Additional changes to seeding

openfold/data/data_modules.py

@@ -7,7 +7,6 @@ import pickle
 from typing import Optional, Sequence, List, Any
 
 import ml_collections as mlc
-import numpy as np
 import pytorch_lightning as pl
 import torch
 from torch.utils.data import RandomSampler
@@ -427,11 +426,7 @@ class OpenFoldDataLoader(torch.utils.data.DataLoader):
     def __init__(self, *args, config, stage="train", generator=None, **kwargs):
         super().__init__(*args, **kwargs)
         self.config = config
-        self.stage = stage    
-
-        if(generator is None):
-            generator = torch.Generator()
-        
+        self.stage = stage
         self.generator = generator
         self._prep_batch_properties_probs()
 
@@ -687,8 +682,9 @@ class OpenFoldDataModule(pl.LightningDataModule):
             )
 
     def _gen_dataloader(self, stage):
-        generator = torch.Generator()
+        generator = None
         if(self.batch_seed is not None):
+            generator = torch.Generator()
             generator = generator.manual_seed(self.batch_seed)
 
         dataset = None

openfold/data/data_transforms.py

@@ -16,7 +16,6 @@
 import itertools
 from functools import reduce, wraps
 from operator import add
-import random
 
 import numpy as np
 import torch
@@ -183,12 +182,14 @@ def randomly_replace_msa_with_unknown(protein, replace_proportion):
 
 @curry1
 def sample_msa(protein, max_seq, keep_extra, seed=None):
-    """Sample MSA randomly, remaining sequences are stored are stored as `extra_*`.""" 
-    if(seed is None):
-        seed = random.randint(0, 2147483647)
+    """Sample MSA randomly, remaining sequences are stored are stored as `extra_*`."""
     num_seq = protein["msa"].shape[0]
-    g = torch.Generator(device=protein["msa"].device)
-    g.manual_seed(seed)
+
+    g = None
+    if seed is not None:
+        g = torch.Generator(device=protein["msa"].device)
+        g.manual_seed(seed)
+
     shuffled = torch.randperm(num_seq - 1, generator=g) + 1
     index_order = torch.cat(
         (torch.tensor([0], device=shuffled.device), shuffled), 
@@ -1141,8 +1142,10 @@ def random_crop_to_size(
 ):
     """Crop randomly to `crop_size`, or keep as is if shorter than that."""
     # We want each ensemble to be cropped the same way
-    g = torch.Generator(device=protein["seq_length"].device)
+
+    g = None
     if seed is not None:
+        g = torch.Generator(device=protein["seq_length"].device)
         g.manual_seed(seed)
 
     seq_length = protein["seq_length"]

openfold/data/input_pipeline.py

@@ -13,7 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from functools import partial
 import random
 
 import torch
@@ -154,7 +153,7 @@ def ensembled_transform_fns(common_cfg, mode_cfg, ensemble_seed):
 def process_tensors_from_config(tensors, common_cfg, mode_cfg):
     """Based on the config, apply filters and transformations to the data."""
 
-    ensemble_seed = random.randint(0, 2147483647)
+    ensemble_seed = random.randint(0, torch.iinfo(torch.int32).max)
 
     def wrap_ensemble_fn(data, i):
         """Function to be mapped over the ensemble dimension."""