Add low-memory attention (still needs to be incorporated)

openfold/model/primitives.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 
 import math
-from typing import Optional, Callable, List
+from typing import Optional, Callable, List, Tuple, Sequence
 import numpy as np
 
 import torch
@@ -24,6 +24,7 @@
 from openfold.utils.tensor_utils import (
     permute_final_dims,
     flatten_final_dims,
+    _chunk_slice,
 )
 
 
@@ -217,7 +218,7 @@ def __init__(
             self.c_hidden * self.no_heads, self.c_q, init="final"
         )
 
-        if self.gating is not None:
+        if self.gating:
             self.linear_g = Linear(
                 self.c_q, self.c_hidden * self.no_heads, init="gating"
             )
@@ -370,3 +371,176 @@ def forward(self, m: torch.Tensor, mask: torch.Tensor) -> torch.Tensor:
         m = self.linear_o(o)
 
         return m
+
+
+@torch.jit.script
+def _lma(
+    q: torch.Tensor, 
+    k: torch.Tensor, 
+    v: torch.Tensor, 
+    biases: List[torch.Tensor], 
+    q_chunk_size: int, 
+    kv_chunk_size: int
+):
+    no_q, no_kv = q.shape[-3], k.shape[-3]
+
+    # [*, Q, H, C_hidden]
+    o = q.new_zeros(q.shape)
+    for q_s in range(0, no_q, q_chunk_size):
+        q_chunk = q[..., q_s: q_s + q_chunk_size, :, :]
+        big_bias_chunks = [
+            b[..., q_s: q_s + q_chunk_size, :] for b in biases
+        ] 
+
+        maxes = []
+        weights = []
+        values = []
+        for kv_s in range(0, no_kv, kv_chunk_size):
+            k_chunk = k[..., kv_s: kv_s + kv_chunk_size, :, :]
+            v_chunk = v[..., kv_s: kv_s + kv_chunk_size, :, :] 
+            small_bias_chunks = [
+                b[..., kv_s: kv_s + kv_chunk_size] for b in big_bias_chunks
+            ]
+
+            a = torch.einsum(
+                "...qhd,...khd->...hqk", q_chunk, k_chunk
+            )
+
+            for b in small_bias_chunks:
+                a += b
+
+            a = a.transpose(-2, -3)
+
+            max_a = torch.max(a, dim=-1, keepdim=True)[0].detach()
+            exp_a = torch.exp(a - max_a)
+            exp_v = torch.einsum("...vhf,...qhv->...qhf", v_chunk, exp_a)
+
+            maxes.append(max_a.squeeze(-1))
+            weights.append(torch.sum(exp_a, dim=-1))
+            values.append(exp_v)
+
+        chunk_max = torch.stack(maxes, dim=-3)
+        chunk_weights = torch.stack(weights, dim=-3)
+        chunk_values = torch.stack(values, dim=-4)
+
+        global_max = torch.max(chunk_max, dim=-3, keepdim=True)[0]
+        max_diffs = torch.exp(chunk_max - global_max)
+        chunk_values *= max_diffs.unsqueeze(-1)
+        chunk_weights *= max_diffs
+
+        all_values = torch.sum(chunk_values, dim=-4)
+        all_weights = torch.sum(chunk_weights.unsqueeze(-1), dim=-4)
+
+        q_chunk_out = all_values / all_weights
+
+        o[..., q_s: q_s + q_chunk_size, :, :] = q_chunk_out
+
+    return o
+
+
+class LowMemoryAttention(nn.Module):
+    """
+    Standard multi-head attention using AlphaFold's default layer
+    initialization. Allows multiple bias vectors. Implements Rabe and Staats'
+    low-memory self-attention algorithm.
+    """
+    def __init__(
+        self,
+        c_q: int,
+        c_k: int,
+        c_v: int,
+        c_hidden: int,
+        no_heads: int,
+        gating: bool = True,
+    ):
+        """
+        Args:
+            c_q:
+                Input dimension of query data
+            c_k:
+                Input dimension of key data
+            c_v:
+                Input dimension of value data
+            c_hidden:
+                Per-head hidden dimension
+            no_heads:
+                Number of attention heads
+            gating:
+                Whether the output should be gated using query data
+            chunk_size:
+                Trades memory for better parallelization. A low value
+                corresponds to lower memory usage.
+        """
+        super().__init__()
+
+        self.c_q = c_q
+        self.c_k = c_k
+        self.c_v = c_v
+        self.c_hidden = c_hidden
+        self.no_heads = no_heads
+        self.gating = gating
+
+        self.linear_q = Linear(
+            self.c_q, self.c_hidden * self.no_heads, bias=False, init="glorot"
+        )
+        self.linear_k = Linear(
+            self.c_k, self.c_hidden * self.no_heads, bias=False, init="glorot"
+        )
+        self.linear_v = Linear(
+            self.c_v, self.c_hidden * self.no_heads, bias=False, init="glorot"
+        )
+        self.linear_o = Linear(
+            self.c_hidden * self.no_heads, self.c_q, init="final"
+        )
+
+        if self.gating:
+            self.linear_g = Linear(
+                self.c_q, self.c_hidden * self.no_heads, init="gating"
+            )
+
+        self.sigmoid = nn.Sigmoid()
+        self.softmax = nn.Softmax(dim=-1)
+
+    def forward(self, 
+        q_x: torch.Tensor,
+        k_x: torch.Tensor,
+        v_x: torch.Tensor,
+        q_chunk_size: int,
+        kv_chunk_size: int,
+        biases: Optional[List[torch.Tensor]] = None,
+    ):
+        if(biases is None):
+            biases = []
+        else:
+            biases = [
+                b.expand(b.shape[:-2] + (q_x.shape[-2],) + (k_x.shape[-2],)) 
+                for b in biases
+            ]
+
+        # [*, Q/K/V, H * C_hidden]
+        q = self.linear_q(q_x)
+        k = self.linear_k(k_x)
+        v = self.linear_v(v_x)
+
+        # [*, Q/K, H, C_hidden]
+        q = q.view(q.shape[:-1] + (self.no_heads, -1))
+        k = k.view(k.shape[:-1] + (self.no_heads, -1))
+        v = v.view(v.shape[:-1] + (self.no_heads, -1))
+
+        q = q / math.sqrt(q.shape[-1])
+
+        o = _lma(q, k, v, biases, q_chunk_size, kv_chunk_size)
+
+        if self.gating:
+            g = self.sigmoid(self.linear_g(q_x))
+            # [*, Q, H, C_hidden]
+            g = g.view(g.shape[:-1] + (self.no_heads, -1))
+            o = o * g
+
+        # [*, Q, H * C_hidden]
+        o = flatten_final_dims(o, 2)
+
+        # [*, Q, C_q]
+        o = self.linear_o(o)
+
+        return o

openfold/utils/tensor_utils.py

@@ -124,6 +124,7 @@ def _fetch_dims(tree):
     return shapes
 
 
+@torch.jit.ignore
 def _flat_idx_to_idx(
     flat_idx: int,
     dims: Tuple[int],
@@ -135,6 +136,8 @@ def _flat_idx_to_idx(
 
     return tuple(reversed(idx))
 
+
+@torch.jit.ignore
 def _get_minimal_slice_set(
     start: Sequence[int],
     end: Sequence[int],
@@ -252,18 +255,19 @@ def lower():
     return [tuple(s) for s in slices]
 
 
+@torch.jit.ignore
 def _chunk_slice(
     t: torch.Tensor,
     flat_start: int,
     flat_end: int,
     no_batch_dims: int,
-):
+) -> torch.Tensor:
     """
         Equivalent to
         
             t.reshape((-1,) + t.shape[no_batch_dims:])[flat_start:flat_end]
 
-        but without the need for the reshape call, which can be 
+        but without the need for the initial reshape call, which can be 
         memory-intensive in certain situations. The only reshape operations
         in this function are performed on sub-tensors that scale with
         (flat_end - flat_start), the chunk size.
@@ -281,7 +285,6 @@ def _chunk_slice(
         batch_dims,
     )
 
-    #
     sliced_tensors = [t[s] for s in slices]
 
     return torch.cat(
@@ -352,7 +355,6 @@ def _prep_inputs(t):
 
     i = 0
     out = None
-
     for _ in range(no_chunks):
         # Chunk the input
         if(not low_mem):
@@ -382,7 +384,6 @@ def _prep_inputs(t):
         # Put the chunk in its pre-allocated space
         out_type = type(output_chunk)
         if out_type is dict:
-
             def assign(d1, d2):
                 for k, v in d1.items():
                     if type(v) is dict:

scripts/run_unit_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-#CUDA_VISIBLE_DEVICES="5"
+CUDA_VISIBLE_DEVICES="0"
 
 python3 -m unittest "$@" || \
 echo -e "\nTest(s) failed. Make sure you've installed all Python dependencies."

tests/compare_utils.py

@@ -1,7 +1,5 @@
 import os
 
-os.environ["CUDA_VISIBLE_DEVICES"] = "4,"
-
 import importlib
 import pkgutil
 import sys

tests/test_primitives.py

@@ -0,0 +1,70 @@
+# Copyright 2021 AlQuraishi Laboratory
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import torch
+import numpy as np
+import unittest
+
+from openfold.model.primitives import (
+    Attention,
+    LowMemoryAttention,
+)
+from tests.config import consts
+
+
+class TestLMA(unittest.TestCase):
+    def test_lma_vs_attention(self):
+        batch_size = consts.batch_size
+        c_hidden = 32 
+        n = 2**12
+        no_heads = 4
+
+        q = torch.rand(batch_size, n, c_hidden).cuda()
+        k = torch.rand(batch_size, n, c_hidden).cuda()
+        v = torch.rand(batch_size, n, c_hidden).cuda()
+
+        bias = [torch.rand(no_heads, 1, n)]
+        bias = [b.cuda() for b in bias]
+
+        gating_fill = torch.rand(c_hidden * no_heads, c_hidden)
+        o_fill = torch.rand(c_hidden, c_hidden * no_heads)
+
+        lma = LowMemoryAttention(
+            c_hidden, c_hidden, c_hidden, c_hidden, no_heads
+        ).cuda()
+        a = Attention(
+            c_hidden, c_hidden, c_hidden, c_hidden, no_heads
+        ).cuda()
+
+        with torch.no_grad():
+            for n, p in lma.named_parameters():
+                attrs = n.split('.')
+                param = a
+                for attr in attrs:
+                    param = getattr(param, attr)
+                param.copy_(p)
+
+            for m in [lma, a]:
+                m.linear_g.weight.copy_(gating_fill)
+                m.linear_o.weight.copy_(o_fill)
+
+        with torch.no_grad():
+            l = lma(q, k, v, 1024, 4096, biases=bias)
+            real = a(q, k, v, biases=bias)
+
+        self.assertTrue(torch.max(torch.abs(l - real)) < consts.eps)
+
+
+if __name__ == "__main__":
+    unittest.main()