import os os.environ["DGLBACKEND"] = "pytorch" import argparse import math 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 from train_dist import DistSAGE, NeighborSampler, compute_acc 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, DistEmbedding class TransDistSAGE(DistSAGE): def __init__( self, in_feats, n_hidden, n_classes, n_layers, activation, dropout ): super(TransDistSAGE, self).__init__( in_feats, n_hidden, n_classes, n_layers, activation, dropout ) def inference(self, standalone, 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, load_feat=False, ) 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 initializer(shape, dtype): arr = th.zeros(shape, dtype=dtype) arr.uniform_(-1, 1) return arr class DistEmb(nn.Module): def __init__(self, num_nodes, emb_size, dgl_sparse_emb=False, dev_id="cpu"): super().__init__() self.dev_id = dev_id self.emb_size = emb_size self.dgl_sparse_emb = dgl_sparse_emb if dgl_sparse_emb: self.sparse_emb = DistEmbedding( num_nodes, emb_size, name="sage", init_func=initializer ) else: self.sparse_emb = th.nn.Embedding(num_nodes, emb_size, sparse=True) nn.init.uniform_(self.sparse_emb.weight, -1.0, 1.0) def forward(self, idx): # embeddings are stored in cpu idx = idx.cpu() if self.dgl_sparse_emb: return self.sparse_emb(idx, device=self.dev_id) else: return self.sparse_emb(idx).to(self.dev_id) def load_embs(standalone, emb_layer, g): nodes = dgl.distributed.node_split( np.arange(g.number_of_nodes()), g.get_partition_book(), force_even=True ) x = dgl.distributed.DistTensor( ( g.number_of_nodes(), emb_layer.module.emb_size if isinstance(emb_layer, th.nn.parallel.DistributedDataParallel) else emb_layer.emb_size, ), th.float32, "eval_embs", persistent=True, ) num_nodes = nodes.shape[0] for i in range((num_nodes + 1023) // 1024): idx = nodes[ i * 1024 : (i + 1) * 1024 if (i + 1) * 1024 < num_nodes else num_nodes ] embeds = emb_layer(idx).cpu() x[idx] = embeds if not standalone: g.barrier() return x def evaluate( standalone, model, emb_layer, g, 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() emb_layer.eval() with th.no_grad(): inputs = load_embs(standalone, emb_layer, g) pred = model.inference(standalone, g, inputs, batch_size, device) model.train() emb_layer.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, n_classes, g = data # Create sampler sampler = NeighborSampler( g, [int(fanout) for fanout in args.fan_out.split(",")], dgl.distributed.sample_neighbors, device, load_feat=False, ) # Create DataLoader for constructing blocks dataloader = DistDataLoader( dataset=train_nid.numpy(), batch_size=args.batch_size, collate_fn=sampler.sample_blocks, shuffle=True, drop_last=False, ) # Define model and optimizer emb_layer = DistEmb( g.num_nodes(), args.num_hidden, dgl_sparse_emb=args.dgl_sparse, dev_id=device, ) model = TransDistSAGE( args.num_hidden, 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: dev_id = g.rank() % args.num_gpus model = th.nn.parallel.DistributedDataParallel( model, device_ids=[dev_id], output_device=dev_id ) if not args.dgl_sparse: emb_layer = th.nn.parallel.DistributedDataParallel(emb_layer) loss_fcn = nn.CrossEntropyLoss() loss_fcn = loss_fcn.to(device) optimizer = optim.Adam(model.parameters(), lr=args.lr) if args.dgl_sparse: emb_optimizer = dgl.distributed.optim.SparseAdam( [emb_layer.sparse_emb], lr=args.sparse_lr ) print("optimize DGL sparse embedding:", emb_layer.sparse_emb) elif args.standalone: emb_optimizer = th.optim.SparseAdam( list(emb_layer.sparse_emb.parameters()), lr=args.sparse_lr ) print("optimize Pytorch sparse embedding:", emb_layer.sparse_emb) else: emb_optimizer = th.optim.SparseAdam( list(emb_layer.module.sparse_emb.parameters()), lr=args.sparse_lr ) print("optimize Pytorch sparse embedding:", emb_layer.module.sparse_emb) train_size = th.sum(g.ndata["train_mask"][0 : g.number_of_nodes()]) # 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 = [] 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[dgl.NID] 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() batch_inputs = emb_layer(batch_inputs) batch_pred = model(blocks, batch_inputs) loss = loss_fcn(batch_pred, batch_labels) forward_end = time.time() emb_optimizer.zero_grad() optimizer.zero_grad() loss.backward() compute_end = time.time() forward_time += forward_end - start backward_time += compute_end - forward_end emb_optimizer.step() 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( args.standalone, model.module, emb_layer, g, 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): dgl.distributed.initialize(args.ip_config) if not args.standalone: th.distributed.init_process_group(backend="gloo") g = dgl.distributed.DistGraph(args.graph_name, part_config=args.part_config) print("rank:", g.rank()) pb = g.get_partition_book() 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)), ) ) if args.num_gpus == -1: device = th.device("cpu") else: device = th.device("cuda:" + str(args.local_rank)) labels = g.ndata["labels"][np.arange(g.number_of_nodes())] n_classes = len(th.unique(labels[th.logical_not(th.isnan(labels))])) print("#labels:", n_classes) # Pack data data = train_nid, val_nid, test_nid, 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, help="the number of classes") 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( "--dgl_sparse", action="store_true", help="Whether to use DGL sparse embedding", ) parser.add_argument( "--sparse_lr", type=float, default=1e-2, help="sparse lr rate" ) args = parser.parse_args() print(args) main(args)