Merge branch 'main' of ssh://github.com/aqlaboratory/openfold into main

README.md

@@ -137,9 +137,9 @@ python3 train_openfold.py mmcif_dir/ alignment_dir/ template_mmcif_dir/ \
     --template_release_dates_cache_path mmcif_cache.json \ 
     --precision 16 \
     --gpus 8 --replace_sampler_ddp=True \
-    --accelerator ddp \ 
     --seed 42 \ # in multi-gpu settings, the seed must be specified
-    --deepspeed_config_path deepspeed_config.json
+    --deepspeed_config_path deepspeed_config.json \
+    --resume_from_ckpt ckpt_dir/
 ```
 
 where `--template_release_dates_cache_path` is a path to the `.json` file

openfold/utils/argparse.py

+from argparse import HelpFormatter
+from operator import attrgetter
+
+class ArgparseAlphabetizer(HelpFormatter):
+    """
+        Sorts the optional arguments of an argparse parser alphabetically
+    """
+
+    @staticmethod
+    def sort_actions(actions):
+        return sorted(actions, key=attrgetter("option_strings"))
+
+    # Formats the help message
+    def add_arguments(self, actions):
+        actions = ArgparseAlphabetizer.sort_actions(actions)
+        super(ArgparseAlphabetizer, self).add_arguments(actions)
+
+    # Formats the usage message
+    def add_usage(self, usage, actions, groups, prefix=None):
+        actions = ArgparseAlphabetizer.sort_actions(actions)
+        args = usage, actions, groups, prefix
+        super(ArgparseAlphabetizer, self).add_usage(*args)
+
+
+def remove_arguments(parser, args):
+    for arg in args:
+        for action in parser._actions:
+            opts = vars(action)["option_strings"]
+            if(arg in opts):
+                parser._handle_conflict_resolve(None, [(arg, action)])

requirements.txt

@@ -26,4 +26,4 @@ tqdm==4.62.2
 triton==1.0.0
 typing-extensions==3.10.0.2
 urllib3==1.26.6
-pytorch_lightning==1.4.8
+pytorch_lightning==1.5.0

scripts/zero_to_fp32.py

+#!/usr/bin/env python
+
+# This script extracts fp32 consolidated weights from a zero 2 and 3 DeepSpeed checkpoints. It gets
+# copied into the top level checkpoint dir, so the user can easily do the conversion at any point in
+# the future. Once extracted, the weights don't require DeepSpeed and can be used in any
+# application.
+#
+# example: python zero_to_fp32.py . pytorch_model.bin
+
+import argparse
+import torch
+import glob
+import math
+import os
+from collections import OrderedDict
+
+# while this script doesn't use deepspeed to recover data, since the checkpoints are pickled with
+# DeepSpeed data structures it has to be available in the current python environment.
+import deepspeed
+from deepspeed.utils import logger
+
+debug = 0
+
+# load to cpu
+device = torch.device('cpu')
+
+
+def get_model_state_file(checkpoint_dir, zero_stage):
+    if not os.path.isdir(checkpoint_dir):
+        raise FileNotFoundError(f"Directory '{checkpoint_dir}' doesn't exist")
+
+    # there should be only one file
+    if zero_stage == 2:
+        file = os.path.join(checkpoint_dir, "mp_rank_00_model_states.pt")
+    elif zero_stage == 3:
+        file = os.path.join(checkpoint_dir, "zero_pp_rank_0_mp_rank_00_model_states.pt")
+
+    if not os.path.exists(file):
+        raise FileNotFoundError(f"can't find model states file at '{file}'")
+
+    return file
+
+
+def get_optim_files(checkpoint_dir):
+    # XXX: need to test that this simple glob rule works for multi-node setup too
+    optim_files = sorted(glob.glob(os.path.join(checkpoint_dir, "*_optim_states.pt")))
+
+    if len(optim_files) == 0:
+        raise FileNotFoundError(
+            f"can't find '*_optim_states.pt' files in directory '{checkpoint_dir}'")
+
+    return optim_files
+
+
+def parse_model_state(file):
+    state_dict = torch.load(file, map_location=device)
+
+    if "buffer_names" not in state_dict:
+        raise ValueError(f"{file} is not a model state checkpoint")
+    buffer_names = state_dict["buffer_names"]
+    if debug:
+        print("Found buffers:", buffer_names)
+
+    # recover just the buffers while restoring them to fp32 if they were saved in fp16
+    buffers = {
+        k: v.float()
+        for k,
+        v in state_dict["module"].items() if k in buffer_names
+    }
+    return buffers
+
+
+def parse_optim_states(files, ds_checkpoint_dir):
+
+    total_files = len(files)
+    state_dicts = []
+    for f in files:
+        state_dicts.append(torch.load(f, map_location=device))
+
+    if not "zero_stage" in state_dicts[0]['optimizer_state_dict']:
+        raise ValueError(f"{files[0]} is not a zero checkpoint")
+    zero_stage = state_dicts[0]['optimizer_state_dict']["zero_stage"]
+    world_size = state_dicts[0]['optimizer_state_dict']["partition_count"]
+    param_shapes = state_dicts[0]["param_shapes"]
+    # For ZeRO-2 each param group can have different partition_count as data parallelism for expert
+    # parameters can be different from data parallelism for non-expert parameters. So we can just
+    # use the max of the partition_count to get the dp world_size.
+
+    if type(world_size) is list:
+        world_size = max(world_size)
+
+    if world_size != total_files:
+        raise ValueError(
+            f"Expected {world_size} of '*_optim_states.pt' under '{ds_checkpoint_dir}' but found {total_files} files. "
+            "Possibly due to an overwrite of an old checkpoint, or a checkpoint didn't get saved by one or more processes."
+        )
+
+    # the groups are named differently in each stage
+    if zero_stage == 2:
+        fp32_groups_key = "single_partition_of_fp32_groups"
+    elif zero_stage == 3:
+        fp32_groups_key = "fp32_flat_groups"
+    else:
+        raise ValueError(f"unknown zero stage {zero_stage}")
+
+    if zero_stage == 2:
+        fp32_flat_groups = [
+            state_dicts[i]['optimizer_state_dict'][fp32_groups_key]
+            for i in range(len(state_dicts))
+        ]
+    elif zero_stage == 3:
+        # if there is more than one param group, there will be multiple flattened tensors - one
+        # flattened tensor per group - for simplicity merge them into a single tensor
+        #
+        # XXX: could make the script more memory efficient for when there are multiple groups - it
+        # will require matching the sub-lists of param_shapes for each param group flattened tensor
+
+        fp32_flat_groups = [
+            torch.cat(state_dicts[i]['optimizer_state_dict'][fp32_groups_key],
+                      0) for i in range(len(state_dicts))
+        ]
+
+    return zero_stage, world_size, param_shapes, fp32_flat_groups
+
+
+def _get_fp32_state_dict_from_zero_checkpoint(ds_checkpoint_dir):
+    """
+    Returns fp32 state_dict reconstructed from ds checkpoint
+
+    Args:
+        - ``ds_checkpoint_dir``: path to the deepspeed checkpoint folder (where the optimizer files are)
+
+    """
+    print(f"Processing zero checkpoint '{ds_checkpoint_dir}'")
+
+    optim_files = get_optim_files(ds_checkpoint_dir)
+    zero_stage, world_size, param_shapes, fp32_flat_groups = parse_optim_states(optim_files, ds_checkpoint_dir)
+    print(
+        f"Detected checkpoint of type zero stage {zero_stage}, world_size: {world_size}")
+
+    model_file = get_model_state_file(ds_checkpoint_dir, zero_stage)
+    buffers = parse_model_state(model_file)
+
+    if zero_stage == 2:
+        return _get_fp32_state_dict_from_zero2_checkpoint(world_size,
+                                                          param_shapes,
+                                                          fp32_flat_groups,
+                                                          buffers)
+    elif zero_stage == 3:
+        return _get_fp32_state_dict_from_zero3_checkpoint(world_size,
+                                                          param_shapes,
+                                                          fp32_flat_groups,
+                                                          buffers)
+
+
+def _get_fp32_state_dict_from_zero2_checkpoint(world_size,
+                                               param_shapes,
+                                               fp32_flat_groups,
+                                               buffers):
+
+    # Reconstruction protocol:
+    #
+    # XXX: document this
+
+    if debug:
+        for i in range(world_size):
+            for j in range(len(fp32_flat_groups[0])):
+                print(f"fp32_flat_groups[{i}][{j}].shape={fp32_flat_groups[i][j].shape}")
+
+    # XXX: memory usage doubles here (zero2)
+    num_param_groups = len(fp32_flat_groups[0])
+    merged_single_partition_of_fp32_groups = []
+    for i in range(num_param_groups):
+        merged_partitions = [sd[i] for sd in fp32_flat_groups]
+        full_single_fp32_vector = torch.cat(merged_partitions, 0)
+        merged_single_partition_of_fp32_groups.append(full_single_fp32_vector)
+    avail_numel = sum([
+        full_single_fp32_vector.numel()
+        for full_single_fp32_vector in merged_single_partition_of_fp32_groups
+    ])
+
+    if debug:
+        wanted_params = sum([len(shapes) for shapes in param_shapes])
+        wanted_numel = sum(
+            [sum(shape.numel() for shape in shapes.values()) for shapes in param_shapes])
+        # not asserting if there is a mismatch due to possible padding
+        print(f"Have {avail_numel} numels to process.")
+        print(f"Need {wanted_numel} numels in {wanted_params} params.")
+
+    state_dict = OrderedDict()
+
+    # buffers
+    state_dict.update(buffers)
+    if debug:
+        print(f"added {len(buffers)} buffers")
+
+    # params
+    # XXX: for huge models that can't fit into the host's RAM we will have to recode this to support
+    # out-of-core computing solution
+    total_numel = 0
+    total_params = 0
+    for shapes, full_single_fp32_vector in zip(param_shapes, merged_single_partition_of_fp32_groups):
+        offset = 0
+        avail_numel = full_single_fp32_vector.numel()
+        for name, shape in shapes.items():
+
+            unpartitioned_numel = shape.numel()
+            total_numel += unpartitioned_numel
+            total_params += 1
+
+            if debug:
+                print(
+                    f"{name} full shape: {shape} unpartitioned numel {unpartitioned_numel} "
+                )
+            state_dict[name] = full_single_fp32_vector.narrow(
+                0,
+                offset,
+                unpartitioned_numel).view(shape)
+            offset += unpartitioned_numel
+
+        # Z2 started to align to 2*world_size to improve nccl performance. Therefore both offset and
+        # avail_numel can differ by anywhere between 0..2*world_size. Due to two unrelated complex
+        # paddings performed in the code it's almost impossible to predict the exact numbers w/o the
+        # live optimizer object, so we are checking that the numbers are within the right range
+        align_to = 2 * world_size
+
+        def zero2_align(x):
+            return align_to * math.ceil(x / align_to)
+
+        if debug:
+            print(f"original offset={offset}, avail_numel={avail_numel}")
+
+        offset = zero2_align(offset)
+        avail_numel = zero2_align(avail_numel)
+
+        if debug:
+            print(f"aligned  offset={offset}, avail_numel={avail_numel}")
+
+        # Sanity check
+        if offset != avail_numel:
+            raise ValueError(
+                f"consumed {offset} numels out of {avail_numel} - something is wrong")
+
+    print(
+        f"Reconstructed fp32 state dict with {total_params} params {total_numel} elements"
+    )
+
+    return state_dict
+
+
+def zero3_partitioned_param_info(unpartitioned_numel, world_size):
+    remainder = unpartitioned_numel % world_size
+    padding_numel = (world_size - remainder) if remainder else 0
+    partitioned_numel = math.ceil(unpartitioned_numel / world_size)
+    return partitioned_numel, padding_numel
+
+
+def _get_fp32_state_dict_from_zero3_checkpoint(world_size,
+                                               param_shapes,
+                                               fp32_flat_groups,
+                                               buffers):
+
+    # Reconstruction protocol: For zero3 we need to zip the partitions together at boundary of each
+    # param, re-consolidating each param, while dealing with padding if any
+
+    avail_numel = fp32_flat_groups[0].numel() * world_size
+    # merge list of dicts, preserving order
+    param_shapes = {k: v for d in param_shapes for k, v in d.items()}
+
+    if debug:
+        for i in range(world_size):
+            print(f"fp32_flat_groups[{i}].shape={fp32_flat_groups[i].shape}")
+
+        wanted_params = len(param_shapes)
+        wanted_numel = sum(shape.numel() for shape in param_shapes.values())
+        # not asserting if there is a mismatch due to possible padding
+        print(f"Have {avail_numel} numels to process.")
+        print(f"Need {wanted_numel} numels in {wanted_params} params.")
+
+    state_dict = OrderedDict()
+
+    # buffers
+    state_dict.update(buffers)
+    if debug:
+        print(f"added {len(buffers)} buffers")
+
+    # params
+    # XXX: for huge models that can't fit into the host's RAM we will have to recode this to support
+    # out-of-core computing solution
+    offset = 0
+    total_numel = 0
+    total_params = 0
+    for name, shape in param_shapes.items():
+
+        unpartitioned_numel = shape.numel()
+        total_numel += unpartitioned_numel
+        total_params += 1
+
+        partitioned_numel, partitioned_padding_numel = zero3_partitioned_param_info(unpartitioned_numel, world_size)
+
+        if debug:
+            print(
+                f"{total_params} {name} full shape: {shape} partition0 numel={partitioned_numel} partitioned_padding_numel={partitioned_padding_numel}"
+            )
+
+        # XXX: memory usage doubles here
+        state_dict[name] = torch.cat(
+            tuple(fp32_flat_groups[i].narrow(0,
+                                             offset,
+                                             partitioned_numel)
+                  for i in range(world_size)),
+            0).narrow(0,
+                      0,
+                      unpartitioned_numel).view(shape)
+        offset += partitioned_numel
+
+    offset *= world_size
+
+    # Sanity check
+    if offset != avail_numel:
+        raise ValueError(
+            f"consumed {offset} numels out of {avail_numel} - something is wrong")
+
+    print(
+        f"Reconstructed fp32 state dict with {total_params} params {total_numel} elements"
+    )
+
+    return state_dict
+
+
+def get_fp32_state_dict_from_zero_checkpoint(checkpoint_dir, tag=None):
+    """
+    Convert ZeRO 2 or 3 checkpoint into a single fp32 consolidated state_dict that can be loaded with
+    ``load_state_dict()`` and used for training without DeepSpeed or shared with others, for example
+    via a model hub.
+
+    Args:
+        - ``checkpoint_dir``: path to the desired checkpoint folder
+        - ``tag``: checkpoint tag used as a unique identifier for checkpoint. If not provided will attempt to load tag in 'latest' file. e.g., ``global_step14``
+
+    Returns:
+        - pytorch ``state_dict``
+
+    Note: this approach may not work if your application doesn't have sufficient free CPU memory and
+    you may need to use the offline approach using the ``zero_to_fp32.py`` script that is saved with
+    the checkpoint.
+
+    A typical usage might be ::
+
+        from deepspeed.utils.zero_to_fp32 import get_fp32_state_dict_from_zero_checkpoint
+        # do the training and checkpoint saving
+        state_dict = get_fp32_state_dict_from_zero_checkpoint(checkpoint_dir) # already on cpu
+        model = model.cpu() # move to cpu
+        model.load_state_dict(state_dict)
+        # submit to model hub or save the model to share with others
+
+    In this example the ``model`` will no longer be usable in the deepspeed context of the same
+    application. i.e. you will need to re-initialize the deepspeed engine, since
+    ``model.load_state_dict(state_dict)`` will remove all the deepspeed magic from it.
+
+    If you want it all done for you, use ``load_state_dict_from_zero_checkpoint`` instead.
+
+    """
+    if tag is None:
+        latest_path = os.path.join(checkpoint_dir, 'latest')
+        if os.path.isfile(latest_path):
+            with open(latest_path, 'r') as fd:
+                tag = fd.read().strip()
+        else:
+            raise ValueError(f"Unable to find 'latest' file at {latest_path}")
+
+    ds_checkpoint_dir = os.path.join(checkpoint_dir, tag)
+
+    if not os.path.isdir(ds_checkpoint_dir):
+        raise FileNotFoundError(f"Directory '{ds_checkpoint_dir}' doesn't exist")
+
+    return _get_fp32_state_dict_from_zero_checkpoint(ds_checkpoint_dir)
+
+
+def convert_zero_checkpoint_to_fp32_state_dict(checkpoint_dir, output_file, tag=None):
+    """
+    Convert ZeRO 2 or 3 checkpoint into a single fp32 consolidated ``state_dict`` file that can be
+    loaded with ``torch.load(file)`` + ``load_state_dict()`` and used for training without DeepSpeed.
+
+    Args:
+        - ``checkpoint_dir``: path to the desired checkpoint folder. (one that contains the tag-folder, like ``global_step14``)
+        - ``output_file``: path to the pytorch fp32 state_dict output file (e.g. path/pytorch_model.bin)
+        - ``tag``: checkpoint tag used as a unique identifier for checkpoint. If not provided will attempt to load tag in the file named ``latest`` in the checkpoint folder, e.g., ``global_step14``
+    """
+
+    state_dict = get_fp32_state_dict_from_zero_checkpoint(checkpoint_dir, tag)
+    print(f"Saving fp32 state dict to {output_file}")
+    torch.save(state_dict, output_file)
+
+
+def load_state_dict_from_zero_checkpoint(model, checkpoint_dir, tag=None):
+    """
+    1. Put the provided model to cpu
+    2. Convert ZeRO 2 or 3 checkpoint into a single fp32 consolidated ``state_dict``
+    3. Load it into the provided model
+
+    Args:
+        - ``model``: the model object to update
+        - ``checkpoint_dir``: path to the desired checkpoint folder. (one that contains the tag-folder, like ``global_step14``)
+        - ``tag``: checkpoint tag used as a unique identifier for checkpoint. If not provided will attempt to load tag in the file named ``latest`` in the checkpoint folder, e.g., ``global_step14``
+
+    Returns:
+        - ``model`: modified model
+
+    Make sure you have plenty of CPU memory available before you call this function. If you don't
+    have enough use the ``zero_to_fp32.py`` utility to do the conversion. You will find it
+    conveniently placed for you in the checkpoint folder.
+
+    A typical usage might be ::
+
+        from deepspeed.utils.zero_to_fp32 import load_state_dict_from_zero_checkpoint
+        model = load_state_dict_from_zero_checkpoint(trainer.model, checkpoint_dir)
+        # submit to model hub or save the model to share with others
+
+    Note, that once this was run, the ``model`` will no longer be usable in the deepspeed context
+    of the same application. i.e. you will need to re-initialize the deepspeed engine, since
+    ``model.load_state_dict(state_dict)`` will remove all the deepspeed magic from it.
+
+    """
+    logger.info(f"Extracting fp32 weights")
+    state_dict = get_fp32_state_dict_from_zero_checkpoint(checkpoint_dir, tag)
+
+    logger.info(f"Overwriting model with fp32 weights")
+    model = model.cpu()
+    model.load_state_dict(state_dict, strict=False)
+
+    return model
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "checkpoint_dir",
+        type=str,
+        help="path to the desired checkpoint folder, e.g., path/checkpoint-12")
+    parser.add_argument(
+        "output_file",
+        type=str,
+        help=
+        "path to the pytorch fp32 state_dict output file (e.g. path/checkpoint-12/pytorch_model.bin)"
+    )
+    parser.add_argument("-d", "--debug", action='store_true', help="enable debug")
+    args = parser.parse_args()
+
+    debug = args.debug
+
+    convert_zero_checkpoint_to_fp32_state_dict(args.checkpoint_dir, args.output_file)

train_openfold.py

@@ -2,12 +2,11 @@ import argparse
 import logging
 import os
 
-#os.environ["CUDA_VISIBLE_DEVICES"] = "5"
+#os.environ["CUDA_VISIBLE_DEVICES"] = "7"
 #os.environ["MASTER_ADDR"]="10.119.81.14"
 #os.environ["MASTER_PORT"]="42069"
 #os.environ["NODE_RANK"]="0"
 
-
 import random
 import time
 
@@ -27,9 +26,13 @@ from openfold.utils.callbacks import (
     EarlyStoppingVerbose,
 )
 from openfold.utils.exponential_moving_average import ExponentialMovingAverage
+from openfold.utils.argparse import remove_arguments
 from openfold.utils.loss import AlphaFoldLoss
 from openfold.utils.seed import seed_everything
 from openfold.utils.tensor_utils import tensor_tree_map
+from scripts.zero_to_fp32 import (
+    get_fp32_state_dict_from_zero_checkpoint
+)
 
 
 class OpenFoldWrapper(pl.LightningModule):
@@ -104,8 +107,12 @@ def main(args):
         train=True, 
         low_prec=(args.precision == 16)
     ) 
-
-    model_module = OpenFoldWrapper(config) 
+    model_module = OpenFoldWrapper(config)
+    if(args.resume_from_ckpt and args.resume_model_weights_only):
+        sd = get_fp32_state_dict_from_zero_checkpoint(args.resume_from_ckpt)
+        sd = {k[len("module."):]:v for k,v in sd.items()}
+        model_module.load_state_dict(sd)
+        logging.info("Successfully loaded model weights...")
     #data_module = DummyDataLoader("batch.pickle")
     data_module = OpenFoldDataModule(
         config=config.data, 
@@ -114,7 +121,7 @@ def main(args):
     )
     data_module.prepare_data()
     data_module.setup()
-   
+
     callbacks = []
     if(args.checkpoint_best_val):
         checkpoint_dir = os.path.join(args.output_dir, "checkpoints")
@@ -137,17 +144,30 @@ def main(args):
         )
         callbacks.append(es)
 
-    plugins = []
     if(args.deepspeed_config_path is not None):
-        plugins.append(DeepSpeedPlugin(config=args.deepspeed_config_path))
+        strategy = DeepSpeedPlugin(config=args.deepspeed_config_path)
+    else:
+        strategy = "ddp"
     
     trainer = pl.Trainer.from_argparse_args(
         args,
-        plugins=plugins,
+        strategy=strategy,
+    )
+
+    if(args.resume_model_weights_only):
+        ckpt_path = None
+    else:
+        ckpt_path = args.resume_from_ckpt
+
+    trainer.fit(
+        model_module, 
+        datamodule=data_module,
+        ckpt_path=ckpt_path,
     )
 
-    trainer.fit(model_module, datamodule=data_module)
-    trainer.save_checkpoint("final.ckpt")
+    trainer.save_checkpoint(
+        os.path.join(trainer.logger.log_dir, "checkpoints", "final.ckpt")
+    )
 
 
 if __name__ == "__main__":
@@ -239,12 +259,24 @@ if __name__ == "__main__":
         "--patience", type=int, default=3,
         help="Early stopping patience"
     )
+    parser.add_argument(
+        "--resume_from_ckpt", type=str, default=None,
+        help="Path to a model checkpoint from which to restore training state"
+    )
+    parser.add_argument(
+        "--resume_model_weights_only", type=bool, default=False,
+        help="Whether to load just model weights as opposed to training state"
+    )
     parser = pl.Trainer.add_argparse_args(parser)
-    
+   
+    # Disable the initial validation pass
     parser.set_defaults(
         num_sanity_val_steps=0,
     )
 
+    # Remove some buggy/redundant arguments introduced by the Trainer
+    remove_arguments(parser, ["--accelerator", "--resume_from_checkpoint"]) 
+
     args = parser.parse_args()
 
     if(args.seed is None and