MegaMolBART/examples/chem/megamolbart_pretrain.py

# Copyright (c) 2022, NVIDIA CORPORATION.
# SPDX-License-Identifier: Apache-2.0

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.


from omegaconf.omegaconf import OmegaConf, open_dict
from pytorch_lightning import Trainer
from pytorch_lightning.callbacks import ModelSummary
from pytorch_lightning.callbacks.timer import Timer
from pytorch_lightning.plugins.environments.torchelastic_environment import TorchElasticEnvironment
from pytorch_lightning.plugins.precision.native_amp import NativeMixedPrecisionPlugin
from pytorch_lightning.trainer.connectors.checkpoint_connector import CheckpointConnector

from nemo.collections.nlp.parts.nlp_overrides import (
    GradScaler,
    MegatronHalfPrecisionPlugin,
    NLPDDPPlugin,
    PipelineMixedPrecisionPlugin,
)
from nemo.core.config import hydra_runner
from nemo.utils import logging
from nemo.utils.exp_manager import StatelessTimer, exp_manager

from nemo_chem.models.megamolbart import MegaMolBARTModel
from nemo_chem.data import MoleculeCsvDatasetConfig
from nemo_chem.utils import recursive_make_dirs, update_dataclass_config
from nemo_chem.data import Preprocess, CsvToBinary
import os

def setup_trainer(cfg):
    """Trainer setup functions"""
    megatron_amp_o2 = cfg.model.get('megatron_amp_O2', False)
    plugins = [
        NLPDDPPlugin(
            no_ddp_communication_hook=True,
            gradient_as_bucket_view=cfg.model.gradient_as_bucket_view,
            find_unused_parameters=False,
        )
    ]
    if cfg.trainer.precision in [16, 'bf16']:
        scaler = None
        if cfg.trainer.precision == 16:
            scaler = GradScaler(
                init_scale=cfg.model.get('native_amp_init_scale', 2 ** 32),
                growth_interval=cfg.model.get('native_amp_growth_interval', 1000),
                hysteresis=cfg.model.get('hysteresis', 2),
            )
        if megatron_amp_o2:
            plugins.append(MegatronHalfPrecisionPlugin(precision=cfg.trainer.precision, device='cuda', scaler=scaler))
        else:
            plugins.append(PipelineMixedPrecisionPlugin(precision=cfg.trainer.precision, device='cuda', scaler=scaler))

    if cfg.get('cluster_type', None) == 'BCP':
        plugins.append(TorchElasticEnvironment())

    trainer = Trainer(plugins=plugins, **cfg.trainer, callbacks=[ModelSummary(max_depth=3)])
    exp_manager(trainer, cfg.get("exp_manager", None))
    # recursive_make_dirs(log_dir)
    # recursive_make_dirs(trainer.checkpoint_callback.dirpath)

    # update resume from checkpoint found by exp_manager
    if cfg.model.resume_from_checkpoint is not None:
        resume_from_checkpoint = cfg.model.resume_from_checkpoint
    else:
        resume_from_checkpoint = trainer._checkpoint_connector.resume_from_checkpoint_fit_path
    logging.info(f'Resuming training from checkpoint: {resume_from_checkpoint}')

    trainer._checkpoint_connector = CheckpointConnector(trainer, resume_from_checkpoint=resume_from_checkpoint)
    # Override timer callback to a stateless one
    for idx, callback in enumerate(trainer.callbacks):
        if isinstance(callback, Timer):
            trainer.callbacks[idx] = StatelessTimer(cfg.trainer.max_time,)

    # hydra interpolation does not work here as the interpolation key is lost when PTL saves hparams
    with open_dict(cfg):
        cfg.model.precision = cfg.trainer.precision

    return trainer


@hydra_runner(config_path="conf", config_name="megamolbart_pretrain_xsmall_span_aug")
def main(cfg) -> None:
    with open_dict(cfg):
        cfg.model.data = update_dataclass_config(cfg.model.data, MoleculeCsvDatasetConfig)

    logging.info("\n\n************** Experiment configuration ***********")
    logging.info(f'\n{OmegaConf.to_yaml(cfg)}')

    trainer = setup_trainer(cfg)
    model = MegaMolBARTModel(cfg.model, trainer)

    logging.info("************** Model parameters and their sizes ***********")
    for name, param in model.named_parameters():
        logging.info(f'{name}: {param.size()}')
        logging.info("***********************************************************")

    if cfg.do_training:
        logging.info("************** Starting Training ***********")
        trainer.fit(model)
        logging.info("************** Finished Training ***********")
    else:
        logging.info("************** Starting Data PreProcessing ***********")
        logging.info("Processing data into CSV files")
        preprocess = Preprocess()
        preprocess.prepare_dataset(links_file=cfg.model.data.links_file,
                                   output_dir=cfg.model.data.dataset_path)
        if cfg.model.data.dataset_format == "bin":
            logging.info("Converting CSV data into Binary")
            csvtobin = CsvToBinary(input_dir=cfg.model.data.dataset_path,
                                   out_dir=cfg.model.data.dataset_path,
                                   config=cfg,
                                   num_enumerations=cfg.model.data.num_enumerations,
                                   num_workers=cfg.model.data.num_workers)
            csvtobin.prepare_dataset()
        logging.info("************** Finished Data PreProcessing ***********")

    if cfg.do_testing:
        logging.info("************** Starting Testing ***********")
        trainer.test(model)
        logging.info("************** Finished Testing ***********")


if __name__ == '__main__':
    main()