graphsage_sampling.py

import dgl
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 torch.multiprocessing as mp
import dgl.function as fn
import dgl.nn.pytorch as dglnn
import time
import argparse
from _thread import start_new_thread
from functools import wraps
from dgl.data import RedditDataset
from torch.nn.parallel import DistributedDataParallel
import tqdm

#### Neighbor sampler

class NeighborSampler(object):
    def __init__(self, g, fanouts):
        self.g = g
        self.fanouts = fanouts

    def sample_blocks(self, seeds):
        blocks = []
        for fanout in self.fanouts:
            # For each seed node, sample ``fanout`` neighbors.
            frontier = dgl.sampling.sample_neighbors(g, seeds, fanout)
            # Then we compact the frontier into a bipartite graph for message passing.
            block = dgl.to_block(frontier, seeds)
            # Obtain the seed nodes for next layer.
            seeds = block.srcdata[dgl.NID]

            blocks.insert(0, block)
        return blocks

class SAGE(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', feat_drop=dropout, activation=activation))
        for i in range(1, n_layers - 1):
            self.layers.append(dglnn.SAGEConv(
                n_hidden, n_hidden, 'mean', feat_drop=dropout, activation=activation))
        self.layers.append(dglnn.SAGEConv(
            n_hidden, n_classes, 'mean', feat_drop=dropout))

    def forward(self, blocks, x):
        h = x
        for layer, block in zip(self.layers, blocks):
            # We need to first copy the representation of nodes on the RHS from the
            # appropriate nodes on the LHS.
            # Note that the shape of h is (num_nodes_LHS, D) and the shape of h_dst
            # would be (num_nodes_RHS, D)
            h_dst = h[:block.number_of_nodes(block.dsttype)]
            # Then we compute the updated representation on the RHS.
            # The shape of h now becomes (num_nodes_RHS, D)
            h = layer(block, (h, h_dst))
        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.

        The inference code is written in a fashion that it could handle any number of nodes and
        layers.
        """
        # 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 = th.arange(g.number_of_nodes())
        for l, layer in enumerate(self.layers):
            y = th.zeros(g.number_of_nodes(), self.n_hidden if l != len(self.layers) - 1 else self.n_classes)

            for start in tqdm.trange(0, len(nodes), batch_size):
                end = start + batch_size
                batch_nodes = nodes[start:end]
                block = dgl.to_block(dgl.in_subgraph(g, batch_nodes), batch_nodes)
                induced_nodes = block.srcdata[dgl.NID]

                h = x[induced_nodes].to(device)
                h_dst = h[:block.number_of_nodes(block.dsttype)]
                h = layer(block, (h, h_dst))

                y[start:end] = h.cpu()

            x = y
        return y

#### Miscellaneous functions

# According to https://github.com/pytorch/pytorch/issues/17199, this decorator
# is necessary to make fork() and openmp work together.
#
# TODO: confirm if this is necessary for MXNet and Tensorflow.  If so, we need
# to standardize worker process creation since our operators are implemented with
# OpenMP.
def thread_wrapped_func(func):
    """
    Wraps a process entry point to make it work with OpenMP.
    """
    @wraps(func)
    def decorated_function(*args, **kwargs):
        queue = mp.Queue()
        def _queue_result():
            exception, trace, res = None, None, None
            try:
                res = func(*args, **kwargs)
            except Exception as e:
                exception = e
                trace = traceback.format_exc()
            queue.put((res, exception, trace))

        start_new_thread(_queue_result, ())
        result, exception, trace = queue.get()
        if exception is None:
            return result
        else:
            assert isinstance(exception, Exception)
            raise exception.__class__(trace)
    return decorated_function

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

def evaluate(model, g, inputs, labels, val_mask, batch_size, device):
    """
    Evaluate the model on the validation set specified by ``val_mask``.
    g : The entire graph.
    inputs : The features of all the nodes.
    labels : The labels of all the nodes.
    val_mask : A 0-1 mask indicating which nodes do we actually compute the accuracy for.
    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_mask], labels[val_mask])

def load_subtensor(g, labels, seeds, induced_nodes, dev_id):
    """
    Copys features and labels of a set of nodes onto GPU.
    """
    batch_inputs = g.ndata['features'][induced_nodes].to(dev_id)
    batch_labels = labels[seeds].to(dev_id)
    return batch_inputs, batch_labels

#### Entry point

@thread_wrapped_func
def run(proc_id, n_gpus, args, devices, data):
    dropout = 0.2

    # Start up distributed training, if enabled.
    dev_id = devices[proc_id]
    if n_gpus > 1:
        dist_init_method = 'tcp://{master_ip}:{master_port}'.format(
            master_ip='127.0.0.1', master_port='12345')
        world_size = n_gpus
        th.distributed.init_process_group(backend="nccl",
                                          init_method=dist_init_method,
                                          world_size=world_size,
                                          rank=dev_id)
    th.cuda.set_device(dev_id)

    # Unpack data
    train_mask, val_mask, in_feats, labels, n_classes, g = data
    train_nid = th.LongTensor(np.nonzero(train_mask)[0])
    val_nid = th.LongTensor(np.nonzero(val_mask)[0])
    train_mask = th.BoolTensor(train_mask)
    val_mask = th.BoolTensor(val_mask)

    # Split train_nid
    train_nid = th.split(train_nid, len(train_nid) // n_gpus)[dev_id]

    # Create sampler
    sampler = NeighborSampler(g, [args.fan_out] * args.num_layers)

    # Define model and optimizer
    model = SAGE(in_feats, args.num_hidden, n_classes, args.num_layers, F.relu, dropout)
    model = model.to(dev_id)
    if n_gpus > 1:
        model = DistributedDataParallel(model, device_ids=[dev_id], output_device=dev_id)
    loss_fcn = nn.CrossEntropyLoss()
    loss_fcn = loss_fcn.to(dev_id)
    optimizer = optim.Adam(model.parameters(), lr=args.lr)

    # Training loop
    avg = 0
    iter_tput = []
    for epoch in range(args.num_epochs):
        tic = time.time()
        train_nid_batches = train_nid[th.randperm(len(train_nid))]
        n_batches = (len(train_nid_batches) + args.batch_size - 1) // args.batch_size
        for step in range(n_batches):
            seeds = train_nid_batches[step * args.batch_size:(step+1) * args.batch_size]
            if proc_id == 0:
                tic_step = time.time()

            # Sample blocks for message propagation
            blocks = sampler.sample_blocks(seeds)
            induced_nodes = blocks[0].srcdata[dgl.NID]
            # Load the input features as well as output labels
            batch_inputs, batch_labels = load_subtensor(g, labels, seeds, induced_nodes, dev_id)

            # Compute loss and prediction
            batch_pred = model(blocks, batch_inputs)
            loss = loss_fcn(batch_pred, batch_labels)
            optimizer.zero_grad()
            loss.backward()

            if n_gpus > 1:
                for param in model.parameters():
                    if param.requires_grad and param.grad is not None:
                        th.distributed.all_reduce(param.grad.data,
                                                  op=th.distributed.ReduceOp.SUM)
                        param.grad.data /= n_gpus
            optimizer.step()

            if proc_id == 0:
                iter_tput.append(len(seeds) * n_gpus / (time.time() - tic_step))
            if step % args.log_every == 0 and proc_id == 0:
                acc = compute_acc(batch_pred, batch_labels)
                print('Epoch {:05d} | Step {:05d} | Loss {:.4f} | Train Acc {:.4f} | Speed (samples/sec) {:.4f}'.format(
                    epoch, step, loss.item(), acc.item(), np.mean(iter_tput[3:])))

        if n_gpus > 1:
            th.distributed.barrier()

        toc = time.time()
        if proc_id == 0:
            print('Epoch Time(s): {:.4f}'.format(toc - tic))
            if epoch >= 5:
                avg += toc - tic
            if epoch % args.eval_every == 0 and epoch != 0:
                eval_acc = evaluate(model, g, g.ndata['features'], labels, val_mask, args.batch_size, 0)
                print('Eval Acc {:.4f}'.format(eval_acc))

    if n_gpus > 1:
        th.distributed.barrier()
    if proc_id == 0:
        print('Avg epoch time: {}'.format(avg / (epoch - 4)))

if __name__ == '__main__':
    argparser = argparse.ArgumentParser("multi-gpu training")
    argparser.add_argument('--gpu', type=str, default='0')
    argparser.add_argument('--num-epochs', type=int, default=20)
    argparser.add_argument('--num-hidden', type=int, default=16)
    argparser.add_argument('--num-layers', type=int, default=2)
    argparser.add_argument('--fan-out', type=int, default=10)
    argparser.add_argument('--batch-size', type=int, default=1000)
    argparser.add_argument('--log-every', type=int, default=20)
    argparser.add_argument('--eval-every', type=int, default=5)
    argparser.add_argument('--lr', type=float, default=0.003)
    args = argparser.parse_args()
    
    devices = list(map(int, args.gpu.split(',')))
    n_gpus = len(devices)

    # load reddit data
    data = RedditDataset(self_loop=True)
    train_mask = data.train_mask
    val_mask = data.val_mask
    features = th.Tensor(data.features)
    in_feats = features.shape[1]
    labels = th.LongTensor(data.labels)
    n_classes = data.num_labels
    # Construct graph
    g = dgl.graph(data.graph.all_edges())
    g.ndata['features'] = features
    # Pack data
    data = train_mask, val_mask, in_feats, labels, n_classes, g

    if n_gpus == 1:
        run(0, n_gpus, args, devices, data)
    else:
        procs = []
        for proc_id in range(n_gpus):
            p = mp.Process(target=run, args=(proc_id, n_gpus, args, devices, data))
            p.start()
            procs.append(p)
        for p in procs:
            p.join()