node_classification.py

import argparse
import socket
import time

import dgl
import dgl.nn.pytorch as dglnn
import numpy as np
import torch as th
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import tqdm


def load_subtensor(g, seeds, input_nodes, device, load_feat=True):
    """
    Copys features and labels of a set of nodes onto GPU.
    """
    batch_inputs = (
        g.ndata["features"][input_nodes].to(device) if load_feat else None
    )
    batch_labels = g.ndata["labels"][seeds].to(device)
    return batch_inputs, batch_labels


class DistSAGE(nn.Module):
    def __init__(
        self, in_feats, n_hidden, n_classes, n_layers, activation, dropout
    ):
        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 _ 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"))
        self.dropout = nn.Dropout(dropout)
        self.activation = activation

    def forward(self, blocks, x):
        h = x
        for i, (layer, block) in enumerate(zip(self.layers, blocks)):
            h = layer(block, h)
            if i != len(self.layers) - 1:
                h = self.activation(h)
                h = self.dropout(h)
        return h

    def inference(self, g, x, batch_size, device):
        """
        Inference with the GraphSAGE model on full neighbors (i.e. without
        neighbor sampling).

        g : the entire graph.
        x : the input of entire node set.

        Distributed layer-wise inference.
        """
        # During inference with sampling, multi-layer blocks are very
        # inefficient because lots of computations in the first few layers
        # are repeated. Therefore, we compute the representation of all nodes
        # layer by layer.  The nodes on each layer are of course splitted in
        # batches.
        # TODO: can we standardize this?
        nodes = dgl.distributed.node_split(
            np.arange(g.num_nodes()),
            g.get_partition_book(),
            force_even=True,
        )
        y = dgl.distributed.DistTensor(
            (g.num_nodes(), self.n_hidden),
            th.float32,
            "h",
            persistent=True,
        )
        for i, layer in enumerate(self.layers):
            if i == len(self.layers) - 1:
                y = dgl.distributed.DistTensor(
                    (g.num_nodes(), self.n_classes),
                    th.float32,
                    "h_last",
                    persistent=True,
                )
            print(f"|V|={g.num_nodes()}, eval batch size: {batch_size}")

            sampler = dgl.dataloading.NeighborSampler([-1])
            dataloader = dgl.dataloading.DistNodeDataLoader(
                g,
                nodes,
                sampler,
                batch_size=batch_size,
                shuffle=False,
                drop_last=False,
            )

            for input_nodes, output_nodes, blocks in tqdm.tqdm(dataloader):
                block = blocks[0].to(device)
                h = x[input_nodes].to(device)
                h_dst = h[: block.number_of_dst_nodes()]
                h = layer(block, (h, h_dst))
                if i != len(self.layers) - 1:
                    h = self.activation(h)
                    h = self.dropout(h)

                y[output_nodes] = h.cpu()

            x = y
            g.barrier()
        return y


def compute_acc(pred, labels):
    """
    Compute the accuracy of prediction given the labels.
    """
    labels = labels.long()
    return (th.argmax(pred, dim=1) == labels).float().sum() / len(pred)


def evaluate(model, g, inputs, labels, val_nid, test_nid, batch_size, device):
    """
    Evaluate the model on the validation set specified by ``val_nid``.
    g : The entire graph.
    inputs : The features of all the nodes.
    labels : The labels of all the nodes.
    val_nid : the node Ids for validation.
    batch_size : Number of nodes to compute at the same time.
    device : The GPU device to evaluate on.
    """
    model.eval()
    with th.no_grad():
        pred = model.inference(g, inputs, batch_size, device)
    model.train()
    return compute_acc(pred[val_nid], labels[val_nid]), compute_acc(
        pred[test_nid], labels[test_nid]
    )


def run(args, device, data):
    train_nid, val_nid, test_nid, in_feats, n_classes, g = data
    sampler = dgl.dataloading.NeighborSampler(
        [int(fanout) for fanout in args.fan_out.split(",")]
    )
    dataloader = dgl.dataloading.DistNodeDataLoader(
        g,
        train_nid,
        sampler,
        batch_size=args.batch_size,
        shuffle=True,
        drop_last=False,
    )
    model = DistSAGE(
        in_feats,
        args.num_hidden,
        n_classes,
        args.num_layers,
        F.relu,
        args.dropout,
    )
    model = model.to(device)
    if args.num_gpus == 0:
        model = th.nn.parallel.DistributedDataParallel(model)
    else:
        model = th.nn.parallel.DistributedDataParallel(
            model, device_ids=[device], output_device=device
        )
    loss_fcn = nn.CrossEntropyLoss()
    loss_fcn = loss_fcn.to(device)
    optimizer = optim.Adam(model.parameters(), lr=args.lr)

    # Training loop.
    iter_tput = []
    epoch = 0
    epoch_time = []
    test_acc = 0.0
    for _ in range(args.num_epochs):
        epoch += 1
        tic = time.time()
        sample_time = 0
        forward_time = 0
        backward_time = 0
        update_time = 0
        num_seeds = 0
        num_inputs = 0
        start = time.time()
        # Loop over the dataloader to sample the computation dependency graph
        # as a list of blocks.
        step_time = []

        with model.join():
            for step, (input_nodes, seeds, blocks) in enumerate(dataloader):
                tic_step = time.time()
                sample_time += tic_step - start
                batch_inputs, batch_labels = load_subtensor(
                    g, seeds, input_nodes, "cpu"
                )
                batch_labels = batch_labels.long()
                num_seeds += len(blocks[-1].dstdata[dgl.NID])
                num_inputs += len(blocks[0].srcdata[dgl.NID])
                # Move to target device.
                blocks = [block.to(device) for block in blocks]
                batch_inputs = batch_inputs.to(device)
                batch_labels = batch_labels.to(device)
                # Compute loss and prediction.
                start = time.time()
                batch_pred = model(blocks, batch_inputs)
                loss = loss_fcn(batch_pred, batch_labels)
                forward_end = time.time()
                optimizer.zero_grad()
                loss.backward()
                compute_end = time.time()
                forward_time += forward_end - start
                backward_time += compute_end - forward_end

                optimizer.step()
                update_time += time.time() - compute_end

                step_t = time.time() - tic_step
                step_time.append(step_t)
                iter_tput.append(len(blocks[-1].dstdata[dgl.NID]) / step_t)
                if (step + 1) % args.log_every == 0:
                    acc = compute_acc(batch_pred, batch_labels)
                    gpu_mem_alloc = (
                        th.cuda.max_memory_allocated() / 1000000
                        if th.cuda.is_available()
                        else 0
                    )
                    print(
                        "Part {} | Epoch {:05d} | Step {:05d} | Loss {:.4f} | "
                        "Train Acc {:.4f} | Speed (samples/sec) {:.4f} | GPU "
                        "{:.1f} MB | time {:.3f} s".format(
                            g.rank(),
                            epoch,
                            step,
                            loss.item(),
                            acc.item(),
                            np.mean(iter_tput[3:]),
                            gpu_mem_alloc,
                            np.mean(step_time[-args.log_every :]),
                        )
                    )
                start = time.time()

        toc = time.time()
        print(
            "Part {}, Epoch Time(s): {:.4f}, sample+data_copy: {:.4f}, "
            "forward: {:.4f}, backward: {:.4f}, update: {:.4f}, #seeds: {}, "
            "#inputs: {}".format(
                g.rank(),
                toc - tic,
                sample_time,
                forward_time,
                backward_time,
                update_time,
                num_seeds,
                num_inputs,
            )
        )
        epoch_time.append(toc - tic)

        if epoch % args.eval_every == 0 or epoch == args.num_epochs:
            start = time.time()
            val_acc, test_acc = evaluate(
                model.module,
                g,
                g.ndata["features"],
                g.ndata["labels"],
                val_nid,
                test_nid,
                args.batch_size_eval,
                device,
            )
            print(
                "Part {}, Val Acc {:.4f}, Test Acc {:.4f}, time: {:.4f}".format(
                    g.rank(), val_acc, test_acc, time.time() - start
                )
            )

    return np.mean(epoch_time[-int(args.num_epochs * 0.8) :]), test_acc


def main(args):
    print(socket.gethostname(), "Initializing DistDGL.")
    dgl.distributed.initialize(args.ip_config, net_type=args.net_type)
    print(socket.gethostname(), "Initializing PyTorch process group.")
    th.distributed.init_process_group(backend=args.backend)
    print(socket.gethostname(), "Initializing DistGraph.")
    g = dgl.distributed.DistGraph(args.graph_name, part_config=args.part_config)
    print(socket.gethostname(), "rank:", g.rank())

    pb = g.get_partition_book()
    if "trainer_id" in g.ndata:
        train_nid = dgl.distributed.node_split(
            g.ndata["train_mask"],
            pb,
            force_even=True,
            node_trainer_ids=g.ndata["trainer_id"],
        )
        val_nid = dgl.distributed.node_split(
            g.ndata["val_mask"],
            pb,
            force_even=True,
            node_trainer_ids=g.ndata["trainer_id"],
        )
        test_nid = dgl.distributed.node_split(
            g.ndata["test_mask"],
            pb,
            force_even=True,
            node_trainer_ids=g.ndata["trainer_id"],
        )
    else:
        train_nid = dgl.distributed.node_split(
            g.ndata["train_mask"], pb, force_even=True
        )
        val_nid = dgl.distributed.node_split(
            g.ndata["val_mask"], pb, force_even=True
        )
        test_nid = dgl.distributed.node_split(
            g.ndata["test_mask"], pb, force_even=True
        )
    local_nid = pb.partid2nids(pb.partid).detach().numpy()
    print(
        "part {}, train: {} (local: {}), val: {} (local: {}), test: {} "
        "(local: {})".format(
            g.rank(),
            len(train_nid),
            len(np.intersect1d(train_nid.numpy(), local_nid)),
            len(val_nid),
            len(np.intersect1d(val_nid.numpy(), local_nid)),
            len(test_nid),
            len(np.intersect1d(test_nid.numpy(), local_nid)),
        )
    )
    del local_nid
    if args.num_gpus == 0:
        device = th.device("cpu")
    else:
        dev_id = g.rank() % args.num_gpus
        device = th.device("cuda:" + str(dev_id))
    n_classes = args.n_classes
    if n_classes == 0:
        labels = g.ndata["labels"][np.arange(g.num_nodes())]
        n_classes = len(th.unique(labels[th.logical_not(th.isnan(labels))]))
        del labels
    print(f"Number of classes: {n_classes}")

    # Pack data.
    in_feats = g.ndata["features"].shape[1]
    data = train_nid, val_nid, test_nid, in_feats, n_classes, g

    # Train and evaluate.
    epoch_time, test_acc = run(args, device, data)
    print(
        f"Summary of node classification(GraphSAGE): GraphName "
        f"{args.graph_name} | TrainEpochTime(mean) {epoch_time:.4f} "
        f"| TestAccuracy {test_acc:.4f}"
    )


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Distributed GraphSAGE.")
    parser.add_argument("--graph_name", type=str, help="graph name")
    parser.add_argument(
        "--ip_config", type=str, help="The file for IP configuration"
    )
    parser.add_argument(
        "--part_config", type=str, help="The path to the partition config file"
    )
    parser.add_argument(
        "--n_classes", type=int, default=0, help="the number of classes"
    )
    parser.add_argument(
        "--backend",
        type=str,
        default="gloo",
        help="pytorch distributed backend",
    )
    parser.add_argument(
        "--num_gpus",
        type=int,
        default=0,
        help="the number of GPU device. Use 0 for CPU training",
    )
    parser.add_argument("--num_epochs", type=int, default=20)
    parser.add_argument("--num_hidden", type=int, default=16)
    parser.add_argument("--num_layers", type=int, default=2)
    parser.add_argument("--fan_out", type=str, default="10,25")
    parser.add_argument("--batch_size", type=int, default=1000)
    parser.add_argument("--batch_size_eval", type=int, default=100000)
    parser.add_argument("--log_every", type=int, default=20)
    parser.add_argument("--eval_every", type=int, default=5)
    parser.add_argument("--lr", type=float, default=0.003)
    parser.add_argument("--dropout", type=float, default=0.5)
    parser.add_argument(
        "--local_rank", type=int, help="get rank of the process"
    )
    parser.add_argument(
        "--pad-data",
        default=False,
        action="store_true",
        help="Pad train nid to the same length across machine, to ensure num "
        "of batches to be the same.",
    )
    parser.add_argument(
        "--net_type",
        type=str,
        default="socket",
        help="backend net type, 'socket' or 'tensorpipe'",
    )
    args = parser.parse_args()
    print(f"Arguments: {args}")
    main(args)