1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438
|
import os
import os.path as osp
import random
import warnings
import pytest
import torch
import torch.nn.functional as F
from torch_geometric.data import Data
from torch_geometric.loader import NeighborLoader
from torch_geometric.nn import SAGEConv
from torch_geometric.nn.models import GAT, GCN, GIN, PNA, EdgeCNN, GraphSAGE
from torch_geometric.profile import benchmark
from torch_geometric.testing import (
onlyFullTest,
onlyLinux,
onlyNeighborSampler,
onlyOnline,
withDevice,
withPackage,
)
out_dims = [None, 8]
dropouts = [0.0, 0.5]
acts = [None, 'leaky_relu', torch.relu_, F.elu, torch.nn.ReLU()]
norms = [None, 'batch_norm', 'layer_norm']
jks = [None, 'last', 'cat', 'max', 'lstm']
@pytest.mark.parametrize('out_dim', out_dims)
@pytest.mark.parametrize('dropout', dropouts)
@pytest.mark.parametrize('act', acts)
@pytest.mark.parametrize('norm', norms)
@pytest.mark.parametrize('jk', jks)
def test_gcn(out_dim, dropout, act, norm, jk):
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
out_channels = 16 if out_dim is None else out_dim
model = GCN(8, 16, num_layers=3, out_channels=out_dim, dropout=dropout,
act=act, norm=norm, jk=jk)
assert str(model) == f'GCN(8, {out_channels}, num_layers=3)'
assert model(x, edge_index).size() == (3, out_channels)
@pytest.mark.parametrize('out_dim', out_dims)
@pytest.mark.parametrize('dropout', dropouts)
@pytest.mark.parametrize('act', acts)
@pytest.mark.parametrize('norm', norms)
@pytest.mark.parametrize('jk', jks)
def test_graph_sage(out_dim, dropout, act, norm, jk):
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
out_channels = 16 if out_dim is None else out_dim
model = GraphSAGE(8, 16, num_layers=3, out_channels=out_dim,
dropout=dropout, act=act, norm=norm, jk=jk)
assert str(model) == f'GraphSAGE(8, {out_channels}, num_layers=3)'
assert model(x, edge_index).size() == (3, out_channels)
@pytest.mark.parametrize('out_dim', out_dims)
@pytest.mark.parametrize('dropout', dropouts)
@pytest.mark.parametrize('act', acts)
@pytest.mark.parametrize('norm', norms)
@pytest.mark.parametrize('jk', jks)
def test_gin(out_dim, dropout, act, norm, jk):
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
out_channels = 16 if out_dim is None else out_dim
model = GIN(8, 16, num_layers=3, out_channels=out_dim, dropout=dropout,
act=act, norm=norm, jk=jk)
assert str(model) == f'GIN(8, {out_channels}, num_layers=3)'
assert model(x, edge_index).size() == (3, out_channels)
@pytest.mark.parametrize('out_dim', out_dims)
@pytest.mark.parametrize('dropout', dropouts)
@pytest.mark.parametrize('act', acts)
@pytest.mark.parametrize('norm', norms)
@pytest.mark.parametrize('jk', jks)
def test_gat(out_dim, dropout, act, norm, jk):
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
out_channels = 16 if out_dim is None else out_dim
for v2 in [False, True]:
model = GAT(8, 16, num_layers=3, out_channels=out_dim, v2=v2,
dropout=dropout, act=act, norm=norm, jk=jk)
assert str(model) == f'GAT(8, {out_channels}, num_layers=3)'
assert model(x, edge_index).size() == (3, out_channels)
model = GAT(8, 16, num_layers=3, out_channels=out_dim, v2=v2,
dropout=dropout, act=act, norm=norm, jk=jk, heads=4)
assert str(model) == f'GAT(8, {out_channels}, num_layers=3)'
assert model(x, edge_index).size() == (3, out_channels)
@pytest.mark.parametrize('out_dim', out_dims)
@pytest.mark.parametrize('dropout', dropouts)
@pytest.mark.parametrize('act', acts)
@pytest.mark.parametrize('norm', norms)
@pytest.mark.parametrize('jk', jks)
def test_pna(out_dim, dropout, act, norm, jk):
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
deg = torch.tensor([0, 2, 1])
out_channels = 16 if out_dim is None else out_dim
aggregators = ['mean', 'min', 'max', 'std', 'var', 'sum']
scalers = [
'identity', 'amplification', 'attenuation', 'linear', 'inverse_linear'
]
model = PNA(8, 16, num_layers=3, out_channels=out_dim, dropout=dropout,
act=act, norm=norm, jk=jk, aggregators=aggregators,
scalers=scalers, deg=deg)
assert str(model) == f'PNA(8, {out_channels}, num_layers=3)'
assert model(x, edge_index).size() == (3, out_channels)
@pytest.mark.parametrize('out_dim', out_dims)
@pytest.mark.parametrize('dropout', dropouts)
@pytest.mark.parametrize('act', acts)
@pytest.mark.parametrize('norm', norms)
@pytest.mark.parametrize('jk', jks)
def test_edge_cnn(out_dim, dropout, act, norm, jk):
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
out_channels = 16 if out_dim is None else out_dim
model = EdgeCNN(8, 16, num_layers=3, out_channels=out_dim, dropout=dropout,
act=act, norm=norm, jk=jk)
assert str(model) == f'EdgeCNN(8, {out_channels}, num_layers=3)'
assert model(x, edge_index).size() == (3, out_channels)
def test_jit():
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
model = GCN(8, 16, num_layers=2)
model = torch.jit.script(model)
assert model(x, edge_index).size() == (3, 16)
@pytest.mark.parametrize('out_dim', out_dims)
@pytest.mark.parametrize('jk', jks)
def test_one_layer_gnn(out_dim, jk):
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
out_channels = 16 if out_dim is None else out_dim
model = GraphSAGE(8, 16, num_layers=1, out_channels=out_dim, jk=jk)
assert model(x, edge_index).size() == (3, out_channels)
@pytest.mark.parametrize('norm', [
'BatchNorm',
'GraphNorm',
'InstanceNorm',
'LayerNorm',
])
def test_batch(norm):
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
batch = torch.tensor([0, 0, 1])
model = GraphSAGE(8, 16, num_layers=2, norm=norm)
assert model.supports_norm_batch == (norm != 'BatchNorm')
out = model(x, edge_index, batch=batch)
assert out.size() == (3, 16)
if model.supports_norm_batch:
with pytest.raises(RuntimeError, match="out of bounds"):
model(x, edge_index, batch=batch, batch_size=1)
@onlyOnline
@onlyNeighborSampler
@pytest.mark.parametrize('jk', [None, 'last'])
def test_basic_gnn_inference(get_dataset, jk):
dataset = get_dataset(name='karate')
data = dataset[0]
model = GraphSAGE(dataset.num_features, hidden_channels=16, num_layers=2,
out_channels=dataset.num_classes, jk=jk)
model.eval()
out1 = model(data.x, data.edge_index)
assert out1.size() == (data.num_nodes, dataset.num_classes)
loader = NeighborLoader(data, num_neighbors=[-1], batch_size=128)
out2 = model.inference(loader)
assert out1.size() == out2.size()
assert torch.allclose(out1, out2, atol=1e-4)
assert 'n_id' not in data
@withDevice
@onlyLinux
@onlyFullTest
@withPackage('torch>=2.0.0')
def test_compile_basic(device):
x = torch.randn(3, 8, device=device)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]], device=device)
model = GCN(8, 16, num_layers=3).to(device)
compiled_model = torch.compile(model)
expected = model(x, edge_index)
out = compiled_model(x, edge_index)
assert torch.allclose(out, expected, atol=1e-6)
def test_packaging():
warnings.filterwarnings('ignore', '.*TypedStorage is deprecated.*')
os.makedirs(torch.hub._get_torch_home(), exist_ok=True)
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]])
model = GraphSAGE(8, 16, num_layers=3)
path = osp.join(torch.hub._get_torch_home(), 'pyg_test_model.pt')
torch.save(model, path)
model = torch.load(path, weights_only=False)
with torch.no_grad():
assert model(x, edge_index).size() == (3, 16)
model = GraphSAGE(8, 16, num_layers=3)
path = osp.join(torch.hub._get_torch_home(), 'pyg_test_package.pt')
with torch.package.PackageExporter(path) as pe:
pe.extern('torch_geometric.nn.**')
pe.extern('torch_geometric.inspector')
pe.extern('torch_geometric.utils._trim_to_layer')
pe.extern('_operator')
pe.save_pickle('models', 'model.pkl', model)
pi = torch.package.PackageImporter(path)
model = pi.load_pickle('models', 'model.pkl')
with torch.no_grad():
assert model(x, edge_index).size() == (3, 16)
@onlyLinux
@withPackage('torch>=2.6.0')
@withPackage('onnx', 'onnxruntime', 'onnxscript')
def test_onnx(tmp_path: str) -> None:
import onnx
import onnxruntime as ort
from torch_geometric import safe_onnx_export
warnings.filterwarnings('ignore', '.*tensor to a Python boolean.*')
warnings.filterwarnings('ignore', '.*shape inference of prim::Constant.*')
class MyModel(torch.nn.Module):
def __init__(self):
super().__init__()
self.conv1 = SAGEConv(8, 16)
self.conv2 = SAGEConv(16, 16)
def forward(self, x, edge_index):
x = self.conv1(x, edge_index).relu()
x = self.conv2(x, edge_index)
return x
model = MyModel()
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 1, 2], [1, 0, 2]])
expected = model(x, edge_index)
assert expected.size() == (3, 16)
path = osp.join(tmp_path, 'model.onnx')
success = safe_onnx_export(
model,
(x, edge_index),
path,
input_names=('x', 'edge_index'),
opset_version=18,
dynamo=True, # False is deprecated by PyTorch
skip_on_error=True, # Skip gracefully in CI if upstream issue occurs
)
if not success:
# ONNX export was skipped due to known upstream issue
# This allows CI to pass while the upstream bug exists
warnings.warn(
"ONNX export test skipped due to known upstream onnx_ir issue. "
"This is expected and does not indicate a problem with PyTorch "
"Geometric.", UserWarning, stacklevel=2)
return
onnx_model = onnx.load(path)
onnx.checker.check_model(onnx_model)
providers = ['CPUExecutionProvider']
ort_session = ort.InferenceSession(path, providers=providers)
out = ort_session.run(None, {
'x': x.numpy(),
'edge_index': edge_index.numpy()
})[0]
out = torch.from_numpy(out)
assert torch.allclose(out, expected, atol=1e-6)
@withPackage('pyg_lib')
def test_trim_to_layer():
x = torch.randn(14, 16)
edge_index = torch.tensor([
[2, 3, 4, 5, 7, 7, 10, 11, 12, 13],
[0, 1, 2, 3, 2, 3, 7, 7, 7, 7],
])
data = Data(x=x, edge_index=edge_index)
loader = NeighborLoader(
data,
num_neighbors=[1, 2, 4],
batch_size=2,
shuffle=False,
)
batch = next(iter(loader))
model = GraphSAGE(in_channels=16, hidden_channels=16, num_layers=3)
out1 = model(batch.x, batch.edge_index)[:2]
assert out1.size() == (2, 16)
out2 = model(
batch.x,
batch.edge_index,
num_sampled_nodes_per_hop=batch.num_sampled_nodes,
num_sampled_edges_per_hop=batch.num_sampled_edges,
)[:2]
assert out2.size() == (2, 16)
assert torch.allclose(out1, out2, atol=1e-6)
@withDevice
@onlyLinux
@withPackage('torch>=2.1.0')
@pytest.mark.parametrize('Model', [GCN, GraphSAGE, GIN, GAT, EdgeCNN, PNA])
def test_compile_graph_breaks(Model, device):
import torch._dynamo as dynamo
x = torch.randn(3, 8, device=device)
edge_index = torch.tensor([[0, 1, 1, 2], [1, 0, 2, 1]], device=device)
kwargs = {}
if Model in {GCN, GAT}:
# Adding self-loops inside the model leads to graph breaks :(
kwargs['add_self_loops'] = False
if Model in {PNA}: # `PNA` requires additional arguments:
kwargs['aggregators'] = ['sum', 'mean', 'min', 'max', 'var', 'std']
kwargs['scalers'] = ['identity', 'amplification', 'attenuation']
kwargs['deg'] = torch.tensor([1, 2, 1])
model = Model(
in_channels=8,
hidden_channels=16,
num_layers=2,
**kwargs,
).to(device)
explanation = dynamo.explain(model)(x, edge_index)
assert explanation.graph_break_count == 0
@withPackage('pyg_lib')
def test_basic_gnn_cache():
x = torch.randn(14, 16)
edge_index = torch.tensor([
[2, 3, 4, 5, 7, 7, 10, 11, 12, 13],
[0, 1, 2, 3, 2, 3, 7, 7, 7, 7],
])
loader = NeighborLoader(
Data(x=x, edge_index=edge_index),
num_neighbors=[-1],
batch_size=2,
)
model = GCN(in_channels=16, hidden_channels=16, num_layers=2)
model.eval()
out1 = model.inference(loader, cache=False)
out2 = model.inference(loader, cache=True)
assert torch.allclose(out1, out2)
if __name__ == '__main__':
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--device', type=str, default='cuda')
parser.add_argument('--backward', action='store_true')
parser.add_argument('--dynamic', action='store_true')
args = parser.parse_args()
if args.dynamic:
min_num_nodes, max_num_nodes = 10_000, 15_000
min_num_edges, max_num_edges = 200_000, 300_000
else:
min_num_nodes, max_num_nodes = 10_000, 10_000
min_num_edges, max_num_edges = 200_000, 200_000
def gen_args():
N = random.randint(min_num_nodes, max_num_nodes)
E = random.randint(min_num_edges, max_num_edges)
x = torch.randn(N, 64, device=args.device)
edge_index = torch.randint(N, (2, E), device=args.device)
return x, edge_index
for Model in [GCN, GraphSAGE, GIN, EdgeCNN]:
print(f'Model: {Model.__name__}')
model = Model(64, 64, num_layers=3).to(args.device)
compiled_model = torch.compile(model)
benchmark(
funcs=[model, compiled_model],
func_names=['Vanilla', 'Compiled'],
args=gen_args,
num_steps=50 if args.device == 'cpu' else 500,
num_warmups=10 if args.device == 'cpu' else 100,
backward=args.backward,
)
|