learn_jax/t5_jax.py

# ---
# jupyter:
#   jupytext:
#     formats: ipynb,py:percent
#     text_representation:
#       extension: .py
#       format_name: percent
#       format_version: '1.3'
#       jupytext_version: 1.16.4
#   kernelspec:
#     display_name: jax
#     language: python
#     name: python3
# ---

# %% [markdown]
# # T5 implementation using jax


# %%
import jax
import jax.numpy as jnp
import optax
import numpy as np
from functools import partial
from typing import Callable, Optional
import math

# jax.config.update("jax_default_matmul_precision", "tensorfloat32")
jax.config.update("jax_default_matmul_precision", "bfloat16")
# jax.config.update("jax_enable_x64", False)
# enable cache
jax.config.update("jax_compilation_cache_dir", "/tmp/jax_cache")
jax.config.update("jax_persistent_cache_min_entry_size_bytes", -1)
jax.config.update("jax_persistent_cache_min_compile_time_secs", 0)


# from transformers import FlaxAutoModelForSeq2SeqLM, AutoConfig


import datasets
from datasets import Dataset, load_dataset
import evaluate
from tqdm import tqdm
from datasets import load_from_disk


import nltk  # Here to have a nice missing dependency error message early on

from flax import jax_utils, traverse_util
from flax.jax_utils import pad_shard_unpad, unreplicate
from flax.training import train_state
from flax.training.common_utils import get_metrics, onehot, shard, shard_prng_key
import flax.core


import time



# %%
import os
os.environ['XLA_FLAGS'] = (
    '--xla_gpu_triton_gemm_any=true --xla_gpu_enable_custom_fusions=true --xla_gpu_enable_address_computation_fusion=true'
)

os.environ.update({
    "TOKENIZERS_PARALLELISM" : "false",
    "CUDA_DEVICE_MAX_CONNECTIONS" : "1",
    "NCCL_LL128_BUFFSIZE": "-2",
    "NCCL_LL_BUFFSIZE": "-2",
    "NCCL_PROTO": "SIMPLE,LL,LL128",
    "XLA_PYTHON_CLIENT_MEM_FRACTION" : "0.99",
    # "XLA_PYTHON_CLIENT_PREALLOCATE" : "false"
 })

# %%
# get platform type
from jax.lib import xla_bridge
print(xla_bridge.get_backend().platform)


# %%
try:
    nltk.data.find("tokenizers/punkt")
except (LookupError, OSError):
    print("error")


# %%
# config options
file_path = '/home/richard/Projects/learn_t5/simple_model/combined_data_t5_retrieval'
save_path = 't5_80_1_bf16'
# file_path = 'combined_data'
split_datasets = load_from_disk(file_path)
training_size = len(split_datasets['train'])
# Store some constant
seed = 117
num_epochs = 5
batch_size = 384  # 384 is the best
num_train_epochs = num_epochs
per_device_train_batch_size = batch_size
train_batch_size = per_device_train_batch_size * jax.device_count()
per_device_eval_batch_size = batch_size
eval_batch_size = per_device_eval_batch_size * jax.device_count()
steps_per_epoch = training_size // train_batch_size
total_train_steps = steps_per_epoch * num_epochs

warmup_steps = 0
learning_rate = 2e-5

weight_decay = 0.01
adam_beta1 = 0.9
adam_beta2 = 0.999
adam_epsilon = 1e-8
label_smoothing_factor = 0.0

num_beams = 1
val_max_target_length = 128

predict_with_generate = True



# %%
from transformers import T5TokenizerFast
tokenizer = T5TokenizerFast.from_pretrained("t5-base", return_tensors="np", clean_up_tokenization_spaces=True)
# Define additional special tokens
additional_special_tokens = ["<THING_START>", "<THING_END>", "<PROPERTY_START>", "<PROPERTY_END>", "<NAME>", "<DESC>", "SIG", "UNIT", "DATA_TYPE"]
# Add the additional special tokens to the tokenizer
tokenizer.add_special_tokens({"additional_special_tokens": additional_special_tokens})

max_length = 86

# %%
len(tokenizer)

# %%
# load pytorch model first
# from transformers import AutoModelForSeq2SeqLM
# model_checkpoint = "t5-base"
# model_pt = AutoModelForSeq2SeqLM.from_pretrained(model_checkpoint)
# # important! after extending tokens vocab
# model_pt.resize_token_embeddings(len(tokenizer))
# model_pt.save_pretrained('./modified_t5_model')
# model = FlaxAutoModelForSeq2SeqLM.from_pretrained(
#     pretrained_model_name_or_path="modified_t5_model",
#     dtype=jax.numpy.bfloat16,
#     from_pt=True
# )


# %%
# model_path = './t5_80_1'
# model_path = 't5-base'
# model = FlaxAutoModelForSeq2SeqLM.from_pretrained(
#     pretrained_model_name_or_path=model_path,
#     dtype=jax.numpy.bfloat16
# )
# from t5_model.modeling_t5_flax import FlaxT5ForConditionalGeneration
# from t5_model.configuration_t5 import T5Config
from transformers import FlaxT5ForConditionalGeneration
from transformers import T5Config

config = T5Config()


# %%
# If you want don't want to cast certain parameters (for example layer norm bias and scale)
# then pass the mask as follows
from flax import traverse_util

model = FlaxT5ForConditionalGeneration.from_pretrained("t5-base")
# useful for transformer model
model.enable_gradient_checkpointing()

# enable bf16 except for layer_norm
flat_params = traverse_util.flatten_dict(model.params)
mask = {
    path: not (path[-2] == "layer_norm" and path[-1] == "weight") for path in flat_params
}
mask = traverse_util.unflatten_dict(mask)
model.params = model.to_bf16(model.params, mask)

# %%
# # Function to extract shape and dtype without showing values
# def format_param(param):
#     return f"shape={param.shape}, dtype={param.dtype}"
# 
# # Use jax.tree_map to apply the formatter across the parameter tree
# formatted_params = jax.tree.map(format_param, model.params)
# 
# # Pretty-print the tree
# for k, v in formatted_params.items():
#     print(f"{k}: {v}")

# %%
model_module = __import__(model.__module__, fromlist=["shift_tokens_tight"])
shift_tokens_right_fn = getattr(model_module, "shift_tokens_right")  # noqa: B009



# %%
# In Flax, for seq2seq models we need to pass `decoder_input_ids`
# as the Flax models don't accept `labels`, we need to prepare the decoder_input_ids here
# for that dynamically import the `shift_tokens_right` function from the model file


# given a dataset entry, run it through the tokenizer
# Setting padding="max_length" as we need fixed length inputs for jitted functions
def preprocess_function(example):
    inputs = example['input']
    targets = example['output']
    # text_target sets the corresponding label to inputs
    # there is no need to create a separate 'labels'
    # produce input_ids and decoder_input_ids
    model_inputs = tokenizer(
        inputs,
        max_length=max_length,
        padding="max_length",
        truncation=True,
        return_tensors="np"
    )
    labels = tokenizer(
        text_target=targets, 
        max_length=max_length,
        padding="max_length",
        truncation=True,
        return_tensors="np"
    )

    # for loss computation
    model_inputs["labels"] = labels["input_ids"]
    # make decoder input ids
    decoder_input_ids = shift_tokens_right_fn(
        labels["input_ids"], config.pad_token_id, config.decoder_start_token_id
    )
    # require by model
    model_inputs["decoder_input_ids"] = np.asarray(decoder_input_ids)
    # We need decoder_attention_mask so we can ignore pad tokens from loss
    model_inputs["decoder_attention_mask"] = labels["attention_mask"]

    return model_inputs

# %%
# temp

# map maps function to each "row" in the dataset
# aka the data in the immediate nesting
token_datasets = split_datasets.map(
    preprocess_function,
    batched=True,
    num_proc=1,
    # if we do not remove, we keep the original data
    remove_columns=split_datasets["train"].column_names,
)

train_dataset = token_datasets["train"]

# %%

token_datasets.set_format(
    type='numpy',
    columns=[
    'input_ids', 'attention_mask', 
    'labels', 'decoder_input_ids', 
    'decoder_attention_mask']
)
# %%
# check values
for name in ['input_ids', 'attention_mask', 'labels', 'decoder_input_ids', 'decoder_attention_mask']:
    int_array = train_dataset[name]
    if np.all((int_array >= 0) & (int_array <= 65535)):
        uint16_array = int_array.astype(np.uint16)
    else:
        raise ValueError("Values are out of range for uint16")

# %%

from datasets import ClassLabel, Value, Sequence
features = train_dataset.features.copy()
features['input_ids'] = Sequence(Value('uint16'))
features['attention_mask'] = Sequence(Value('bool'))
features['labels'] = Sequence(Value('uint16'))
features['decoder_input_ids'] = Sequence(Value('uint16'))
features['decoder_attention_mask'] = Sequence(Value('bool'))
train_dataset = train_dataset.cast(features)



# %%
# temp
print('data type check: ', train_dataset['decoder_attention_mask'].dtype)

# %%
def data_loader(rng: jax.random.PRNGKey, dataset: Dataset, batch_size: int, shuffle: bool = False, drop_last=True):
    """
    Returns batches of size `batch_size` from `dataset`. If `drop_last` is set to `False`, the final batch may be incomplete,
    and range in size from 1 to `batch_size`. Shuffle batches if `shuffle` is `True`.
    """
    if shuffle:
        batch_idx = jax.random.permutation(rng, len(dataset))
        batch_idx = np.asarray(batch_idx)
    else:
        batch_idx = np.arange(len(dataset))

    if drop_last:
        steps_per_epoch = len(dataset) // batch_size
        batch_idx = batch_idx[: steps_per_epoch * batch_size]  # Skip incomplete batch.
        batch_idx = batch_idx.reshape((steps_per_epoch, batch_size))
    else:
        steps_per_epoch = math.ceil(len(dataset) / batch_size)
        batch_idx = np.array_split(batch_idx, steps_per_epoch)

    for idx in batch_idx:
        batch = dataset[idx]
        batch = {k: jnp.array(v) for k, v in batch.items()}

        yield batch


# %% [markdown]
# # Model
#
#
#

# %%

# Initialize our training
rng = jax.random.PRNGKey(seed)
rng, dropout_rng = jax.random.split(rng)


# %%
# optimization functions

def create_learning_rate_fn(
    train_ds_size: int, train_batch_size: int, num_train_epochs: int, num_warmup_steps: int, learning_rate: float
) -> Callable[[int], jnp.ndarray]:
    """Returns a linear warmup, linear_decay learning rate function."""
    steps_per_epoch = train_ds_size // train_batch_size
    num_train_steps = steps_per_epoch * num_train_epochs
    warmup_fn = optax.linear_schedule(init_value=0.0, end_value=learning_rate, transition_steps=num_warmup_steps)
    decay_fn = optax.linear_schedule(
        init_value=learning_rate, end_value=0, transition_steps=num_train_steps - num_warmup_steps
    )
    schedule_fn = optax.join_schedules(schedules=[warmup_fn, decay_fn], boundaries=[num_warmup_steps])
    return schedule_fn


# Create learning rate schedule
linear_decay_lr_schedule_fn = create_learning_rate_fn(
    len(train_dataset),
    train_batch_size,
    num_train_epochs,
    warmup_steps,
    learning_rate,
)

# We use Optax's "masking" functionality to not apply weight decay
# to bias and LayerNorm scale parameters. decay_mask_fn returns a
# mask boolean with the same structure as the parameters.
# The mask is True for parameters that should be decayed.
def decay_mask_fn(params):
    flat_params = traverse_util.flatten_dict(params)
    # find out all LayerNorm parameters
    layer_norm_candidates = ["layernorm", "layer_norm", "ln"]
    layer_norm_named_params = {
        layer[-2:]
        for layer_norm_name in layer_norm_candidates
        for layer in flat_params.keys()
        if layer_norm_name in "".join(layer).lower()
    }
    flat_mask = {path: (path[-1] != "bias" and path[-2:] not in layer_norm_named_params) for path in flat_params}
    return traverse_util.unflatten_dict(flat_mask)

# create adam optimizer
adamw = optax.adamw(
    learning_rate=linear_decay_lr_schedule_fn,
    b1=adam_beta1,
    b2=adam_beta2,
    eps=adam_epsilon,
    weight_decay=weight_decay,
    mask=decay_mask_fn,
)


# %%
# Training functions
class TrainState(train_state.TrainState):
    dropout_rng: jnp.ndarray

    # easy way to achieve data parallelism
    # also achieves folding of rng keys
    def replicate(self):
        return jax_utils.replicate(self).replace(dropout_rng=shard_prng_key(self.dropout_rng))

# set bf16 for model params
# model.params = model.to_bf16(model.params)
# Cast parameters to bfloat16 if desired
# params = jax.tree_util.tree_map(lambda x: x.astype(jnp.bfloat16), params)

# Setup train state
state = TrainState.create(apply_fn=model.__call__, params=model.params, tx=adamw, dropout_rng=dropout_rng)

# label smoothed cross entropy
def loss_fn(logits, labels, padding_mask, label_smoothing_factor=0.0):
    """
    The label smoothing implementation is adapted from Flax's official example:
    https://github.com/google/flax/blob/87a211135c6a377c8f29048a1cac3840e38b9da4/examples/wmt/train.py#L104
    """
    vocab_size = logits.shape[-1]
    confidence = 1.0 - label_smoothing_factor
    low_confidence = (1.0 - confidence) / (vocab_size - 1)
    normalizing_constant = -(
        confidence * jnp.log(confidence) + (vocab_size - 1) * low_confidence * jnp.log(low_confidence + 1e-20)
    )
    soft_labels = onehot(labels, vocab_size, on_value=confidence, off_value=low_confidence)

    loss = optax.softmax_cross_entropy(logits, soft_labels)
    loss = loss - normalizing_constant

    # ignore padded tokens from loss
    loss = loss * padding_mask
    loss = loss.sum()
    num_labels = padding_mask.sum()
    return loss, num_labels

# Define gradient update step fn
@jax.jit
def train_step(state, batch, label_smoothing_factor=0.0):
    dropout_rng, new_dropout_rng = jax.random.split(state.dropout_rng)

    def compute_loss(params):
        labels = batch.pop("labels")
        logits = state.apply_fn(**batch, params=params, dropout_rng=dropout_rng, train=True)[0]
        loss, num_labels = loss_fn(logits, labels, batch["decoder_attention_mask"], label_smoothing_factor)
        return loss, num_labels

    # compute gradients through computational graph
    grad_fn = jax.value_and_grad(compute_loss, has_aux=True)
    (loss, num_labels), grad = grad_fn(state.params)
    num_labels = jax.lax.psum(num_labels, "batch")

    # true loss = total loss / total samples
    # loss = jax.lax.psum(loss, "batch")
    # loss = jax.tree_util.tree_map(lambda x: x / num_labels, loss)

    # true grad = total grad / total samples
    grad = jax.lax.psum(grad, "batch")
    grad = jax.tree_util.tree_map(lambda x: x / num_labels, grad)
    new_state = state.apply_gradients(grads=grad, dropout_rng=new_dropout_rng)

    # metrics = {"loss": loss, "learning_rate": linear_decay_lr_schedule_fn(state.step)}
    # return new_state, metrics
    return new_state

# Define generation function
max_length = (
    val_max_target_length if val_max_target_length is not None else model.config.max_length
)
num_beams = num_beams if num_beams is not None else model.config.num_beams
gen_kwargs = {"max_length": max_length, "num_beams": num_beams}

# def generate_step(params, batch):
#     model.params = params
#     output_ids = model.generate(batch["input_ids"], attention_mask=batch["attention_mask"], **gen_kwargs)
#     return output_ids.sequences

# Create parallel version of the train and eval step
p_train_step = jax.pmap(
    partial(train_step, label_smoothing_factor=label_smoothing_factor), "batch", donate_argnums=(0,)
)
# p_eval_step = jax.pmap(partial(eval_step, label_smoothing_factor=label_smoothing_factor), "batch")
# p_generate_step = jax.pmap(generate_step, "batch")

# Replicate the train state on each device
state = state.replicate()



# %%


print("***** Running training *****")
print(f"  Num examples = {len(train_dataset)}")
print(f"  Num Epochs = {num_epochs}")
print(f"  Instantaneous batch size per device = {per_device_train_batch_size}")
print(f"  Total train batch size (w. parallel & distributed) = {train_batch_size}")
print(f"  Total optimization steps = {total_train_steps}")


# %%
# jax.profiler.start_trace("./traces")

rng, input_rng = jax.random.split(rng)
train_time = 0
epochs = tqdm(range(num_epochs), desc=f"Epoch ... (1/{num_epochs})", position=0)
for epoch in epochs:
    train_start = time.time()

    # Create sampling rng
    train_metrics = []
    train_loader = data_loader(input_rng, train_dataset, train_batch_size, shuffle=True)
    steps_per_epoch = len(train_dataset) // train_batch_size
    # Generate an epoch by shuffling sampling indices from the train dataset
    for _ in tqdm(range(steps_per_epoch), desc="Training...", position=1, leave=False):
        batch = next(train_loader)
        batch = shard(batch)
        state = p_train_step(state, batch)
        # train_metrics.append(train_metric)

    train_time = time.time() - train_start

    # train_metric = unreplicate(train_metric)
    # train_metric['loss'].block_until_ready()



    epochs.write(
        # f"Epoch... ({epoch + 1}/{num_epochs} | Loss: {train_metric['loss']}, "
        f"Epoch... ({epoch + 1}/{num_epochs} |  "
        # f"Learning Rate:{train_metric['learning_rate']}, "
        f"Last train time: {train_time})"
    )
# jax.profiler.stop_trace()
# %%

# output_dir = save_path
# # save checkpoint after each epoch and push checkpoint to the hub
# if jax.process_index() == 0:
#     params = jax.device_get(jax.tree_util.tree_map(lambda x: x[0], state.params))
#     params = jax.tree_util.tree_map(lambda x: x.astype(jnp.float32), params)
#     model.save_pretrained(output_dir, params=params)
#     tokenizer.save_pretrained(output_dir)