restruct dir

tests/test_autochunk/autochunk_benchmark.py

@@ -3,13 +3,13 @@ import time
 import torch
 import torch.fx
 
-from autochunk.chunk_codegen import ChunkCodeGen
+from colossalai.autochunk.chunk_codegen import ChunkCodeGen
 from colossalai.fx import ColoTracer
 from colossalai.fx.graph_module import ColoGraphModule
 from colossalai.fx.passes.meta_info_prop import MetaInfoProp
 from colossalai.fx.profiler import MetaTensor
-from autochunk.evoformer.evoformer import evoformer_base
+from tests.test_autochunk.evoformer.evoformer import evoformer_base
-from autochunk.openfold.evoformer import EvoformerBlock
+from tests.test_autochunk.openfold.evoformer import EvoformerBlock
 
 
 def _benchmark_evoformer(model: torch.nn.Module, node, pair, title, chunk_size=None):
@@ -94,7 +94,7 @@ def _build_openfold():
 def benchmark_evoformer():
     # init data and model
     msa_len = 256
-    pair_len = 1024
+    pair_len = 256
     node = torch.randn(1, msa_len, pair_len, 256).cuda()
     pair = torch.randn(1, pair_len, pair_len, 128).cuda()
     model = evoformer_base().cuda()
@@ -106,11 +106,11 @@ def benchmark_evoformer():
 
     # build openfold
     chunk_size = 64
-    # openfold = _build_openfold()
+    openfold = _build_openfold()
 
     # benchmark
-    # _benchmark_evoformer(model, node, pair, "base")
+    _benchmark_evoformer(model, node, pair, "base")
-    # _benchmark_evoformer(openfold, node, pair, "openfold", chunk_size=chunk_size)
+    _benchmark_evoformer(openfold, node, pair, "openfold", chunk_size=chunk_size)
     _benchmark_evoformer(autochunk, node, pair, "autochunk")
 
 

tests/test_autochunk/autochunk_test.py

@@ -12,8 +12,8 @@ from colossalai.core import global_context as gpc
 from colossalai.fx.graph_module import ColoGraphModule
 from colossalai.fx.passes.meta_info_prop import MetaInfoProp, TensorMetadata
 from colossalai.fx.profiler import MetaTensor
-from autochunk.evoformer.evoformer import evoformer_base
+from tests.test_autochunk.evoformer.evoformer import evoformer_base
-from autochunk.chunk_codegen import ChunkCodeGen
+from ...colossalai.autochunk.chunk_codegen import ChunkCodeGen
 with_codegen = True
 
 

tests/test_autochunk/openfold/evoformer.py

@@ -19,25 +19,25 @@ import torch.nn as nn
 from typing import Tuple, Optional
 from functools import partial
 
-from openfold.primitives import Linear, LayerNorm
+from .primitives import Linear, LayerNorm
-from openfold.dropout import DropoutRowwise, DropoutColumnwise
+from .dropout import DropoutRowwise, DropoutColumnwise
-from openfold.msa import (
+from .msa import (
     MSARowAttentionWithPairBias,
     MSAColumnAttention,
     MSAColumnGlobalAttention,
 )
-from openfold.outer_product_mean import OuterProductMean
+from .outer_product_mean import OuterProductMean
-from openfold.pair_transition import PairTransition
+from .pair_transition import PairTransition
-from openfold.triangular_attention import (
+from .triangular_attention import (
     TriangleAttentionStartingNode,
     TriangleAttentionEndingNode,
 )
-from openfold.triangular_multiplicative_update import (
+from .triangular_multiplicative_update import (
     TriangleMultiplicationOutgoing,
     TriangleMultiplicationIncoming,
 )
-from openfold.checkpointing import checkpoint_blocks, get_checkpoint_fn
+from .checkpointing import checkpoint_blocks, get_checkpoint_fn
-from openfold.tensor_utils import chunk_layer
+from .tensor_utils import chunk_layer
 
 
 class MSATransition(nn.Module):

tests/test_autochunk/openfold/msa.py

@@ -18,15 +18,15 @@ import torch
 import torch.nn as nn
 from typing import Optional, List, Tuple
 
-from openfold.primitives import (
+from .primitives import (
     Linear, 
     LayerNorm,
     Attention, 
     GlobalAttention, 
     _attention_chunked_trainable,
 )
-from openfold.checkpointing import get_checkpoint_fn
+from .checkpointing import get_checkpoint_fn
-from openfold.tensor_utils import (
+from .tensor_utils import (
     chunk_layer,
     permute_final_dims,
     flatten_final_dims,

tests/test_autochunk/openfold/outer_product_mean.py

@@ -19,8 +19,8 @@ from typing import Optional
 import torch
 import torch.nn as nn
 
-from openfold.primitives import Linear
+from .primitives import Linear
-from openfold.tensor_utils import chunk_layer
+from .tensor_utils import chunk_layer
 
 
 class OuterProductMean(nn.Module):

tests/test_autochunk/openfold/pair_transition.py

@@ -17,8 +17,8 @@ from typing import Optional
 import torch
 import torch.nn as nn
 
-from openfold.primitives import Linear, LayerNorm
+from .primitives import Linear, LayerNorm
-from openfold.tensor_utils import chunk_layer
+from .tensor_utils import chunk_layer
 
 
 class PairTransition(nn.Module):

tests/test_autochunk/openfold/primitives.py

@@ -21,8 +21,8 @@ import numpy as np
 import torch
 import torch.nn as nn
 
-from openfold.checkpointing import get_checkpoint_fn
+from .checkpointing import get_checkpoint_fn
-from openfold.tensor_utils import (
+from .tensor_utils import (
     permute_final_dims,
     flatten_final_dims,
     _chunk_slice,

tests/test_autochunk/openfold/triangular_attention.py

@@ -20,8 +20,8 @@ from typing import Optional, List
 import torch
 import torch.nn as nn
 
-from openfold.primitives import Linear, LayerNorm, Attention
+from .primitives import Linear, LayerNorm, Attention
-from openfold.tensor_utils import (
+from .tensor_utils import (
     chunk_layer,
     permute_final_dims,
     flatten_final_dims,

tests/test_autochunk/openfold/triangular_multiplicative_update.py

@@ -19,8 +19,8 @@ from typing import Optional
 import torch
 import torch.nn as nn
 
-from openfold.primitives import Linear, LayerNorm
+from .primitives import Linear, LayerNorm
-from openfold.tensor_utils import permute_final_dims
+from .tensor_utils import permute_final_dims
 
 
 class TriangleMultiplicativeUpdate(nn.Module):