protenix / scripts /runner /train.py
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import datetime
import logging
import os
import time
from contextlib import nullcontext
from typing import Any, Mapping
import torch
import torch.distributed as dist
from torch.nn.parallel import DistributedDataParallel as DDP
from tqdm import tqdm
from configs.configs_base import configs as configs_base
from configs.configs_data import data_configs
from models.protenix.config import parse_configs, parse_sys_args
from models.protenix.config.config import save_config
from onescience.datapipes.protenix.dataloader import get_dataloaders
from onescience.metrics.protenix.lddt_metrics import LDDTMetrics
from models.protenix.loss import ProtenixLoss
from models.protenix.protenix import Protenix
from onescience.utils.protenix.distributed import DIST_WRAPPER
from onescience.utils.protenix.lr_scheduler import get_lr_scheduler
from onescience.utils.protenix.metrics import SimpleMetricAggregator
from onescience.utils.protenix.permutation.permutation import SymmetricPermutation
from onescience.utils.protenix.seed import seed_everything
from onescience.utils.protenix.torch_utils import autocasting_disable_decorator, to_device
from onescience.utils.protenix.training import get_optimizer, is_loss_nan_check
from scripts.runner.ema import EMAWrapper
try:
import wandb
except ImportError:
wandb = None
# Disable WANDB's console output capture to reduce unnecessary logging
os.environ["WANDB_CONSOLE"] = "off"
class AF3Trainer(object):
def __init__(self, configs):
self.configs = configs
self.smoke_test = os.environ.get("PROTENIX_SMOKE_TEST", "").lower() in {
"1",
"true",
"yes",
}
self.init_env()
self.init_basics()
self.init_log()
self.init_model()
self.init_loss()
if self.smoke_test:
self.try_load_checkpoint()
self.print("Smoke test completed: skipped external dataset initialization.")
return
self.init_data()
self.try_load_checkpoint()
def init_basics(self):
# 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.run_name = self.configs.run_name + "_" + time.strftime("%Y%m%d_%H%M%S")
run_names = DIST_WRAPPER.all_gather_object(
self.run_name if DIST_WRAPPER.rank == 0 else None
)
self.run_name = [name for name in run_names if name is not None][0]
self.run_dir = f"{self.configs.base_dir}/{self.run_name}"
self.checkpoint_dir = f"{self.run_dir}/checkpoints"
self.prediction_dir = f"{self.run_dir}/predictions"
self.structure_dir = f"{self.run_dir}/structures"
self.dump_dir = f"{self.run_dir}/dumps"
self.error_dir = f"{self.run_dir}/errors"
if DIST_WRAPPER.rank == 0:
os.makedirs(self.run_dir)
os.makedirs(self.checkpoint_dir)
os.makedirs(self.prediction_dir)
os.makedirs(self.structure_dir)
os.makedirs(self.dump_dir)
os.makedirs(self.error_dir)
save_config(
self.configs,
os.path.join(self.configs.base_dir, self.run_name, "config.yaml"),
)
self.print(
f"Using run name: {self.run_name}, run dir: {self.run_dir}, checkpoint_dir: "
+ f"{self.checkpoint_dir}, prediction_dir: {self.prediction_dir}, structure_dir: "
+ f"{self.structure_dir}, error_dir: {self.error_dir}"
)
def init_log(self):
if self.configs.use_wandb and DIST_WRAPPER.rank == 0:
if wandb is None:
raise ImportError(
"wandb is required only when use_wandb=true. "
"Install wandb or run with --use_wandb false."
)
wandb.init(
project=self.configs.project,
name=self.run_name,
config=vars(self.configs),
id=self.configs.wandb_id or None,
)
self.train_metric_wrapper = SimpleMetricAggregator(["avg"])
def init_env(self):
"""Init pytorch/cuda envs."""
logging.info(
f"Distributed environment: world size: {DIST_WRAPPER.world_size}, "
+ f"global rank: {DIST_WRAPPER.rank}, local rank: {DIST_WRAPPER.local_rank}"
)
self.use_cuda = torch.cuda.device_count() > 0
if self.use_cuda:
self.device = torch.device("cuda:{}".format(DIST_WRAPPER.local_rank))
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
all_gpu_ids = ",".join(str(x) for x in range(torch.cuda.device_count()))
devices = os.getenv("CUDA_VISIBLE_DEVICES", all_gpu_ids)
logging.info(
f"LOCAL_RANK: {DIST_WRAPPER.local_rank} - CUDA_VISIBLE_DEVICES: [{devices}]"
)
torch.cuda.set_device(self.device)
else:
self.device = torch.device("cpu")
if DIST_WRAPPER.world_size > 1:
timeout_seconds = int(os.environ.get("NCCL_TIMEOUT_SECOND", 600))
dist.init_process_group(
backend="nccl", timeout=datetime.timedelta(seconds=timeout_seconds)
)
if not self.configs.deterministic_seed:
# use rank-specific seed
rank_seed = hash((self.configs.seed, DIST_WRAPPER.rank, "init_seed"))
rank_seed = rank_seed % (2**32)
else:
rank_seed = self.configs.seed
# All ddp process got the same seed
seed_everything(
seed=rank_seed,
deterministic=self.configs.deterministic,
)
if self.configs.use_deepspeed_evo_attention:
env = os.getenv("CUTLASS_PATH", None)
print(f"env: {env}")
assert (
env is not None
), "if use ds4sci, set env as https://www.deepspeed.ai/tutorials/ds4sci_evoformerattention/"
logging.info("Finished init ENV.")
def init_loss(self):
self.loss = ProtenixLoss(self.configs)
self.symmetric_permutation = SymmetricPermutation(
self.configs, error_dir=self.error_dir
)
self.lddt_metrics = LDDTMetrics(self.configs)
def init_model(self):
self.raw_model = Protenix(self.configs).to(self.device)
self.use_ddp = False
if DIST_WRAPPER.world_size > 1:
self.print(f"Using DDP")
self.use_ddp = True
# Fix DDP/checkpoint https://discuss.pytorch.org/t/ddp-and-gradient-checkpointing/132244
self.model = DDP(
self.raw_model,
find_unused_parameters=self.configs.find_unused_parameters,
device_ids=[DIST_WRAPPER.local_rank],
output_device=DIST_WRAPPER.local_rank,
static_graph=True,
)
else:
self.model = self.raw_model
if self.configs.get("ema_decay", -1) > 0:
assert self.configs.ema_decay < 1
self.ema_wrapper = EMAWrapper(
self.model,
self.configs.ema_decay,
self.configs.ema_mutable_param_keywords,
)
self.ema_wrapper.register()
torch.cuda.empty_cache()
self.optimizer = get_optimizer(self.configs, self.model)
self.init_scheduler()
def init_scheduler(self, **kwargs):
self.lr_scheduler = get_lr_scheduler(self.configs, self.optimizer, **kwargs)
def init_data(self):
self.train_dl, self.test_dls = get_dataloaders(
self.configs,
DIST_WRAPPER.world_size,
seed=self.configs.seed,
error_dir=self.error_dir,
)
def save_checkpoint(self, ema_suffix=""):
if DIST_WRAPPER.rank == 0:
path = f"{self.checkpoint_dir}/{self.step}{ema_suffix}.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 try_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,
):
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)
state_dict = checkpoint["model"] if "model" in checkpoint else checkpoint
state_dict = self._strip_module_prefix(state_dict)
state_dict = self._select_checkpoint_key_format(state_dict)
self.raw_model.load_state_dict(
state_dict=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"])
else:
# reinitialize LR scheduler using the updated optimizer and step
self.init_scheduler(last_epoch=self.step - 1)
self.print(f"Finish loading checkpoint, current step: {self.step}")
# Load EMA model parameters
if self.configs.load_ema_checkpoint_path:
_load_checkpoint(
self.configs.load_ema_checkpoint_path,
load_params_only=True,
)
self.ema_wrapper.register()
# 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,
)
@staticmethod
def _strip_module_prefix(state_dict: Mapping[str, Any]) -> dict:
"""Remove DistributedDataParallel's module. prefix when present."""
if state_dict and all(k.startswith("module.") for k in state_dict.keys()):
return {k[len("module.") :]: v for k, v in state_dict.items()}
return dict(state_dict)
def _select_checkpoint_key_format(self, state_dict: Mapping[str, Any]) -> dict:
"""Pick the checkpoint key format that best matches this model."""
model_keys = set(self.raw_model.state_dict().keys())
candidates = {
"original": dict(state_dict),
"distogram_linear_wrapped": self._distogram_linear_wrapped_key_format(state_dict),
"legacy_wrapped": self._legacy_wrapped_key_format(state_dict),
}
def score(candidate: Mapping[str, Any]) -> tuple[int, int]:
candidate_keys = set(candidate.keys())
matched = len(model_keys & candidate_keys)
missing_or_unexpected = len(model_keys - candidate_keys) + len(candidate_keys - model_keys)
return matched, -missing_or_unexpected
best_name, best_state_dict = max(candidates.items(), key=lambda item: score(item[1]))
best_keys = set(best_state_dict.keys())
self.print(
"Selected checkpoint key format: "
f"{best_name} (matched={len(model_keys & best_keys)}, "
f"missing={len(model_keys - best_keys)}, unexpected={len(best_keys - model_keys)})"
)
return best_state_dict
@staticmethod
def _distogram_linear_wrapped_key_format(state_dict: Mapping[str, Any]) -> dict:
"""Compatibility mapping for checkpoints with an unwrapped distogram linear."""
remapped = {}
for k, v in state_dict.items():
new_key = k
if new_key.startswith("distogram_head.linear.") and not new_key.startswith("distogram_head.linear.Linear."):
new_key = new_key.replace("distogram_head.linear.", "distogram_head.linear.Linear.", 1)
remapped[new_key] = v
return remapped
@staticmethod
def _legacy_wrapped_key_format(state_dict: Mapping[str, Any]) -> dict:
"""Compatibility mapping for older wrappers used in some extracted packages."""
remapped = {}
for k, v in state_dict.items():
new_key = k
if new_key.startswith("input_embedder.") and not new_key.startswith("input_embedder.embedder."):
new_key = new_key.replace("input_embedder.", "input_embedder.embedder.", 1)
elif new_key.startswith("template_embedder.") and not new_key.startswith("template_embedder.embedder."):
new_key = new_key.replace("template_embedder.", "template_embedder.embedder.", 1)
elif new_key.startswith("relative_position_encoding.") and not new_key.startswith("relative_position_encoding.encoder."):
new_key = new_key.replace("relative_position_encoding.", "relative_position_encoding.encoder.", 1)
elif new_key.startswith("msa_module.") and not new_key.startswith("msa_module.msa."):
new_key = new_key.replace("msa_module.", "msa_module.msa.", 1)
elif new_key.startswith("pairformer_stack.") and not new_key.startswith("pairformer_stack.Pairformer."):
new_key = new_key.replace("pairformer_stack.", "pairformer_stack.Pairformer.", 1)
elif new_key.startswith("diffusion_module.") and not new_key.startswith("diffusion_module.Diffusion."):
new_key = new_key.replace("diffusion_module.", "diffusion_module.Diffusion.", 1)
elif new_key.startswith("distogram_head.linear.") and not new_key.startswith("distogram_head.linear.Linear."):
new_key = new_key.replace("distogram_head.linear.", "distogram_head.linear.Linear.", 1)
for prefix in (
"linear_no_bias_sinit.",
"linear_no_bias_zinit1.",
"linear_no_bias_zinit2.",
"linear_no_bias_token_bond.",
"linear_no_bias_z_cycle.",
"linear_no_bias_s.",
):
if new_key.startswith(prefix) and not new_key.startswith(f"{prefix}Linear."):
new_key = new_key.replace(prefix, f"{prefix}Linear.", 1)
break
if new_key.startswith("msa_module.msa.blocks.") and ".pair_stack." in new_key and ".pair_stack.Pairformer." not in new_key:
new_key = new_key.replace(".pair_stack.", ".pair_stack.Pairformer.", 1)
remapped[new_key] = v
return remapped
def print(self, msg: str):
if DIST_WRAPPER.rank == 0:
logging.info(msg)
def model_forward(self, batch: dict, mode: str = "train") -> tuple[dict, dict]:
assert mode in ["train", "eval"]
batch["pred_dict"], batch["label_dict"], log_dict = self.model(
input_feature_dict=batch["input_feature_dict"],
label_dict=batch["label_dict"],
label_full_dict=batch["label_full_dict"],
mode=mode,
current_step=self.step if mode == "train" else None,
symmetric_permutation=self.symmetric_permutation,
)
return batch, log_dict
def get_loss(
self, batch: dict, mode: str = "train"
) -> tuple[torch.Tensor, dict, dict]:
assert mode in ["train", "eval"]
loss, loss_dict = autocasting_disable_decorator(self.configs.skip_amp.loss)(
self.loss
)(
feat_dict=batch["input_feature_dict"],
pred_dict=batch["pred_dict"],
label_dict=batch["label_dict"],
mode=mode,
)
return loss, loss_dict, batch
@torch.no_grad()
def get_metrics(self, batch: dict) -> dict:
lddt_dict = self.lddt_metrics.compute_lddt(
batch["pred_dict"], batch["label_dict"]
)
return lddt_dict
@torch.no_grad()
def aggregate_metrics(self, lddt_dict: dict, batch: dict) -> dict:
simple_metrics, _ = self.lddt_metrics.aggregate_lddt(
lddt_dict, batch["pred_dict"]["summary_confidence"]
)
return simple_metrics
@torch.no_grad()
def evaluate(self, mode: str = "eval"):
if not self.configs.eval_ema_only:
self._evaluate()
if hasattr(self, "ema_wrapper"):
self.ema_wrapper.apply_shadow()
self._evaluate(ema_suffix=f"ema{self.ema_wrapper.decay}_", mode=mode)
self.ema_wrapper.restore()
@torch.no_grad()
def _evaluate(self, ema_suffix: str = "", mode: str = "eval"):
# Init Metric Aggregator
simple_metric_wrapper = SimpleMetricAggregator(["avg"])
eval_precision = {
"fp32": torch.float32,
"bf16": torch.bfloat16,
"fp16": torch.float16,
}[self.configs.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
batch, _ = self.model_forward(batch, mode=mode)
# Loss forward
loss, loss_dict, batch = self.get_loss(batch, mode="eval")
# lDDT metrics
lddt_dict = self.get_metrics(batch)
lddt_metrics = self.aggregate_metrics(lddt_dict, batch)
simple_metrics.update(
{k: v for k, v in lddt_metrics.items() if "diff" not in k}
)
simple_metrics.update(loss_dict)
# Metrics
for key, value in simple_metrics.items():
simple_metric_wrapper.add(
f"{ema_suffix}{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.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.dtype == "float16"),
)
with enable_amp:
batch, _ = self.model_forward(batch, mode="train")
loss, loss_dict, _ = self.get_loss(batch, mode="train")
if self.configs.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 AF3Trainer.
This function handles the training process, evaluation, logging, and checkpoint saving.
"""
if self.configs.eval_only or self.configs.eval_first:
self.evaluate()
if self.configs.eval_only:
return
use_ema = hasattr(self, "ema_wrapper")
self.print(f"Using ema: {use_ema}")
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 use_ema and is_update_step:
self.ema_wrapper.update()
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()[0]
if DIST_WRAPPER.rank == 0:
if self.configs.use_wandb:
wandb.log(
{"train/lr": last_lr},
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 use_ema:
self.ema_wrapper.apply_shadow()
self.save_checkpoint(
ema_suffix=f"_ema_{self.ema_wrapper.decay}"
)
self.ema_wrapper.restore()
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
def main():
LOG_FORMAT = "%(asctime)s,%(msecs)-3d %(levelname)-8s [%(filename)s:%(lineno)s %(funcName)s] %(message)s"
logging.basicConfig(
format=LOG_FORMAT,
level=logging.INFO,
datefmt="%Y-%m-%d %H:%M:%S",
filemode="w",
)
configs_base["use_deepspeed_evo_attention"] = (
os.environ.get("USE_DEEPSPEED_EVO_ATTENTION", False) == "true"
)
configs = {**configs_base, **{"data": data_configs}}
configs = parse_configs(
configs,
parse_sys_args(),
)
print(configs.run_name)
print(configs)
trainer = AF3Trainer(configs)
if getattr(trainer, "smoke_test", False):
logging.info("Smoke test completed; skip train loop.")
return
trainer.run()
if __name__ == "__main__":
main()