster via SSH. Users should follow the instruction
+#in `this document <https://linuxize.com/post/how-to-setup-passwordless-ssh-login/>`_ to set up
+#the passwordless SSH login on every machine in the cluster. After setting up the passwordless SSH,
+#users need to authenticate the connection to each machine and add their key fingerprints to `~/.ssh/known_hosts`.
+#This can be done automatically when we ssh to a machine for the first time.
+#
+#Launch the distributed training job
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+#After everything is ready, we can now use the launch script provided by DGL to launch the distributed
+#training job in the cluster. We can run the launch script on any machine in the cluster. 
+#
+#.. code-block:: shell
+#
+#  python3 ~/workspace/dgl/tools/launch.py \
+#  --workspace ~/workspace/ \
+#  --num_trainers 1 \
+#  --num_samplers 0 \
+#  --num_servers 1 \
+#  --part_config 4part_data/ogbn-products.json \
+#  --ip_config ip_config.txt \
+#  "python3 train_dist.py"
+#
+#If we split the graph into four partitions as demonstrated at the beginning of the tutorial, the cluster has to have four machines. The command above launches one trainer and one server on each machine in the cluster. `ip_config.txt` lists the IP addresses of all machines in the cluster as follows:
+#
+#.. code-block:: shell
+#
+#  ip_addr1
+#  ip_addr2
+#  ip_addr3
+#  ip_addr4

tutorials/dist/README.txt

+Distributed training
+====================