train_dist.py

import argparse
import socket
import time
from contextlib import contextmanager

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 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"))
        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

    @contextmanager
    def join(self):
        """dummy join for standalone"""
        yield


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):
    # Unpack data
    train_nid, val_nid, test_nid, in_feats, n_classes, g = data
    shuffle = True
    # prefetch_node_feats/prefetch_labels are not supported for DistGraph yet.
    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=shuffle,
        drop_last=False,
    )
    # Define model and optimizer
    model = DistSAGE(
        in_feats,
        args.num_hidden,
        n_classes,
        args.num_layers,
        F.relu,
        args.dropout,
    )
    model = model.to(device)
    if not args.standalone:
        if args.num_gpus == -1:
            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
    for epoch in range(args.num_epochs):
        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
                # fetch features/labels
                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 % 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.sum(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 += 1

        if epoch % args.eval_every == 0 and epoch != 0:
            start = time.time()
            val_acc, test_acc = evaluate(
                model if args.standalone else 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
                )
            )


def main(args):
    print(socket.gethostname(), "Initializing DGL dist")
    dgl.distributed.initialize(args.ip_config)
    if not args.standalone:
        print(socket.gethostname(), "Initializing DGL 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 == -1:
        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("#labels:", n_classes)

    # Pack data
    in_feats = g.ndata["features"].shape[1]
    data = train_nid, val_nid, test_nid, in_feats, n_classes, g
    run(args, device, data)
    print("parent ends")


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="GCN")
    parser.add_argument("--graph_name", type=str, help="graph name")
    parser.add_argument("--id", type=int, help="the partition id")
    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=-1,
        help="the number of GPU device. Use -1 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(
        "--standalone", action="store_true", help="run in the standalone mode"
    )
    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.",
    )
    args = parser.parse_args()

    print(args)
    main(args)