ODesign / data /src /utils /train /train_runner.py
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import os
from pathlib import Path
import logging
import wandb
from ml_collections.config_dict import ConfigDict
from contextlib import nullcontext
from tqdm import tqdm
import torch
from torch.utils.data import DataLoader
from src.api.model_interface import LossInput, ODesignOutput, GroundTruth
from src.model.odesign import ODesign
from src.model.modules.loss import ODesignLoss
from src.utils.inference.dumper import DataDumper
from src.utils.model.misc import is_loss_nan_check
from src.utils.train.distributed import DIST_WRAPPER
from src.utils.train.lr_scheduler import get_lr_scheduler
from src.utils.train.metrics import SimpleMetricAggregator
from src.utils.model.torch_utils import (
autocasting_disable_decorator,
to_device,
filter_state_dict,
)
from src.utils.permutation.permutation import SymmetricPermutation
logger = logging.getLogger(__name__)
class TrainRunner(object):
def __init__(
self,
configs: ConfigDict,
ckpt_dir: str | Path,
error_dir: str | Path,
eval_dump_dir: str | Path,
device: torch.device,
train_dl: DataLoader,
test_dls: dict[str, DataLoader],
model: ODesign,
optimizer: torch.optim.Optimizer,
lr_scheduler: torch.optim.lr_scheduler.LRScheduler,
loss: ODesignLoss,
symmetric_permutation: SymmetricPermutation,
train_metric_wrapper: SimpleMetricAggregator,
) -> None:
self.configs = configs
self.ckpt_dir = ckpt_dir
self.error_dir = error_dir
self.eval_dump_dir = eval_dump_dir
self.device = device
self.train_dl = train_dl
self.test_dls = test_dls
self.model = model
self.optimizer = optimizer
self.lr_scheduler = lr_scheduler
self.loss = loss
self.symmetric_permutation = symmetric_permutation
self.train_metric_wrapper = train_metric_wrapper
# Step means effective step considering accumulation
self.step = 0
# Global_step equals to self.step * self.iters_to_accumulate
self.global_step = 0
self.start_step = 0
# Add for grad accumulation, it can increase real batch size
self.iters_to_accumulate = self.configs.iters_to_accumulate
self.load_checkpoint()
def load_checkpoint(self):
def _load_checkpoint(
checkpoint_path: str,
load_params_only: bool,
skip_load_optimizer: bool = False,
skip_load_step: bool = False,
skip_load_scheduler: bool = False,
load_step_for_scheduler: bool = True,
):
if not os.path.exists(checkpoint_path):
raise Exception(f"Given checkpoint path not exist [{checkpoint_path}]")
self.print(
f"Loading from {checkpoint_path}, strict: {self.configs.load_strict}"
)
checkpoint = torch.load(checkpoint_path, self.device)
sample_key = [k for k in checkpoint["model"].keys()][0]
self.print(f"Sampled key: {sample_key}")
if sample_key.startswith("module.") and not (DIST_WRAPPER.world_size > 1):
# DDP checkpoint has module. prefix
checkpoint["model"] = {
k[len("module.") :]: v for k, v in checkpoint["model"].items()
}
# Handle shape mismatches by filtering out parameters with different shapes
filtered_state_dict = filter_state_dict(
model_state_dict=self.model.state_dict(),
ckpt_state_dict=checkpoint["model"],
)
self.model.load_state_dict(
state_dict=filtered_state_dict,
strict=self.configs.load_strict,
)
if not load_params_only:
if not skip_load_optimizer:
self.print(f"Loading optimizer state")
self.optimizer.load_state_dict(checkpoint["optimizer"])
if not skip_load_step:
self.print(f"Loading checkpoint step")
self.step = checkpoint["step"] + 1
self.start_step = self.step
self.global_step = self.step * self.iters_to_accumulate
if not skip_load_scheduler:
self.print(f"Loading scheduler state")
self.lr_scheduler.load_state_dict(checkpoint["scheduler"])
elif load_step_for_scheduler:
assert (
not skip_load_step
), "if load_step_for_scheduler is True, you must load step first"
# reinitialize LR scheduler using the updated optimizer and step
self.lr_scheduler = get_lr_scheduler(
self.configs.lr_scheduler,
self.optimizer,
last_epoch=self.step - 1,
)
self.print(f"Finish loading checkpoint, current step: {self.step}")
# Load model
if self.configs.load_checkpoint_path:
_load_checkpoint(
self.configs.load_checkpoint_path,
self.configs.load_params_only,
skip_load_optimizer=self.configs.skip_load_optimizer,
skip_load_scheduler=self.configs.skip_load_scheduler,
skip_load_step=self.configs.skip_load_step,
load_step_for_scheduler=self.configs.load_step_for_scheduler,
)
def save_checkpoint(self):
if DIST_WRAPPER.rank == 0:
path = f"{self.ckpt_dir}/{self.step}.pt"
checkpoint = {
"model": self.model.state_dict(),
"optimizer": self.optimizer.state_dict(),
"scheduler": (
self.lr_scheduler.state_dict()
if self.lr_scheduler is not None
else None
),
"step": self.step,
}
torch.save(checkpoint, path)
self.print(f"Saved checkpoint to {path}")
def print(self, msg: str):
if DIST_WRAPPER.rank == 0:
logger.info(msg)
def model_forward(
self,
batch: dict,
mode: str = "train",
) -> tuple[ODesignOutput, GroundTruth, LossInput]:
assert mode in ["train", "eval"]
pred_output, ground_truth, loss_input = self.model(
feature_data=batch["feature_data"],
label_data=batch["label_data"],
label_full_data=batch["label_full_data"],
mode=mode,
current_step=self.step if mode == "train" else None,
symmetric_permutation=self.symmetric_permutation,
)
return pred_output, ground_truth, loss_input
def get_loss(
self,
loss_input: LossInput,
pred_output: ODesignOutput,
ground_truth: GroundTruth,
mode: str = "train",
) -> tuple[torch.Tensor, dict]:
assert mode in ["train", "eval"]
loss, loss_dict = autocasting_disable_decorator(self.configs.model.skip_amp.loss)(
self.loss
)(
loss_input=loss_input,
pred_output=pred_output,
ground_truth=ground_truth,
mode=mode,
)
return loss, loss_dict
@torch.no_grad()
def evaluate(self):
# Init Metric Aggregator
simple_metric_wrapper = SimpleMetricAggregator(["avg"])
eval_precision = {
"fp32": torch.float32,
"bf16": torch.bfloat16,
"fp16": torch.float16,
}[self.configs.model.dtype]
enable_amp = (
torch.autocast(device_type="cuda", dtype=eval_precision)
if torch.cuda.is_available()
else nullcontext()
)
self.model.eval()
for test_name, test_dl in self.test_dls.items():
self.print(f"Testing on {test_name}")
evaluated_pids = []
total_batch_num = len(test_dl)
for index, batch in enumerate(tqdm(test_dl)):
batch = to_device(batch, self.device)
pid = batch["basic"]["pdb_id"]
if index + 1 == total_batch_num and DIST_WRAPPER.world_size > 1:
# Gather all pids across ranks for avoiding duplicated evaluations when drop_last = False
all_data_ids = DIST_WRAPPER.all_gather_object(evaluated_pids)
dedup_ids = set(sum(all_data_ids, []))
if pid in dedup_ids:
print(
f"Rank {DIST_WRAPPER.rank}: Drop data_id {pid} as it is already evaluated."
)
break
evaluated_pids.append(pid)
simple_metrics = {}
with enable_amp:
# Model forward
pred_output, ground_truth, loss_input = self.model_forward(batch, mode="eval")
# Loss forward
_, loss_dict = self.get_loss(loss_input, pred_output, ground_truth, mode="eval")
simple_metrics.update(loss_dict)
if self.configs.eval_dump:
dumper = DataDumper(base_dir=self.eval_dump_dir)
dumper.dump(
dataset_name="",
pdb_id=pid,
seed=self.configs.seed,
pred_dict=pred_output.to_dict(),
atom_array=batch["atom_array"],
entity_poly_type=batch["basic"]["entity_poly_type"],
)
# Metrics
for key, value in simple_metrics.items():
simple_metric_wrapper.add(
key, value, namespace=test_name
)
del batch, simple_metrics
if index % 5 == 0:
# Release some memory periodically
torch.cuda.empty_cache()
metrics = simple_metric_wrapper.calc()
self.print(f"Step {self.step}, eval {test_name}: {metrics}")
if self.configs.use_wandb and DIST_WRAPPER.rank == 0:
wandb.log(metrics, step=self.step)
def update(self):
# Clip the gradient
if self.configs.grad_clip_norm != 0.0:
torch.nn.utils.clip_grad_norm_(
self.model.parameters(), self.configs.grad_clip_norm
)
def train_step(self, batch: dict):
self.model.train()
# FP16 training has not been verified yet
train_precision = {
"fp32": torch.float32,
"bf16": torch.bfloat16,
"fp16": torch.float16,
}[self.configs.model.dtype]
enable_amp = (
torch.autocast(
device_type="cuda", dtype=train_precision, cache_enabled=False
)
if torch.cuda.is_available()
else nullcontext()
)
scaler = torch.GradScaler(
device="cuda" if torch.cuda.is_available() else "cpu",
enabled=(self.configs.model.dtype == "float16"),
)
with enable_amp:
pred_output, ground_truth, loss_input = self.model_forward(batch, mode="train")
loss, loss_dict = self.get_loss(loss_input, pred_output, ground_truth, mode="train")
if self.configs.model.dtype in ["bf16", "fp32"]:
if is_loss_nan_check(loss):
self.print(f"Skip iteration with NaN loss: {self.step} steps")
loss = torch.tensor(0.0, device=loss.device, requires_grad=True)
scaler.scale(loss / self.iters_to_accumulate).backward()
# For simplicity, the global training step is used
if (self.global_step + 1) % self.iters_to_accumulate == 0:
self.print(
f"self.step {self.step}, self.iters_to_accumulate: {self.iters_to_accumulate}"
)
# Unscales the gradients of optimizer's assigned parameters in-place
scaler.unscale_(self.optimizer)
# Do grad clip only
self.update()
scaler.step(self.optimizer)
scaler.update()
self.optimizer.zero_grad(set_to_none=True)
self.lr_scheduler.step()
for key, value in loss_dict.items():
if "loss" not in key:
continue
self.train_metric_wrapper.add(key, value, namespace="train")
torch.cuda.empty_cache()
def progress_bar(self, desc: str = ""):
if DIST_WRAPPER.rank != 0:
return
if self.global_step % (
self.configs.eval_interval * self.iters_to_accumulate
) == 0 or (not hasattr(self, "_ipbar")):
# Start a new progress bar
self._pbar = tqdm(
range(
self.global_step
% (self.iters_to_accumulate * self.configs.eval_interval),
self.iters_to_accumulate * self.configs.eval_interval,
)
)
self._ipbar = iter(self._pbar)
step = next(self._ipbar)
self._pbar.set_description(
f"[step {self.step}: {step}/{self.iters_to_accumulate * self.configs.eval_interval}] {desc}"
)
return
def run(self):
"""
Main entry for the TrainRunner.
This function handles the training process, evaluation, logging, and checkpoint saving.
"""
if self.configs.eval_only or self.configs.eval_first or self.configs.eval_dump:
self.evaluate()
if self.configs.eval_only or self.configs.eval_dump:
return
while True:
for batch in self.train_dl:
is_update_step = (self.global_step + 1) % self.iters_to_accumulate == 0
is_last_step = (self.step + 1) == self.configs.max_steps
step_need_log = (self.step + 1) % self.configs.log_interval == 0
step_need_eval = (
self.configs.eval_interval > 0
and (self.step + 1) % self.configs.eval_interval == 0
)
step_need_save = (
self.configs.checkpoint_interval > 0
and (self.step + 1) % self.configs.checkpoint_interval == 0
)
is_last_step &= is_update_step
step_need_log &= is_update_step
step_need_eval &= is_update_step
step_need_save &= is_update_step
batch = to_device(batch, self.device)
self.progress_bar()
self.train_step(batch)
if step_need_log or is_last_step:
metrics = self.train_metric_wrapper.calc()
self.print(f"Step {self.step} train: {metrics}")
last_lr = self.lr_scheduler.get_last_lr()
if DIST_WRAPPER.rank == 0:
if self.configs.use_wandb:
lr_dict = {"train/lr": last_lr[0]}
for group_i, group_lr in enumerate(last_lr):
lr_dict[f"train/group{group_i}_lr"] = group_lr
wandb.log(lr_dict, step=self.step)
self.print(f"Step {self.step}, lr: {last_lr}")
if self.configs.use_wandb and DIST_WRAPPER.rank == 0:
wandb.log(metrics, step=self.step)
if step_need_save or is_last_step:
self.save_checkpoint()
if step_need_eval or is_last_step:
self.evaluate()
self.global_step += 1
if self.global_step % self.iters_to_accumulate == 0:
self.step += 1
if self.step >= self.configs.max_steps:
self.print(f"Finish training after {self.step} steps")
break
if self.step >= self.configs.max_steps:
break