Return to regular kernel usage

environment.yml

@@ -30,7 +30,7 @@ dependencies:
   - bioconda::kalign2==2.04
   - pytorch::pytorch=1.12.*
   - pip:
-      - deepspeed==0.12.2
+      - git+https://github.com/microsoft/DeepSpeed.git@4388a60  # Replace when version becomes available
       - dm-tree==0.1.6
       - git+https://github.com/NVIDIA/dllogger.git
       - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8

openfold/model/primitives.py

@@ -23,7 +23,7 @@
     import deepspeed
 
 if ds4s_is_installed:
-    from deepspeed.ops.deepspeed4science import EvoformerFusedAttention
+    from deepspeed.ops.deepspeed4science import DS4Sci_EvoformerAttention
 
 fa_is_installed = importlib.util.find_spec("flash_attn") is not None
 if fa_is_installed:
@@ -661,19 +661,18 @@ def reshape_dims(x):
         v = reshape_dims(v)
         biases = [reshape_dims(b) for b in biases]
 
-    biases.extend([None] * (2 - len(biases)))
-
     # DeepSpeed attn. kernel requires inputs to be type bf16 or fp16
     # Cast to bf16 so kernel can be used during inference
     orig_dtype = q.dtype
     if orig_dtype not in [torch.bfloat16, torch.float16]:
-        inputs_bf16 = [x.to(dtype=torch.bfloat16) if x is not None else x
-                       for x in (q, k, v, biases[0], biases[1])]
-        o = EvoformerFusedAttention.apply(*inputs_bf16)
+        o = DS4Sci_EvoformerAttention(q.to(dtype=torch.bfloat16),
+                                      k.to(dtype=torch.bfloat16),
+                                      v.to(dtype=torch.bfloat16),
+                                      [b.to(dtype=torch.bfloat16) for b in biases])
 
         o = o.to(dtype=orig_dtype)
     else:
-        o = EvoformerFusedAttention.apply(q, k, v, biases[0], biases[1])
+        o = DS4Sci_EvoformerAttention(q, k, v, biases)
 
     o = o.reshape(orig_shape)
     return o