changes required for pytorch2

environment.yml

@@ -1,4 +1,4 @@
-name: openfold-venv
+name: pytorch1-plupgrade 
 channels:
   - conda-forge
   - bioconda
@@ -11,7 +11,7 @@ dependencies:
   - openmm=7.7
   - pdbfixer
   - cudatoolkit==11.3.*
-  - pytorch-lightning==1.5.10
+  - pytorch-lightning==2.0.9
   - biopython==1.79
   - numpy==1.21
   - pandas==2.0
@@ -19,7 +19,7 @@ dependencies:
   - requests
   - scipy==1.7
   - tqdm==4.62.2
-  - typing-extensions==3.10
+  - typing-extensions==4.0
   - wandb==0.12.21
   - modelcif==0.7
   - awscli
@@ -31,6 +31,7 @@ dependencies:
   - bioconda::kalign2==2.04
   - pytorch::pytorch=1.12.*
   - pip:
+      - mpi4py==3.1.5
       - deepspeed==0.12.4
       - dm-tree==0.1.6
       - git+https://github.com/NVIDIA/dllogger.git

openfold/data/data_modules.py

@@ -937,7 +937,7 @@ class OpenFoldDataModule(pl.LightningDataModule):
             with open(distillation_alignment_index_path, "r") as fp:
                 self.distillation_alignment_index = json.load(fp)
 
-    def setup(self):
+    def setup(self, stage=None):
         # Most of the arguments are the same for the three datasets 
         dataset_gen = partial(OpenFoldSingleDataset,
                               template_mmcif_dir=self.template_mmcif_dir,
@@ -1016,7 +1016,7 @@ class OpenFoldDataModule(pl.LightningDataModule):
                 mode="predict",
             )
 
-    def _gen_dataloader(self, stage):
+    def _gen_dataloader(self, stage=None):
         generator = None
         if self.batch_seed is not None:
             generator = torch.Generator()
@@ -1053,7 +1053,7 @@ class OpenFoldDataModule(pl.LightningDataModule):
     def val_dataloader(self):
         if self.eval_dataset is not None:
             return self._gen_dataloader("eval")
-        return None
+        return [] 
 
     def predict_dataloader(self):
         return self._gen_dataloader("predict")
@@ -1085,7 +1085,7 @@ class OpenFoldMultimerDataModule(OpenFoldDataModule):
         self.training_mode = self.train_data_dir is not None
         self.val_mmcif_data_cache_path = val_mmcif_data_cache_path
 
-    def setup(self):
+    def setup(self, setup=None):
         # Most of the arguments are the same for the three datasets 
         dataset_gen = partial(OpenFoldSingleMultimerDataset,
                               template_mmcif_dir=self.template_mmcif_dir,

openfold/data/data_pipeline.py

@@ -244,7 +244,7 @@ def make_msa_features(msas: Sequence[parsers.Msa]) -> FeatureDict:
     features["num_alignments"] = np.array(
         [num_alignments] * num_res, dtype=np.int32
     )
-    features["msa_species_identifiers"] = np.array(species_ids, dtype=np.object_)
+    features["msa_species_identifiers"] = np.array(species_ids, dtype=object)
     return features
 
 
@@ -590,7 +590,7 @@ def convert_monomer_features(
 ) -> FeatureDict:
     """Reshapes and modifies monomer features for multimer models."""
     converted = {}
-    converted['auth_chain_id'] = np.asarray(chain_id, dtype=np.object_)
+    converted['auth_chain_id'] = np.asarray(chain_id, dtype=object)
     unnecessary_leading_dim_feats = {
         'sequence', 'domain_name', 'num_alignments', 'seq_length'
     }
@@ -1296,7 +1296,7 @@ class DataPipelineMultimer:
         )
 
         mmcif_feats["release_date"] = np.array(
-            [mmcif_object.header["release_date"].encode("utf-8")], dtype=np.object_
+            [mmcif_object.header["release_date"].encode("utf-8")], dtype=object
         )
 
         mmcif_feats["is_distillation"] = np.array(0., dtype=np.float32)

openfold/utils/superimposition.py

@@ -35,8 +35,8 @@ def _superimpose_np(reference, coords):
 
 
 def _superimpose_single(reference, coords):
-    reference_np = reference.detach().cpu().numpy()    
-    coords_np = coords.detach().cpu().numpy()
+    reference_np = reference.detach().to(torch.float).cpu().numpy()    
+    coords_np = coords.detach().to(torch.float).cpu().numpy()
     superimposed, rmsd = _superimpose_np(reference_np, coords_np)
     return coords.new_tensor(superimposed), coords.new_tensor(rmsd)
 

train_openfold.py

@@ -8,8 +8,11 @@ import pytorch_lightning as pl
 from pytorch_lightning.callbacks.lr_monitor import LearningRateMonitor
 from pytorch_lightning.callbacks.model_checkpoint import ModelCheckpoint
 from pytorch_lightning.loggers import WandbLogger
-from pytorch_lightning.plugins.training_type import DeepSpeedPlugin, DDPPlugin
+from pytorch_lightning.strategies import DDPStrategy, DeepSpeedStrategy
+from pytorch_lightning.plugins.environments import MPIEnvironment
+from pytorch_lightning import seed_everything
 import torch
+import wandb
 
 from openfold.config import model_config
 from openfold.data.data_modules import OpenFoldDataModule, OpenFoldMultimerDataModule
@@ -24,7 +27,6 @@ from openfold.utils.exponential_moving_average import ExponentialMovingAverage
 from openfold.utils.loss import AlphaFoldLoss, lddt_ca
 from openfold.utils.lr_schedulers import AlphaFoldLRScheduler
 from openfold.utils.multi_chain_permutation import multi_chain_permutation_align
-from openfold.utils.seed import seed_everything
 from openfold.utils.superimposition import superimpose
 from openfold.utils.tensor_utils import tensor_tree_map
 from openfold.utils.validation_metrics import (
@@ -59,7 +61,7 @@ class OpenFoldWrapper(pl.LightningModule):
         
         self.cached_weights = None
         self.last_lr_step = -1
-        self.save_hyperparameters
+        self.save_hyperparameters()
 
     def forward(self, batch):
         return self.model(batch)
@@ -70,14 +72,15 @@ class OpenFoldWrapper(pl.LightningModule):
             self.log(
                 f"{phase}/{loss_name}", 
                 indiv_loss, 
-                on_step=train, on_epoch=(not train), logger=True,
+                prog_bar=(loss_name == 'loss'),
+                on_step=train, on_epoch=(not train), logger=True, sync_dist=False,
             )
 
             if(train):
                 self.log(
                     f"{phase}/{loss_name}_epoch",
                     indiv_loss,
-                    on_step=False, on_epoch=True, logger=True,
+                    on_step=False, on_epoch=True, logger=True, sync_dist=False,
                 )
 
         with torch.no_grad():
@@ -91,7 +94,8 @@ class OpenFoldWrapper(pl.LightningModule):
             self.log(
                 f"{phase}/{k}",
                 torch.mean(v),
-                on_step=False, on_epoch=True, logger=True
+                prog_bar = (k == 'loss'),
+                on_step=False, on_epoch=True, logger=True, sync_dist=False,
             )
 
     def training_step(self, batch, batch_idx):
@@ -154,7 +158,7 @@ class OpenFoldWrapper(pl.LightningModule):
 
         self._log(loss_breakdown, batch, outputs, train=False)
         
-    def validation_epoch_end(self, _):
+    def on_validation_epoch_end(self):
         # Restore the model weights to normal
         self.model.load_state_dict(self.cached_weights)
         self.cached_weights = None
@@ -377,40 +381,59 @@ def main(args):
         callbacks.append(lr_monitor)
 
     loggers = []
+    is_rank_zero = int(os.environ.get("PMI_RANK")) == 0
     if(args.wandb):
+        if args.mpi_plugin and is_rank_zero:
+            wandb_init_dict = dict(
+                name=args.experiment_name,
+                project=args.wandb_project,
+                id=args.wandb_id,
+                dir=args.output_dir,
+                resume="allow",
+                anonymous=None,
+                entity=args.wandb_entity
+            )
+            wandb.run = wandb.init(**wandb_init_dict)
+
         wdb_logger = WandbLogger(
             name=args.experiment_name,
             save_dir=args.output_dir,
             id=args.wandb_id,
             project=args.wandb_project,
-            config=config.to_dict(),
             **{"entity": args.wandb_entity}
         )
         loggers.append(wdb_logger)
 
+    cluster_environment = MPIEnvironment() if args.mpi_plugin else None
     if(args.deepspeed_config_path is not None):
-        strategy = DeepSpeedPlugin(
+        strategy = DeepSpeedStrategy(
             config=args.deepspeed_config_path,
+            cluster_environment=cluster_environment,
         )
-        if(args.wandb):
+        if(args.wandb and is_rank_zero):
             wdb_logger.experiment.save(args.deepspeed_config_path)
             wdb_logger.experiment.save("openfold/config.py")
     elif (args.gpus is not None and args.gpus > 1) or args.num_nodes > 1:
-        strategy = DDPPlugin(find_unused_parameters=False)
+        strategy = DDPStrategy(find_unused_parameters=False,
+                               cluster_environment=cluster_environment)
     else:
         strategy = None
  
-    if(args.wandb):
+    if(args.wandb and is_rank_zero):
         freeze_path = f"{wdb_logger.experiment.dir}/package_versions.txt"
         os.system(f"{sys.executable} -m pip freeze > {freeze_path}")
         wdb_logger.experiment.save(f"{freeze_path}")
 
-    trainer = pl.Trainer.from_argparse_args(
-        args,
+    trainer = pl.Trainer(
+        num_nodes=args.num_nodes,
+        devices=args.gpus,
+        precision=args.precision,
+        max_epochs=args.max_epochs,
         default_root_dir=args.output_dir,
         strategy=strategy,
         callbacks=callbacks,
         logger=loggers,
+        profiler='simple',
     )
 
     if(args.resume_model_weights_only):
@@ -621,7 +644,16 @@ if __name__ == "__main__":
     parser.add_argument(
         "--experiment_config_json", default="", help="Path to a json file with custom config values to overwrite config setting",
     )
-    parser = pl.Trainer.add_argparse_args(parser)
+    parser.add_argument("--num_nodes", type=int, default=1)
+    parser.add_argument("--gpus", type=int, default=None)
+    parser.add_argument("--max_epochs", type=int, default=None)
+    parser.add_argument("--precision", type=str, default="32")
+    parser.add_argument("--log_every_n_steps", type=int, default=50)
+    parser.add_argument("--accumulate_grad_batches", type=int, default=1)
+    parser.add_argument("--flush_logs_every_n_steps", type=int, default=5)
+    parser.add_argument("--num_sanity_val_steps", type=int, default=0)
+    parser.add_argument("--mpi_plugin", action="store_true", default=False)
+    # parser = pl.Trainer.add_argparse_args(parser)
    
     # Disable the initial validation pass
     parser.set_defaults(