def main(args):
dataname = os.path.basename(args.dataset)
g = dgl.contrib.graph_store.create_graph_from_store(dataname, "shared_mem")
labels = data.get_labels(args.dataset)
n_classes = len(np.unique(labels))
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
train_nid = np.nonzero(train_mask)[0].astype(np.int64)
vnum = train_mask.shape[0]
num_hops = args.n_layers if args.preprocess else args.n_layers + 1
for epoch in range(args.n_epochs):
#epoch_load_vnum = 0
freq = np.zeros(vnum, dtype=np.int64)
for nf in dgl.contrib.sampling.NeighborSampler(g,
args.batch_size,
args.num_neighbors,
neighbor_type='in',
shuffle=True,
num_workers=16,
num_hops=num_hops,
seed_nodes=train_nid,
prefetch=False):
#epoch_load_vnum += count_nf_vnum(nf)
count_vertex_freq(nf, freq)
hit_rate = optimal_cache_hit(freq, 0.2)
print('Oracle cache hit rate: ', hit_rate)
def main(args):
dataname = os.path.basename(args.dataset)
g = dgl.contrib.graph_store.create_graph_from_store(dataname, "shared_mem")
labels = data.get_labels(args.dataset)
n_classes = len(np.unique(labels))
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
test_nid = np.nonzero(test_mask)[0].astype(np.int64)
labels = torch.LongTensor(labels)
if args.arch == 'gcn-nssc':
from PaGraph.model.gcn_nssc import GCNSampling, GCNInfer
infer_model = GCNInfer(args.feat_size, 32, n_classes, args.n_layers,
F.relu, args.preprocess)
elif args.arch == 'gs-nssc':
from PaGraph.model.graphsage_nssc import GraphSageSampling
infer_model = GraphSageSampling(args.feat_size, 16, n_classes,
args.n_layers, F.relu, 0, 'mean',
args.preprocess)
else:
print('Unknown arch')
sys.exit(-1)
gnneval(args, infer_model, g, labels, 0, test_nid)
def main(args):
dataname = os.path.basename(args.dataset)
g = dgl.contrib.graph_store.create_graph_from_store(dataname, "shared_mem")
labels = data.get_labels(args.dataset)
n_classes = len(np.unique(labels))
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
train_nid = np.nonzero(train_mask)[0].astype(np.int64)
num_hops = args.n_layers if args.preprocess else args.n_layers + 1
for epoch in range(args.n_epochs):
epoch_load_vnum = 0
for nf in dgl.contrib.sampling.NeighborSampler(g,
args.batch_size,
args.num_neighbors,
neighbor_type='in',
shuffle=True,
num_workers=16,
num_hops=num_hops,
seed_nodes=train_nid,
prefetch=False):
epoch_load_vnum += count_nf_vnum(nf)
print('Epoch loaded vertex#: ', epoch_load_vnum)
help="dataset dir")
parser.add_argument("--partition",
type=int,
default=2,
help="num of partitions")
parser.add_argument("--num-hops",
type=int,
default=1,
help="num of hop neighbors required for a batch")
parser.add_argument("--ordering", dest='ordering', action='store_true')
parser.set_defaults(ordering=False)
args = parser.parse_args()
# get data
adj = spsp.load_npz(os.path.join(args.dataset, 'adj.npz'))
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
train_nids = np.nonzero(train_mask)[0].astype(np.int64)
labels = data.get_labels(args.dataset)
# ordering
if args.ordering:
print('re-ordering graphs...')
adj = adj.tocsc()
adj, vmap = ordering.reordering(
adj, depth=args.num_hop) # vmap: orig -> new
# save to files
mapv = np.zeros(vmap.shape, dtype=np.int64)
mapv[vmap] = np.arange(vmap.shape[0]) # mapv: new -> orig
train_nids = np.sort(vmap[train_nids])
spsp.save_npz(os.path.join(args.dataset, 'adj.npz'), adj)
np.save(os.path.join(args.dataset, 'labels.npy'), labels[mapv])
def trainer(rank, world_size, args, backend='nccl'):
# init multi process
init_process(rank, world_size, backend)
# load data
dataname = os.path.basename(args.dataset)
g = dgl.contrib.graph_store.create_graph_from_store(dataname, "shared_mem")
labels = data.get_labels(args.dataset)
n_classes = len(np.unique(labels))
# masks for semi-supervised learning
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
train_nid = np.nonzero(train_mask)[0].astype(np.int64)
test_nid = np.nonzero(test_mask)[0].astype(np.int64)
chunk_size = int(train_nid.shape[0] / world_size) - 1
train_nid = train_nid[chunk_size * rank:chunk_size * (rank + 1)]
# to torch tensor
labels = torch.LongTensor(labels)
train_mask = torch.ByteTensor(train_mask)
val_mask = torch.ByteTensor(val_mask)
test_mask = torch.ByteTensor(test_mask)
# prepare model
num_hops = args.n_layers if args.preprocess else args.n_layers + 1
model = GCNSampling(args.feat_size, args.n_hidden, n_classes,
args.n_layers, F.relu, args.dropout, args.preprocess)
infer_model = GCNInfer(args.feat_size, args.n_hidden, n_classes,
args.n_layers, F.relu)
loss_fcn = torch.nn.CrossEntropyLoss()
optimizer = torch.optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
model.cuda(rank)
infer_model.cuda(rank)
model = torch.nn.parallel.DistributedDataParallel(model, device_ids=[rank])
ctx = torch.device(rank)
# start training
epoch_dur = []
sock = PaGraph.utils.trainer(port=8200 + rank)
port = 8760
sampler = dgl.contrib.sampling.SamplerReceiver(g,
'127.0.0.1:' +
str(port + rank),
1,
net_type='socket')
with torch.autograd.profiler.profile(enabled=(rank == 0),
use_cuda=True) as prof:
for epoch in range(args.n_epochs):
model.train()
epoch_start_time = time.time()
step = 0
for nf in sampler:
with torch.autograd.profiler.record_function('gpu-load'):
nf.copy_from_parent(ctx=ctx)
batch_nids = nf.layer_parent_nid(-1)
label = labels[batch_nids]
label = label.cuda(rank, non_blocking=True)
with torch.autograd.profiler.record_function('gpu-compute'):
pred = model(nf)
loss = loss_fcn(pred, label)
optimizer.zero_grad()
loss.backward()
optimizer.step()
step += 1
if rank == 0 and step % 20 == 0:
print('epoch [{}] step [{}]. Loss: {:.4f}'.format(
epoch + 1, step, loss.item()))
if step % 100 == 0:
PaGraph.utils.barrier(sock, role='trainer')
if rank == 0:
epoch_dur.append(time.time() - epoch_start_time)
print('Epoch average time: {:.4f}'.format(
np.mean(np.array(epoch_dur[2:]))))
# epoch barrier
PaGraph.utils.barrier(sock, role='trainer')
if rank == 0:
print(prof.key_averages().table(sort_by='cuda_time_total'))
def trainer(rank, world_size, args, backend='nccl'):
# init multi process
init_process(rank, world_size, backend)
# load data
dataname = os.path.basename(args.dataset)
g = dgl.contrib.graph_store.create_graph_from_store(dataname, "shared_mem")
labels = data.get_labels(args.dataset)
n_classes = args.n_classes
# masks for semi-supervised learning
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
train_nid = np.nonzero(train_mask)[0].astype(np.int64)
chunk_size = int(train_nid.shape[0] / world_size) - 1
train_nid = train_nid[chunk_size * rank:chunk_size * (rank + 1)]
test_nid = np.nonzero(test_mask)[0].astype(np.int64)
# to torch tensor
labels = torch.LongTensor(labels)
train_mask = torch.ByteTensor(train_mask)
val_mask = torch.ByteTensor(val_mask)
test_mask = torch.ByteTensor(test_mask)
# cacher
embed_names = ['features', 'norm']
vnum = train_mask.size(0)
maps = torch.arange(vnum)
cacher = storage.GraphCacheServer(g, vnum, maps, rank)
cacher.init_field(embed_names)
cacher.log = False
# prepare model
model = GCNSampling(args.feat_size,
args.n_hidden,
n_classes,
args.n_layers,
F.relu,
args.dropout,
args.preprocess)
loss_fcn = torch.nn.CrossEntropyLoss()
optimizer = torch.optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
model.cuda(rank)
model = torch.nn.parallel.DistributedDataParallel(model, device_ids=[rank])
# sampler
num_hops = args.n_layers if args.preprocess else args.n_layers + 1
if args.remote_sample:
sampler = SampleLoader(g, rank, one2all=False)
else:
sampler = dgl.contrib.sampling.NeighborSampler(
g, args.batch_size,
args.num_neighbors, neighbor_type='in',
shuffle=True, num_workers=16, num_hops=num_hops,
seed_nodes=train_nid, prefetch=True)
# start training
epoch_dur = []
tic = time.time()
with torch.autograd.profiler.profile(enabled=(rank==0), use_cuda=True) as prof:
for epoch in range(args.n_epochs):
model.train()
epoch_start_time = time.time()
step = 0
for nf in sampler:
with torch.autograd.profiler.record_function('gpu-load'):
cacher.fetch_data(nf)
batch_nids = nf.layer_parent_nid(-1)
label = labels[batch_nids]
label = label.cuda(rank, non_blocking=True)
with torch.autograd.profiler.record_function('gpu-compute'):
pred = model(nf)
loss = loss_fcn(pred, label)
optimizer.zero_grad()
loss.backward()
optimizer.step()
step += 1
if epoch == 0 and step == 1:
cacher.auto_cache(g, embed_names)
if rank == 0 and step % 20 == 0:
print('epoch [{}] step [{}]. Loss: {:.4f}'
.format(epoch + 1, step, loss.item()))
if rank == 0:
epoch_dur.append(time.time() - epoch_start_time)
print('Epoch average time: {:.4f}'.format(np.mean(np.array(epoch_dur[2:]))))
if cacher.log:
miss_rate = cacher.get_miss_rate()
print('Epoch average miss rate: {:.4f}'.format(miss_rate))
toc = time.time()
if rank == 0:
print(prof.key_averages().table(sort_by='cuda_time_total'))
print('Total Time: {:.4f}s'.format(toc - tic))
def main(args):
coo_adj, feat = data.get_graph_data(args.dataset)
graph = dgl.DGLGraph(coo_adj, readonly=True)
features = torch.FloatTensor(feat)
graph_name = os.path.basename(args.dataset)
vnum = graph.number_of_nodes()
enum = graph.number_of_edges()
feat_size = feat.shape[1]
print('=' * 30)
print("Graph Name: {}\nNodes Num: {}\tEdges Num: {}\nFeature Size: {}".
format(graph_name, vnum, enum, feat_size))
print('=' * 30)
# create server
g = dgl.contrib.graph_store.create_graph_store_server(graph,
graph_name,
'shared_mem',
args.num_workers,
False,
edge_dir='in')
# calculate norm for gcn
dgl_g = DGLGraph(graph, readonly=True)
if args.model == 'gcn':
dgl_g = DGLGraph(graph, readonly=True)
norm = 1. / dgl_g.in_degrees().float().unsqueeze(1)
# preprocess
if args.preprocess:
print('Preprocessing features...')
dgl_g.ndata['norm'] = norm
dgl_g.ndata['features'] = features
dgl_g.update_all(
fn.copy_src(src='features', out='m'),
fn.sum(msg='m', out='preprocess'), lambda node:
{'preprocess': node.data['preprocess'] * node.data['norm']})
features = dgl_g.ndata['preprocess']
g.ndata['norm'] = norm
g.ndata['features'] = features
del dgl_g
elif args.model == 'graphsage':
if args.preprocess: # for simple preprocessing
print('preprocessing: warning: jusy copy')
g.ndata['neigh'] = features
g.ndata['features'] = features
# remote sampler
if args.sample:
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
train_nid = np.nonzero(train_mask)[0].astype(np.int64)
print('Expected trainer#: {}. Start sampling at server end...'.format(
args.num_workers))
if args.one2all:
sampler_proc = multiprocessing.Process(target=sample_one2all,
args=(graph, train_nid,
args))
sampler_proc.start()
else:
sampler_proc = sample_one2one(graph, train_nid, args)
print('start running graph server on dataset: {}'.format(graph_name))
g.run()
sampler_proc.close()
sampler_proc.join()
def trainer(rank, world_size, args, backend='nccl'):
# init multi process
init_process(rank, world_size, backend)
# load data
dataname = os.path.basename(args.dataset)
g = dgl.contrib.graph_store.create_graph_from_store(dataname, "shared_mem")
labels = data.get_labels(args.dataset)
n_classes = len(np.unique(labels))
# masks for semi-supervised learning
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
train_nid = np.nonzero(train_mask)[0].astype(np.int64)
chunk_size = int(train_nid.shape[0] / world_size) - 1
train_nid = train_nid[chunk_size * rank:chunk_size * (rank + 1)]
test_nid = np.nonzero(test_mask)[0].astype(np.int64)
# to torch tensor
labels = torch.LongTensor(labels)
train_mask = torch.ByteTensor(train_mask)
val_mask = torch.ByteTensor(val_mask)
test_mask = torch.ByteTensor(test_mask)
# prepare model
num_hops = args.n_layers if args.preprocess else args.n_layers + 1
model = GCNSampling(args.feat_size, args.n_hidden, n_classes,
args.n_layers, F.relu, args.dropout, args.preprocess)
loss_fcn = torch.nn.CrossEntropyLoss()
optimizer = torch.optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
model.cuda(rank)
model = torch.nn.parallel.DistributedDataParallel(model, device_ids=[rank])
ctx = torch.device(rank)
# start training
epoch_dur = []
sampler = dgl.contrib.sampling.NeighborSampler(
g,
args.batch_size,
args.num_neighbors,
neighbor_type='in',
shuffle=True,
num_workers=args.num_workers,
num_hops=num_hops,
seed_nodes=train_nid,
prefetch=False)
profile_begin = time.time()
with torch.autograd.profiler.profile(enabled=(rank == 0),
use_cuda=True) as prof:
for epoch in range(args.n_epochs):
model.train()
epoch_start_time = time.time()
step = 0
for nf in sampler:
with torch.autograd.profiler.record_function('gpu-load'):
nf.copy_from_parent(ctx=ctx)
batch_nids = nf.layer_parent_nid(-1)
label = labels[batch_nids]
label = label.cuda(rank, non_blocking=True)
step += 1
if rank == 0 and step % 20 == 0:
print('epoch [{}] step [{}]'.format(epoch + 1, step))
if rank == 0:
epoch_dur.append(time.time() - epoch_start_time)
print('Epoch average time: {:.4f}'.format(
np.mean(np.array(epoch_dur[2:]))))
print('Total Time: {:.4f}s'.format(time.time() - profile_begin))
if rank == 0:
print(prof.key_averages().table(sort_by='cuda_time_total'))
def trainer(rank, world_size, args, backend='nccl'):
# init multi process
init_process(rank, world_size, backend)
# load data
dataname = os.path.basename(args.dataset)
g = dgl.contrib.graph_store.create_graph_from_store(dataname, "shared_mem")
labels = data.get_labels(args.dataset)
n_classes = len(np.unique(labels))
# masks for semi-supervised learning
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
train_nid = np.nonzero(train_mask)[0].astype(np.int64)
chunk_size = int(train_nid.shape[0] / world_size) - 1
train_nid = train_nid[chunk_size * rank:chunk_size * (rank + 1)]
test_nid = np.nonzero(test_mask)[0].astype(np.int64)
# to torch tensor
labels = torch.LongTensor(labels)
train_mask = torch.ByteTensor(train_mask)
val_mask = torch.ByteTensor(val_mask)
test_mask = torch.ByteTensor(test_mask)
# generate data
vnum = 4036538
data1 = torch.rand((vnum, args.feat_size))
data2 = torch.rand((vnum, 1)) # norm
# start training
epoch_dur = []
num_hops = args.n_layers if args.preprocess else args.n_layers + 1
sampler = dgl.contrib.sampling.NeighborSampler(
g,
args.batch_size,
args.num_neighbors,
neighbor_type='in',
shuffle=True,
num_workers=args.num_workers,
num_hops=num_hops,
seed_nodes=train_nid,
prefetch=False)
profile_begin = time.time()
with torch.autograd.profiler.profile(enabled=(rank == 0),
use_cuda=True) as prof:
for epoch in range(args.n_epochs):
epoch_start_time = time.time()
step = 0
for nf in sampler:
datas = []
for i in range(nf.num_layers):
with torch.autograd.profiler.record_function(
'index-select'):
tnid = nf.layer_parent_nid(i)
fdata1 = data1[tnid]
fdata2 = data2[tnid]
datas.append([fdata1, fdata2])
with torch.autograd.profiler.record_function('h2d-load'):
fdata1 = fdata1.cuda()
fdata2 = fdata2.cuda()
with torch.autograd.profiler.record_function('index-select'):
label = labels[tnid]
with torch.autograd.profiler.record_function('h2d-load'):
label = label.cuda()
# clear data
del label
for d in datas:
del d
step += 1
if rank == 0 and step % 20 == 0:
print('epoch [{}] step [{}]'.format(epoch + 1, step))
if rank == 0:
epoch_dur.append(time.time() - epoch_start_time)
print('Epoch average time: {:.4f}'.format(
np.mean(np.array(epoch_dur[2:]))))
print('Total Time: {:.4f}s'.format(time.time() - profile_begin))
if rank == 0:
print(prof.key_averages().table(sort_by='cuda_time_total'))
def main(args):
coo_adj, feat = data.get_graph_data(args.dataset)
graph = dgl.DGLGraph(coo_adj, readonly=True)
features = torch.FloatTensor(feat)
graph_name = os.path.basename(args.dataset)
vnum = graph.number_of_nodes()
enum = graph.number_of_edges()
feat_size = feat.shape[1]
print('=' * 30)
print("Graph Name: {}\nNodes Num: {}\tEdges Num: {}\nFeature Size: {}".
format(graph_name, vnum, enum, feat_size))
print('=' * 30)
# create server
g = dgl.contrib.graph_store.create_graph_store_server(graph,
graph_name,
'shared_mem',
args.num_workers,
False,
edge_dir='in')
# calculate norm for gcn
dgl_g = DGLGraph(graph, readonly=True)
if args.model == 'gcn':
dgl_g = DGLGraph(graph, readonly=True)
norm = 1. / dgl_g.in_degrees().float().unsqueeze(1)
# preprocess
if args.preprocess:
print('Preprocessing features...')
dgl_g.ndata['norm'] = norm
dgl_g.ndata['features'] = features
dgl_g.update_all(
fn.copy_src(src='features', out='m'),
fn.sum(msg='m', out='preprocess'), lambda node:
{'preprocess': node.data['preprocess'] * node.data['norm']})
features = dgl_g.ndata['preprocess']
g.ndata['norm'] = norm
g.ndata['features'] = features
del dgl_g
elif args.model == 'graphsage':
if args.preprocess: # for simple preprocessing
print('preprocessing: warning: jusy copy')
g.ndata['neigh'] = features
g.ndata['features'] = features
# remote sampler
if args.sample:
train_mask, val_mask, test_mask = data.get_masks(args.dataset)
train_nid = np.nonzero(train_mask)[0].astype(np.int64)
chunk_size = int(train_nid.shape[0] / args.num_workers) - 1
subgraph = []
sub_trainnid = []
for rank in range(args.num_workers):
train_nid = train_nid[chunk_size * rank:chunk_size * (rank + 1)]
sub_trainnid.append(train_nid)
hops = args.gnn_layers - 1 if args.preprocess else args.gnn_layers
print('Expected trainer#: {}. Start sampling at server end...'.format(
args.num_workers))
deliver = SampleDeliver(graph, sub_trainnid, args.num_neighbors, hops,
args.num_workers)
deliver.async_sample(args.n_epochs,
args.batch_size,
one2all=args.one2all)
print('start running graph server on dataset: {}'.format(graph_name))
g.run()
