import os os.environ["DGLBACKEND"] = "pytorch" import argparse import math import socket import time from functools import wraps from multiprocessing import Process import numpy as np import torch as th import torch.multiprocessing as mp import torch.nn as nn import torch.nn.functional as F import torch.optim as optim import tqdm from torch.utils.data import DataLoader import dgl import dgl.function as fn import dgl.nn.pytorch as dglnn from dgl import DGLGraph from dgl.data import load_data, register_data_args from dgl.data.utils import load_graphs from dgl.distributed import DistDataLoader 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 NeighborSampler(object): def __init__(self, g, fanouts, sample_neighbors, device, load_feat=True): self.g = g self.fanouts = fanouts self.sample_neighbors = sample_neighbors self.device = device self.load_feat = load_feat def sample_blocks(self, seeds): seeds = th.LongTensor(np.asarray(seeds)) blocks = [] for fanout in self.fanouts: # For each seed node, sample ``fanout`` neighbors. frontier = self.sample_neighbors( self.g, seeds, fanout, replace=True ) # 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) input_nodes = blocks[0].srcdata[dgl.NID] seeds = blocks[-1].dstdata[dgl.NID] batch_inputs, batch_labels = load_subtensor( self.g, seeds, input_nodes, "cpu", self.load_feat ) if self.load_feat: blocks[0].srcdata["features"] = batch_inputs blocks[-1].dstdata["labels"] = batch_labels return blocks 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 l, (layer, block) in enumerate(zip(self.layers, blocks)): h = layer(block, h) if l != 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. 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 = dgl.distributed.node_split( np.arange(g.number_of_nodes()), g.get_partition_book(), force_even=True, ) y = dgl.distributed.DistTensor( (g.number_of_nodes(), self.n_hidden), th.float32, "h", persistent=True, ) for l, layer in enumerate(self.layers): if l == len(self.layers) - 1: y = dgl.distributed.DistTensor( (g.number_of_nodes(), self.n_classes), th.float32, "h_last", persistent=True, ) sampler = NeighborSampler( g, [-1], dgl.distributed.sample_neighbors, device ) print( "|V|={}, eval batch size: {}".format( g.number_of_nodes(), batch_size ) ) # Create PyTorch DataLoader for constructing blocks dataloader = DistDataLoader( dataset=nodes, batch_size=batch_size, collate_fn=sampler.sample_blocks, shuffle=False, drop_last=False, ) for blocks in tqdm.tqdm(dataloader): block = blocks[0].to(device) input_nodes = block.srcdata[dgl.NID] output_nodes = block.dstdata[dgl.NID] h = x[input_nodes].to(device) h_dst = h[: block.number_of_dst_nodes()] h = layer(block, (h, h_dst)) if l != 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): # Unpack data train_nid, val_nid, test_nid, in_feats, n_classes, g = data shuffle = True # Create sampler sampler = NeighborSampler( g, [int(fanout) for fanout in args.fan_out.split(",")], dgl.distributed.sample_neighbors, device, ) # Create DataLoader for constructing blocks dataloader = DistDataLoader( dataset=train_nid.numpy(), batch_size=args.batch_size, collate_fn=sampler.sample_blocks, 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, blocks in enumerate(dataloader): tic_step = time.time() sample_time += tic_step - start # The nodes for input lies at the LHS side of the first block. # The nodes for output lies at the RHS side of the last block. batch_inputs = blocks[0].srcdata["features"] batch_labels = blocks[-1].dstdata["labels"] batch_labels = batch_labels.long() num_seeds += len(blocks[-1].dstdata[dgl.NID]) num_inputs += len(blocks[0].srcdata[dgl.NID]) blocks = [block.to(device) for block in blocks] batch_labels = batch_labels.to(device) # Compute loss and prediction start = time.time() # print(g.rank(), blocks[0].device, model.module.layers[0].fc_neigh.weight.device, dev_id) 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.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, net_type=args.net_type) 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 == -1: labels = g.ndata["labels"][np.arange(g.number_of_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") register_data_args(parser) 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("--num_clients", type=int, help="The number of clients") parser.add_argument( "--n_classes", type=int, default=-1, help="The number of classes. If not specified, this" " value will be calculated via scaning all the labels" " in the dataset which probably causes memory burst.", ) 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.", ) parser.add_argument( "--net_type", type=str, default="socket", help="backend net type, 'socket' or 'tensorpipe'", ) args = parser.parse_args() print(args) main(args)