Make FlashAttention installation optional

environment.yml

@@ -27,5 +27,4 @@ dependencies:
       - typing-extensions==3.10.0.2
       - pytorch_lightning==1.5.10
       - wandb==0.12.21
-      - git+https://github.com/HazyResearch/flash-attention.git@5b838a8bef78186196244a4156ec35bbb58c337d
       - git+https://github.com/NVIDIA/dllogger.git

openfold/config.py

@@ -1,4 +1,5 @@
 import copy
+import importlib
 import ml_collections as mlc
 
 
@@ -36,6 +37,10 @@ def string_to_setting(s):
         if(s1_setting and s2_setting):
             raise ValueError(f"Only one of {s1} and {s2} may be set at a time")
 
+    fa_is_installed = importlib.util.find_spec("flash_attn") is not None
+    if(config.globals.use_flash and not fa_is_installed):
+        raise ValueError("use_flash requires that FlashAttention is installed")
+
 
 def model_config(name, train=False, low_prec=False):
     c = copy.deepcopy(config)
@@ -57,6 +62,24 @@ def model_config(name, train=False, low_prec=False):
         c.loss.experimentally_resolved.weight = 0.01
         c.model.heads.tm.enabled = True
         c.loss.tm.weight = 0.1
+    elif name == "finetuning_no_templ":
+        # AF2 Suppl. Table 4, "finetuning" setting
+        c.data.train.max_extra_msa = 5120
+        c.data.train.crop_size = 384
+        c.data.train.max_msa_clusters = 512
+        c.model.template.enabled = False
+        c.loss.violation.weight = 1.
+        c.loss.experimentally_resolved.weight = 0.01
+    elif name == "finetuning_no_templ_ptm":
+        # AF2 Suppl. Table 4, "finetuning" setting
+        c.data.train.max_extra_msa = 5120
+        c.data.train.crop_size = 384
+        c.data.train.max_msa_clusters = 512
+        c.model.template.enabled = False
+        c.loss.violation.weight = 1.
+        c.loss.experimentally_resolved.weight = 0.01
+        c.model.heads.tm.enabled = True
+        c.loss.tm.weight = 0.1
     elif name == "model_1":
         # AF2 Suppl. Table 5, Model 1.1.1
         c.data.train.max_extra_msa = 5120
@@ -324,7 +347,7 @@ def model_config(name, train=False, low_prec=False):
             "use_lma": False,
             # Use FlashAttention in selected modules. Mutually exclusive with 
             # use_lma.
-            "use_flash": True,
+            "use_flash": False,
             "offload_inference": False,
             "c_z": c_z,
             "c_m": c_m,

openfold/model/primitives.py

@@ -13,14 +13,19 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 from functools import partial
+import importlib
 import math
 from typing import Optional, Callable, List, Tuple, Sequence
 import numpy as np
 
 import deepspeed
-from flash_attn.bert_padding import unpad_input, pad_input
-from flash_attn.flash_attention import FlashAttention
-from flash_attn.flash_attn_interface import flash_attn_unpadded_kvpacked_func
+
+fa_is_installed = importlib.util.find_spec("flash_attn") is not None
+if(fa_is_installed):
+    from flash_attn.bert_padding import unpad_input, pad_input
+    from flash_attn.flash_attention import FlashAttention
+    from flash_attn.flash_attn_interface import flash_attn_unpadded_kvpacked_func
+
 import torch
 import torch.nn as nn
 from scipy.stats import truncnorm
@@ -643,6 +648,11 @@ def _lma(
 
 @torch.jit.ignore
 def _flash_attn(q, k, v, kv_mask):
+    if(not fa_is_installed):
+        raise ValueError(
+            "_flash_attn requires that FlashAttention be installed"
+        )
+
     batch_dims = q.shape[:-3]
     no_heads, n, c = q.shape[-3:]
     dtype = q.dtype

scripts/install_third_party_dependencies.sh

@@ -17,6 +17,9 @@ lib/conda/bin/python3 -m pip install nvidia-pyindex
 conda env create --name=${ENV_NAME} -f environment.yml
 source activate ${ENV_NAME}
 
+echo "Attempting to install FlashAttention"
+pip install git+https://github.com/HazyResearch/flash-attention.git@5b838a8bef78186196244a4156ec35bbb58c337d && echo "Installation successful"
+
 # Install DeepMind's OpenMM patch
 OPENFOLD_DIR=$PWD
 pushd lib/conda/envs/$ENV_NAME/lib/python3.7/site-packages/ \