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train.py
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"""Main training entry point for pre-training and downstream fine-tuning.
"""
import json
import os
import random
import time
from functools import wraps
from typing import Callable, List, Sequence
import fsspec
import hydra
import pytorch_lightning as pl
import torch
import wandb
from omegaconf import OmegaConf
from pytorch_lightning.loggers import WandbLogger
from pytorch_lightning.utilities import rank_zero_only, rank_zero_warn
import src.models.nn.utils as U
import src.utils as utils
import src.utils.train
from src.dataloaders import SequenceDataset # TODO make registry
from src.tasks import decoders, encoders, tasks
from src.utils import registry
from src.utils.optim_groups import add_optimizer_hooks
log = src.utils.train.get_logger(__name__)
# Turn on TensorFloat32 (speeds up large model training substantially)
import torch.backends
torch.backends.cuda.matmul.allow_tf32 = True
torch.backends.cudnn.allow_tf32 = True
OmegaConf.register_new_resolver('eval', eval)
OmegaConf.register_new_resolver('div_up', lambda x, y: (x + y - 1) // y)
OmegaConf.register_new_resolver('min', lambda x, y: min([x, y]))
# Lots of annoying hacks to get WandbLogger to continuously retry on failure
class DummyExperiment:
"""Dummy experiment."""
def nop(self, *args, **kw):
pass
def __getattr__(self, _):
return self.nop
def __getitem__(self, idx) -> "DummyExperiment":
# enables self.logger.experiment[0].add_image(...)
return self
def __setitem__(self, *args, **kwargs) -> None:
pass
def rank_zero_experiment(fn: Callable) -> Callable:
"""Returns the real experiment on rank 0 and otherwise the DummyExperiment."""
@wraps(fn)
def experiment(self):
@rank_zero_only
def get_experiment():
return fn(self)
return get_experiment() or DummyExperiment()
return experiment
class CustomWandbLogger(WandbLogger):
def __init__(self, *args, **kwargs):
"""Modified logger that insists on a wandb.init() call and catches wandb's error if thrown."""
super().__init__(*args, **kwargs)
@property
@rank_zero_experiment
def experiment(self):
r"""
Actual wandb object. To use wandb features in your
:class:`~pytorch_lightning.core.lightning.LightningModule` do the following.
Example::
code-block:: python
self.logger.experiment.some_wandb_function()
"""
if self._experiment is None:
if self._offline:
os.environ["WANDB_MODE"] = "dryrun"
attach_id = getattr(self, "_attach_id", None)
if wandb.run is not None:
# wandb process already created in this instance
rank_zero_warn(
"There is a wandb run already in progress and newly created instances of `WandbLogger` will reuse"
" this run. If this is not desired, call `wandb.finish()` before instantiating `WandbLogger`."
)
self._experiment = wandb.run
elif attach_id is not None and hasattr(wandb, "_attach"):
# attach to wandb process referenced
self._experiment = wandb._attach(attach_id)
else:
# create new wandb process
while True:
try:
self._experiment = wandb.init(**self._wandb_init)
break
except Exception as e:
log.error("wandb Exception:\n", e)
t = random.randint(30, 60)
log.warning(f"Sleeping for {t} seconds")
time.sleep(t)
# define default x-axis
if getattr(self._experiment, "define_metric", None):
self._experiment.define_metric("trainer/global_step")
self._experiment.define_metric("*", step_metric="trainer/global_step", step_sync=True)
return self._experiment
class SequenceLightningModule(pl.LightningModule):
def __init__(self, config):
# Disable profiling executor. This reduces memory and increases speed.
try:
torch._C._jit_set_profiling_executor(False)
torch._C._jit_set_profiling_mode(False)
except AttributeError:
pass
super().__init__()
# Passing in config expands it one level: access by self.hparams.train instead of self.hparams.config.train
self.save_hyperparameters(config, logger=False)
# Dataset arguments
self.dataset = SequenceDataset.registry[self.hparams.dataset._name_](
**self.hparams.dataset
)
# Check hparams
self._check_config()
# PL has some bugs, so add hooks and make sure they're only called once
self._has_setup = False
# To be set in `setup`
self.encoder, self.decoder, self.model = None, None, None
self.task, self.loss, self.loss_val = None, None, None
self.metrics, self.train_torchmetrics, self.val_torchmetrics, self.test_torchmetrics = None, None, None, None
self.setup()
self._state = None
self.val_loader_names, self.test_loader_names = None, None
def setup(self, stage=None):
if not self.hparams.train.disable_dataset:
self.dataset.setup()
# We need to set up the model in setup() because for some reason when training with DDP, one GPU uses much more
# memory than the others.
# In order to not overwrite the model multiple times during different stages, we need this hack
# TODO PL 1.5 seems to have an option to skip hooks to avoid this
# https://github.com/PyTorchLightning/pytorch-lightning/issues/5410#issuecomment-762257024
if self._has_setup:
return
else:
self._has_setup = True
# Convenience feature: if model specifies encoder, combine it with main encoder
encoder_cfg = utils.to_list(self.hparams.encoder) + utils.to_list(
self.hparams.model.pop("encoder", None)
)
decoder_cfg = utils.to_list(
self.hparams.model.pop("decoder", None)
) + utils.to_list(self.hparams.decoder)
# Instantiate model
config_path = self.hparams.model.pop("config_path", None)
if config_path is not None:
with open(config_path) as f:
model_config_from_file = json.load(f)
self.hparams.model.update(model_config_from_file)
# Check if dropout_layer_norm is compiled
try:
from flash_attn.ops.layer_norm import dropout_add_layer_norm
except ImportError:
if self.hparams.model.get("fused_dropout_add_ln", None) is not None:
self.hparams.model.update({"fused_dropout_add_ln": False})
# TODO: Hacky way to get complement_map for Caduceus models; need to find a more elegant implementation
if "caduceus" in self.hparams.model.get("_name_"):
OmegaConf.update(
self.hparams.model.config, "complement_map", self.dataset.tokenizer.complement_map, force_add=True
)
# Instantiate the config class if using hydra's _target_ paradigm for the config
if self.hparams.model.get("config", None) is not None and self.hparams.model.config.get("_target_", None) is not None:
model_hparams = OmegaConf.to_container(self.hparams.model, resolve=True)
model_hparams["config"] = hydra.utils.instantiate(model_hparams["config"])
self.model = utils.instantiate(registry.model, model_hparams)
else:
self.model = utils.instantiate(registry.model, self.hparams.model)
if (name := self.hparams.train.post_init_hook['_name_']) is not None:
kwargs = self.hparams.train.post_init_hook.copy()
del kwargs['_name_']
for module in self.modules():
if hasattr(module, name):
getattr(module, name)(**kwargs)
# if self.hparams.train.get("compile_model", False):
# self.model = torch.compile(self.model, dynamic=False)
# Instantiate the task
self.task = utils.instantiate(
tasks.registry, self.hparams.task, dataset=self.dataset, model=self.model
)
# Create encoders and decoders
encoder = encoders.instantiate(
encoder_cfg, dataset=self.dataset, model=self.model
)
decoder = decoders.instantiate(
decoder_cfg, model=self.model, dataset=self.dataset
)
# Extract the modules, so they show up in the top level parameter count
self.encoder = U.PassthroughSequential(self.task.encoder, encoder)
self.decoder = U.PassthroughSequential(decoder, self.task.decoder)
self.loss = self.task.loss
self.loss_val = self.task.loss
if hasattr(self.task, 'loss_val'):
self.loss_val = self.task.loss_val
self.metrics = self.task.metrics
self.train_torchmetrics = self.task.train_torchmetrics
self.val_torchmetrics = self.task.val_torchmetrics
self.test_torchmetrics = self.task.test_torchmetrics
def load_state_dict(self, state_dict, strict=False):
if self.hparams.train.pretrained_model_state_hook['_name_'] is not None:
model_state_hook = utils.instantiate(
registry.model_state_hook,
self.hparams.train.pretrained_model_state_hook.copy(),
partial=True,
)
state_dict = model_state_hook(self.model, state_dict)
log.info("Custom load_state_dict function is running.")
# strict==True will require all modules to match
# strict==False can allow encoder/decoder to be loaded from scratch too
return super().load_state_dict(state_dict, strict=strict)
def _check_config(self):
assert self.hparams.train.state.mode in [None, "none", "null", "reset", "bptt", "tbptt"]
assert (
(n := self.hparams.train.state.n_context) is None
or isinstance(n, int)
and n >= 0
)
assert (
(n := self.hparams.train.state.n_context_eval) is None
or isinstance(n, int)
and n >= 0
)
def _initialize_state(self):
"""Called at model setup and start of epoch to completely reset state"""
self._state = None
self._memory_chunks = []
def _reset_state(self, batch, device=None):
"""Called to construct default_state when necessary, e.g. during BPTT"""
device = device or batch[0].device
self._state = self.model.default_state(*batch[0].shape[:1], device=device)
def _detach_state(self, state):
if isinstance(state, torch.Tensor):
return state.detach()
elif isinstance(state, tuple):
return tuple(self._detach_state(s) for s in state)
elif isinstance(state, list):
return [self._detach_state(s) for s in state]
elif isinstance(state, dict):
return {k: self._detach_state(v) for k, v in state.items()}
elif state is None:
return None
else:
raise NotImplementedError
def _process_state(self, batch, batch_idx, training=True):
"""Handle logic for state context."""
# Number of context steps
key = "n_context" if training else "n_context_eval"
n_context = self.hparams.train.state.get(key)
# Don't need to do anything if 0 context steps. Make sure there is no state
if n_context == 0 and self.hparams.train.state.mode not in ['tbptt']:
self._initialize_state()
return
# Reset state if needed
if self.hparams.train.state.mode == "reset":
if batch_idx % (n_context + 1) == 0:
self._reset_state(batch)
# Pass through memory chunks
elif self.hparams.train.state.mode == "bptt":
self._reset_state(batch)
with torch.no_grad(): # should be unnecessary because individual modules should handle this
for _batch in self._memory_chunks:
self.forward(_batch)
# Prepare for next step
self._memory_chunks.append(batch)
self._memory_chunks = self._memory_chunks[-n_context:]
elif self.hparams.train.state.mode == 'tbptt':
_, _, z = batch
reset = z["reset"]
if reset:
self._reset_state(batch)
else:
self._state = self._detach_state(self._state)
def forward(self, batch):
return self.task.forward(batch, self.encoder, self.model, self.decoder, self._state)
def step(self, x_t):
x_t, *_ = self.encoder(x_t) # Potential edge case for encoders that expect (B, L, H)?
x_t, state = self.model.step(x_t, state=self._state)
self._state = state
x_t, *_ = self.decoder.step(x_t, state=state)
return x_t
def _shared_step(self, batch, batch_idx, prefix="train"):
"""Shared step logic between training, validation, and test"""
self._process_state(batch, batch_idx, training=(prefix == "train"))
x, y, w = self.forward(batch)
# Loss
if prefix == 'train':
loss = self.loss(x, y, **w)
else:
loss = self.loss_val(x, y, **w)
# Metrics
metrics = self.metrics(x, y, **w)
metrics["loss"] = loss
metrics = {f"{prefix}/{k}": v for k, v in metrics.items()}
# Calculate torchmetrics
torchmetrics = getattr(self, f'{prefix}_torchmetrics')
torchmetrics(x, y, loss=loss)
log_on_step = 'eval' in self.hparams and self.hparams.eval.get('log_on_step', False) and prefix == 'train'
self.log_dict(
metrics,
on_step=log_on_step,
on_epoch=True,
prog_bar=True,
add_dataloader_idx=False,
sync_dist=True,
)
# log the whole dict, otherwise lightning takes the mean to reduce it
# https://pytorch-lightning.readthedocs.io/en/stable/visualize/logging_advanced.html#enable-metrics-for-distributed-training
self.log_dict(
torchmetrics,
on_step=log_on_step,
on_epoch=True,
prog_bar=True,
add_dataloader_idx=False,
sync_dist=True,
)
return loss
def on_train_epoch_start(self):
# Reset training torchmetrics
self.task._reset_torchmetrics("train")
def training_epoch_end(self, outputs):
# Log training torchmetrics
super().training_epoch_end(outputs)
def on_validation_epoch_start(self):
# Reset all validation torchmetrics
for name in self.val_loader_names:
self.task._reset_torchmetrics(name)
def validation_epoch_end(self, outputs):
# Log all validation torchmetrics
super().validation_epoch_end(outputs)
def on_test_epoch_start(self):
# Reset all test torchmetrics
for name in self.test_loader_names:
self.task._reset_torchmetrics(name)
def test_epoch_end(self, outputs):
# Log all test torchmetrics
super().test_epoch_end(outputs)
def training_step(self, batch, batch_idx, dataloader_idx=0):
loss = self._shared_step(batch, batch_idx, prefix="train")
# Log the loss explicitly so that it shows up in WandB
# Note that this currently runs into a bug in the progress bar with ddp (as of 1.4.6)
# https://github.com/PyTorchLightning/pytorch-lightning/pull/9142
# We additionally log the epochs under 'trainer' to get a consistent prefix with 'global_step'
loss_epoch = {"trainer/loss": loss, "trainer/epoch": float(self.current_epoch)}
self.log_dict(
loss_epoch,
on_step=True,
on_epoch=False,
prog_bar=False,
add_dataloader_idx=False,
sync_dist=True,
)
# Log any extra info that the models want to expose (e.g. output norms)
metrics = {}
for module in list(self.modules())[1:]:
if hasattr(module, "metrics"):
metrics.update(module.metrics)
self.log_dict(
metrics,
on_step=True,
on_epoch=False,
prog_bar=False,
add_dataloader_idx=False,
sync_dist=True,
)
return loss
def validation_step(self, batch, batch_idx, dataloader_idx=0):
# There's a bit of an annoying edge case with the first (0-th) epoch; it has to be excluded due to the initial
# sanity check
ema = (
self.val_loader_names[dataloader_idx].endswith("/ema")
and self.optimizers().optimizer.stepped
)
if ema:
self.optimizers().swap_ema()
loss = self._shared_step(
batch, batch_idx, prefix=self.val_loader_names[dataloader_idx]
)
if ema:
self.optimizers().swap_ema()
return loss
def test_step(self, batch, batch_idx, dataloader_idx=0):
return self._shared_step(
batch, batch_idx, prefix=self.test_loader_names[dataloader_idx]
)
def configure_optimizers(self):
# Set zero weight decay for some params
if 'optimizer_param_grouping' in self.hparams.train:
add_optimizer_hooks(self.model, **self.hparams.train.optimizer_param_grouping)
# Normal parameters
all_params = list(self.parameters())
params = [p for p in all_params if not hasattr(p, "_optim")]
optimizer = utils.instantiate(registry.optimizer, self.hparams.optimizer, params)
del self.hparams.optimizer._name_
# Add parameters with special hyperparameters
hps = [getattr(p, "_optim") for p in all_params if hasattr(p, "_optim")]
hps = [
# dict(s) for s in set(frozenset(hp.items()) for hp in hps)
dict(s) for s in sorted(list(dict.fromkeys(frozenset(hp.items()) for hp in hps)))
# dict(s) for s in dict.fromkeys(frozenset(hp.items()) for hp in hps)
] # Unique dicts
print("Hyperparameter groups:", hps) # TODO: log.info throws error because hps is list of dicts
for hp in hps:
params = [p for p in all_params if getattr(p, "_optim", None) == hp]
optimizer.add_param_group(
{"params": params, **self.hparams.optimizer, **hp}
)
# Layer Decay
if self.hparams.train.layer_decay['_name_'] is not None:
get_num_layer = utils.instantiate(
registry.layer_decay,
self.hparams.train.layer_decay['_name_'],
partial=True,
)
# Go through all parameters and get num layer
layer_wise_groups = {}
num_max_layers = 0
for name, p in self.named_parameters():
# Get layer id for each parameter in the model
layer_id = get_num_layer(name)
# Add to layer wise group
if layer_id not in layer_wise_groups:
layer_wise_groups[layer_id] = {
'params': [],
'lr': None,
'weight_decay': self.hparams.optimizer.weight_decay
}
layer_wise_groups[layer_id]['params'].append(p)
if layer_id > num_max_layers:
num_max_layers = layer_id
# Update lr for each layer
for layer_id, group in layer_wise_groups.items():
group['lr'] = self.hparams.optimizer.lr * (
self.hparams.train.layer_decay.decay ** (num_max_layers - layer_id))
# Reset the torch optimizers param groups
optimizer.param_groups = []
for layer_id, group in layer_wise_groups.items():
optimizer.add_param_group(group)
# Print optimizer info for debugging
keys = set([k for hp in hps for k in hp.keys()]) # Special hparams
utils.train.log_optimizer(log, optimizer, keys)
# Configure scheduler
if "scheduler" not in self.hparams:
return optimizer
lr_scheduler = utils.instantiate(
registry.scheduler, self.hparams.scheduler, optimizer
)
scheduler = {
"scheduler": lr_scheduler,
"interval": self.hparams.train.interval, # 'epoch' or 'step'
"monitor": self.hparams.train.monitor,
"name": "trainer/lr", # default is e.g. 'lr-AdamW'
}
# See documentation for how to configure the return
# https://pytorch-lightning.readthedocs.io/en/latest/api/pytorch_lightning.core.lightning.html#pytorch_lightning.core.lightning.LightningModule.configure_optimizers
return [optimizer], [scheduler]
def train_dataloader(self):
return self.dataset.train_dataloader(**self.hparams.loader)
def _eval_dataloaders_names(self, loaders, prefix):
"""Process loaders into a list of names and loaders"""
if utils.is_dict(loaders):
return [
f"{prefix}/{k}" if k is not None else prefix for k in loaders.keys()
], list(loaders.values())
elif utils.is_list(loaders):
return [f"{prefix}/{i}" for i in range(len(loaders))], loaders
else:
return [prefix], [loaders]
def _eval_dataloaders(self):
# Return all val + test loaders
val_loaders = self.dataset.val_dataloader(**self.hparams.loader)
test_loaders = self.dataset.test_dataloader(**self.hparams.loader)
val_loader_names, val_loaders = self._eval_dataloaders_names(val_loaders, "val")
test_loader_names, test_loaders = self._eval_dataloaders_names(
test_loaders, "test"
)
# Duplicate datasets for ema
if self.hparams.train.ema > 0.0:
val_loader_names += [name + "/ema" for name in val_loader_names]
val_loaders = val_loaders + val_loaders
test_loader_names += [name + "/ema" for name in test_loader_names]
test_loaders = test_loaders + test_loaders
# adding option to only have val loader at eval (e.g., if test is duplicate)
eval_loader_names = []
eval_loaders = []
if not self.hparams.train.get("remove_val_loader_in_eval", False):
eval_loader_names += val_loader_names
eval_loaders += val_loaders
if not self.hparams.train.get("remove_test_loader_in_eval", False):
eval_loader_names += test_loader_names
eval_loaders += test_loaders
return eval_loader_names, eval_loaders
def val_dataloader(self):
val_loader_names, val_loaders = self._eval_dataloaders()
self.val_loader_names = val_loader_names
return val_loaders
def test_dataloader(self):
test_loader_names, test_loaders = self._eval_dataloaders()
self.test_loader_names = ["final/" + name for name in test_loader_names]
return test_loaders
# pytorch-lightning utils and entrypoint
def create_trainer(config, **kwargs):
callbacks: List[pl.Callback] = []
logger = None
# WandB Logging
if config.get("wandb") is not None:
# Pass in wandb.init(config=) argument to get the nice 'x.y.0.z' hparams logged
# Can pass in config_exclude_keys='wandb' to remove certain groups
import wandb
logger = CustomWandbLogger(
config=utils.to_dict(config, recursive=True),
settings=wandb.Settings(start_method="fork"),
**config.wandb,
)
# Lightning callbacks
if "callbacks" in config:
for _name_, callback in config.callbacks.items():
if config.get("wandb") is None and _name_ in ["learning_rate_monitor"]:
continue
log.info(f"Instantiating callback <{registry.callbacks[_name_]}>")
callback._name_ = _name_
callbacks.append(utils.instantiate(registry.callbacks, callback))
# Add ProgressiveResizing callback
if config.callbacks.get("progressive_resizing", None) is not None:
num_stages = len(config.callbacks.progressive_resizing.stage_params)
log.info(f"Progressive Resizing: {num_stages} stages")
for i, e in enumerate(config.callbacks.progressive_resizing.stage_params):
# Stage params are resolution and epochs, pretty print
log.info(f"\tStage {i}: {e['resolution']} @ {e['epochs']} epochs")
# Configure ddp automatically
n_devices = config.trainer.get('devices', 1)
if isinstance(n_devices, Sequence): # trainer.devices could be [1, 3] for example
n_devices = len(n_devices)
if n_devices > 1 and config.trainer.get('strategy', None) is None:
config.trainer.strategy = dict(
_target_='pytorch_lightning.strategies.DDPStrategy',
find_unused_parameters=False,
# https://pytorch-lightning.readthedocs.io/en/stable/advanced/advanced_gpu.html#ddp-optimizations
gradient_as_bucket_view=True,
)
# Init lightning trainer
log.info(f"Instantiating trainer <{config.trainer._target_}>")
# special processing for seqlen warmup scheduler (reload)
trainer = hydra.utils.instantiate(config.trainer, callbacks=callbacks, logger=logger)
return trainer
def fsspec_exists(filename):
fs, _ = fsspec.core.url_to_fs(filename)
return fs.exists(filename)
def train(config):
if config.train.seed is not None:
pl.seed_everything(config.train.seed, workers=True)
trainer = create_trainer(config)
model = SequenceLightningModule(config)
# Load pretrained_model if specified
if config.train.get("pretrained_model_path", None) is not None:
# PTL style. Note, method returns a new model object, and need to pass config.
model = SequenceLightningModule.load_from_checkpoint(
config.train.pretrained_model_path,
config=config,
strict=config.train.pretrained_model_strict_load,
)
# Run initial validation epoch (useful for debugging, fine-tuning)
if config.train.validate_at_start:
log.info("Running validation before training")
trainer.validate(model)
log.info(f'{config.train.ckpt=} {fsspec_exists(config.train.ckpt)=}')
# if config.train.get("compile_model", False):
# model = torch.compile(model, mode="reduce-overhead")
if config.train.ckpt is not None and fsspec_exists(config.train.ckpt):
trainer.fit(model, ckpt_path=config.train.ckpt)
else:
trainer.fit(model)
if config.train.test:
if config.train.get("cross_validation", False): # First, load the best validation model
best_val_ckpt = os.path.join(
model.hparams.callbacks.model_checkpoint.dirpath,
f"{model.hparams.callbacks.model_checkpoint.filename}.ckpt",
)
# Update config so we do not load just the backbone
config.train.pretrained_model_state_hook.update({"_name_": None})
# Remove validation loader
config.train.update({"remove_val_loader_in_eval": True})
config.train.update({"remove_test_loader_in_eval": False})
ckpt = torch.load(best_val_ckpt)
log.info(f"Loaded best validation checkpoint from epoch {ckpt['epoch']}")
trainer.validate(model, ckpt_path=best_val_ckpt)
else:
trainer.validate(model)
@hydra.main(config_path="configs", config_name="config.yaml")
def main(config: OmegaConf):
# Process config:
# - register evaluation resolver
# - filter out keys used only for interpolation
# - optional hooks, including disabling python warnings or debug friendly configuration
config = utils.train.process_config(config)
# if config.train.get("compile_model", False):
# # See: https://github.com/arogozhnikov/einops/wiki/Using-torch.compile-with-einops
# from einops._torch_specific import allow_ops_in_compiled_graph # requires einops>=0.6.1
# allow_ops_in_compiled_graph()
# Pretty print config using Rich library
utils.train.print_config(config, resolve=True)
train(config)
if __name__ == "__main__":
main()