BioReason-0813/model/blip2_opt.py

"""
 Copyright (c) 2023, salesforce.com, inc.
 All rights reserved.
 SPDX-License-Identifier: BSD-3-Clause
 For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
"""
import logging
import torch
import torch.nn as nn
from torch.cuda.amp import autocast as autocast
# from peft import get_peft_config, get_peft_model, get_peft_model_state_dict, LoraConfig, TaskType, PeftModel
from lavis.models.blip2_models.blip2 import disabled_train
from model.blip2 import Blip2Base
from transformers import AutoTokenizer
from transformers import OPTForCausalLM
from transformers import AutoTokenizer, AutoModelForCausalLM
from opendelta import LoraModel
from opendelta.delta_models.lora import LoraConfig as DeltaLoraConfig
from transformers import BertTokenizer, BitsAndBytesConfig
from model.help_funcs import hf_enable_gradient_checkpointing
import json
# from accelerate import Accelerator
# import torch.distributed as dist

# from peft.tuners.lora import LoraLayer
# from peft import (
#     prepare_model_for_kbit_training,
#     LoraConfig as PeftLoraConfig,
#     get_peft_model,
#     PeftModel
# )

# from opendelta.delta_configs

opt_model_list = [
    "facebook/galactica-125m",
    "facebook/galactica-1.3b",
    "facebook/galactica-6.7b",
    "facebook/galactica-30b",
]

def get_gpu_memory(device=0):
    # t = torch.cuda.get_device_properties(device).total_memory
    # r = torch.cuda.memory_reserved(device)
    # a = torch.cuda.memory_allocated(device)
    # f = r-a  # free inside reserved
    free, total = torch.cuda.mem_get_info(device)
    free = free / (1024 ** 3)
    total = total / (1024 ** 3)
    return free, total-free, total

def mask_by_len(input, lens, fill_value=0):
    '''
    input: shape = [N, D]
    lens: shape = [N]
    '''
    mask = torch.arange(input.shape[1], device=input.device).reshape(1, -1)
    mask = mask < lens.reshape(-1, 1)
    input[mask] = fill_value
    return input



class Blip2OPT(Blip2Base):
    """
    BLIP2 first-stage model with Q-former and ViT.
    Supported model types:
        - pretrained: pretrained model with vit-g
        - pretrain_vitL: pretrained model with vit-large
        - coco: fintuned model on coco
    Usage:
        >>> from lavis.models import load_model
        >>> model = load_model("blip2", "pretrain")
    """
    def __init__(
        self,
        bert_name,
        num_query_token=32,
        cross_attention_freq=2,
        plm_model="facebook/esm2_t30_150M_UR50D",
        plm_tune='freeze',
        llm_name="facebook/galactica-1.3b",
        llm_tune='freeze',
        qformer_tune='train',
        peft_dir='',
        args=None,
    ):
        super().__init__()
        self.args = args
        self.enbale_gradient_checkpointing = args.enbale_gradient_checkpointing

        self.plm_tokenizer, self.plm, self.ln_layer = self.init_protein_encoder(plm_model)
        self.plm_tune = plm_tune
        if plm_tune == 'freeze':
            for name, param in self.plm.named_parameters():
                param.requires_grad = False
            self.plm = self.plm.eval()
            self.plm.train = disabled_train
            logging.info("freeze plm encoder")
        elif plm_tune == 'lora':
            lora_config = DeltaLoraConfig(args.lora_r, 
                                          args.lora_alpha, 
                                          args.lora_dropout,
                                          modified_modules=["query", "value"])
            self.delta = LoraModel.from_config(lora_config, self.plm)
            self.delta.freeze_module(set_state_dict=False)
            self.delta.log()
        else:
            raise NotImplementedError()
        
        self.num_query_token = num_query_token
        self.qformer_tokenizer, self.Qformer, self.query_tokens = self.init_Qformer(bert_name, num_query_token, self.plm.num_features, cross_attention_freq)
        ### remove the unused parameters
        self.Qformer.cls = None
        self.Qformer.bert.embeddings.word_embeddings = None
        self.Qformer.bert.embeddings.position_embeddings = None
        for layer in self.Qformer.bert.encoder.layer:
            layer.output = None
            layer.intermediate = None

        # === 3. 控制 Qformer 是否冻结 ===
        self.qformer_tune = qformer_tune
        if self.qformer_tune == 'freeze':
            for name, param in self.Qformer.named_parameters():
                param.requires_grad = False
            self.Qformer = self.Qformer.eval()
            self.Qformer.train = disabled_train
            logging.info("freeze Qformer encoder")
        elif self.qformer_tune == 'train':
            logging.info("train Qformer encoder")
        else:
            raise NotImplementedError(f"Unsupported qformer_tune mode: {self.qformer_tune}")

        ## initialize llm model
        # self.init_distributed()
        self.llm_model, self.llm_tokenizer = self.load_llm(llm_name)
        
        #self.llm_model, self.llm_tokenizer = self.load_model_on_single_gpu(llm_name)
        self.eos_token_id = self.llm_tokenizer.eos_token_id
        self.pad_token_id = self.llm_tokenizer.pad_token_id

        if llm_tune == 'freeze':
            for name, param in self.llm_model.named_parameters():
                param.requires_grad = False
        elif llm_tune == 'full':
            for name, param in self.llm_model.named_parameters():
                param.requires_grad = True
        elif llm_tune == 'lora':
            lora_config = DeltaLoraConfig(args.lora_r, 
                                          args.lora_alpha, 
                                          args.lora_dropout,)
            self.delta = LoraModel.from_config(lora_config, self.llm_model)
            self.delta.freeze_module(set_state_dict=False)
            self.delta.log()
        elif llm_tune == 'mid_lora':
            print("================")
            print("加载了小lora")
            print("=================")
            lora_config = DeltaLoraConfig(args.lora_r, args.lora_alpha, args.lora_dropout, modified_modules=["q_proj", "v_proj", 'k_proj', "out_proj", "fc1", "fc2"])
            self.delta = LoraModel.from_config(lora_config, self.llm_model)
            self.delta.freeze_module(set_state_dict=False)
            self.delta.log()
        elif llm_tune == 'peft_lora':
            config = PeftLoraConfig(
                r=args.lora_r,
                lora_alpha=args.lora_alpha,
                # target_modules=modules,
                lora_dropout=args.lora_dropout,
                bias="none",
                task_type="CAUSAL_LM",
            )
            self.llm_model = get_peft_model(self.llm_model, config)
            for name, module in self.llm_model.named_modules():
                if isinstance(module, LoraLayer):
                    if True:
                        module = module.to(torch.bfloat16)
                if 'norm' in name:
                    module = module.to(torch.float32)
                if 'lm_head' in name or 'embed_tokens' in name:
                    if hasattr(module, 'weight'):
                        if True and module.weight.dtype == torch.float32:
                            module = module.to(torch.bfloat16)
        else:
            raise NotImplementedError()

        ## fixme: this is different from the original BLIP2
        # self.eos_token_id = self.llm_tokenizer(
        #     "\n", add_special_tokens=False
        # ).input_ids[0]
        self.opt_proj = nn.Linear(self.Qformer.config.hidden_size, self.llm_model.config.hidden_size)

    def load_llm(self, llm_model, load_4bit=False, enable_gradient_checkpointing=True):
        llm_tokenizer = AutoTokenizer.from_pretrained(llm_model, use_fast=False, padding_side='right')
        llm_tokenizer.add_special_tokens({'pad_token': '<pad>'})
        
        special_tokens_dict = {'additional_special_tokens': ['<PROT>', '<TEXT>']}
        llm_tokenizer.add_special_tokens(special_tokens_dict)
        
        llm_model = AutoModelForCausalLM.from_pretrained(llm_model, torch_dtype=torch.bfloat16)
        llm_model.resize_token_embeddings(len(llm_tokenizer)) ## this will cause bug when 
       
        return llm_model, llm_tokenizer


    # def forward(self, batch):
    #     prot_batch, text_batch = batch
    #     prot_embeds = self.plm(**prot_batch, return_dict=True)
    #     prot_embeds = prot_embeds.last_hidden_state
    #     if self.plm_tune == 'freeze':
    #         prot_embeds = prot_embeds.detach()
    #     prot_embeds = self.ln_layer(prot_embeds)
    #     device = prot_embeds.device
    #     query_tokens = self.query_tokens.expand(prot_embeds.shape[0], -1, -1)
    #     query_output = self.Qformer.bert(
    #         query_embeds=query_tokens,
    #         encoder_hidden_states=prot_embeds,
    #         encoder_attention_mask=prot_batch.attention_mask,
    #         return_dict=True,
    #     )
    #     prot_tokens = self.opt_proj(query_output.last_hidden_state)
    #     prot_mask = torch.ones(prot_tokens.shape[:2], dtype=text_batch.attention_mask.dtype, device=device)
    #     prot_empty_targets = torch.ones(prot_tokens.shape[:2], dtype=torch.long, device=device).fill_(-100)
        
    #     targets = text_batch.input_ids.masked_fill(text_batch.input_ids == self.llm_tokenizer.pad_token_id, -100)
    #     targets = targets.masked_fill(text_batch.token_type_ids == 0, -100)
    #     targets = torch.cat([prot_empty_targets, targets], dim=1)

    #     inputs_embeds = self.llm_model.get_input_embeddings()(text_batch.input_ids)
    #     inputs_embeds = torch.cat((prot_tokens, inputs_embeds), dim=1)
    #     attention_mask = torch.cat([prot_mask, text_batch.attention_mask], dim=1)
        
    #     outputs = self.llm_model(
    #         inputs_embeds=inputs_embeds,
    #         attention_mask=attention_mask,
    #         return_dict=True,
    #         labels=targets,
    #     )
    #     loss = outputs.loss
    #     return loss

    def forward(self, batch):
        prot_batch, prompt_batch, text_dict = batch
        text_seqs = text_dict['targets']
        batch_size = prompt_batch['input_ids'].size(0)
        # print("{{{{{}}}}}")
        # print(batch_size)

        prot_embeds = self.plm(**prot_batch, return_dict=True)
        prot_embeds = prot_embeds.last_hidden_state
        if self.plm_tune == 'freeze':
            prot_embeds = prot_embeds.detach()
        prot_embeds = self.ln_layer(prot_embeds)
        device = prot_embeds.device
        query_tokens = self.query_tokens.expand(prot_embeds.shape[0], -1, -1)
        query_output = self.Qformer.bert(
            query_embeds=query_tokens,
            encoder_hidden_states=prot_embeds,
            encoder_attention_mask=prot_batch.attention_mask,
            return_dict=True,
        )
        prot_tokens = self.opt_proj(query_output.last_hidden_state)
        prot_mask = torch.ones(prot_tokens.shape[:2], dtype=torch.long, device=device)

        # === Step 3: 编码 prompt 输入 ===
        prompt_embeds = self.llm_model.get_input_embeddings()(prompt_batch.input_ids)  # [B, L_prompt, D_llm]
        prompt_mask = prompt_batch['attention_mask']


        text_batch = self.llm_tokenizer(
            list(text_seqs),
            padding='longest',
            truncation=True,
            max_length=1024,
            return_tensors='pt'
        ).to(device)
        target_embeds = self.llm_model.get_input_embeddings()(text_batch['input_ids'])  # [B, T, D]
        target_mask = text_batch['attention_mask']
        targets = text_batch['input_ids'].masked_fill(text_batch['input_ids'] == self.llm_tokenizer.pad_token_id, -100)

        # === : 加入 ChatML 特殊 token embedding ===
        embedding_layer = self.llm_model.get_input_embeddings()

        def embed_special_str(token_str):
            # 先 tokenize，得到一系列 ID
            ids = self.llm_tokenizer(token_str, add_special_tokens=False).input_ids
            # 把它变成 [1, N] tensor
            ids_tensor = torch.tensor([ids], device=device)
            # 查 embedding 层：
            embs = embedding_layer(ids_tensor)  # shape [1, N, D]
            # Expand 到 batch 大小
            return embs.expand(batch_size, -1, -1)

        # 示例
        embed_im_start = embed_special_str("<|im_start|>user\n protein sequence is:<protein>")   # 可能对应多个 sub-tokens
        embed_protein = embed_special_str("</protein>")
        embed_im_end   = embed_special_str("<|im_end|>\n")
        embed_assistant= embed_special_str("<|im_start|>assistant\n")

         
        user_embeds = torch.cat([embed_im_start, prot_tokens , embed_protein, prompt_embeds,embed_im_end, embed_assistant], dim=1)
        user_mask = torch.ones(user_embeds.shape[:2], dtype=torch.long, device=device)

        assistant_embeds = target_embeds
        assistant_mask = target_mask

        inputs_embeds = torch.cat([user_embeds, assistant_embeds], dim=1)
        attention_mask = torch.cat([user_mask, assistant_mask], dim=1)

        # === Step 6: 构造 labels，只监督 assistant 部分 ===
        ignore_labels = torch.full(user_embeds.shape[:2], -100, dtype=torch.long, device=device)
        assistant_labels = targets
        labels = torch.cat([ignore_labels, assistant_labels], dim=1)

        # print("embed_im_start:", embed_im_start.shape)
        # print("prompt_embeds:", prompt_embeds.shape)
        # print("prot_tokens:", prot_tokens.shape)
        # print("embed_im_end:", embed_im_end.shape)
        # print("embed_assistant:", embed_assistant.shape)
        # print("target_embeds:", target_embeds.shape)
        # print("labels:", labels.shape)
        # print("inputs_embeds:", inputs_embeds.shape)

        #============================

        # inputs_embeds = torch.cat([prot_tokens, prompt_embeds, target_embeds], dim=1)
        # attention_mask = torch.cat([prot_mask, prompt_mask, target_mask], dim=1)

        # # === Step 7: 构造 labels，只监督 target 部分 ===
        # prot_label_pad = torch.full(prot_tokens.shape[:2], -100, dtype=torch.long, device=device)
        # prompt_label_pad = torch.full(prompt_mask.shape, -100, dtype=torch.long, device=device)
        # labels = torch.cat([prot_label_pad, prompt_label_pad, targets], dim=1)

        # === Step 8: 送入 LLM ===
        outputs = self.llm_model(
            inputs_embeds=inputs_embeds,
            attention_mask=attention_mask,
            labels=labels,
            return_dict=True,
        )
        loss = outputs.loss
        # prot_mask = torch.ones(prot_tokens.shape[:2], dtype=text_batch.attention_mask.dtype, device=device)
        # prot_empty_targets = torch.ones(prot_tokens.shape[:2], dtype=torch.long, device=device).fill_(-100)
        # empty_targets = torch.ones(prompt_batch.attention_mask.shape, dtype=torch.long, device=device).fill_(-100)
        # targets = text_batch.input_ids.masked_fill(text_batch.input_ids == self.llm_tokenizer.pad_token_id, -100)
        # targets = torch.cat([prot_empty_targets, empty_targets, targets], dim=1)

        # prompt_embeds = self.llm_model.get_input_embeddings()(prompt_batch.input_ids)
        # inputs_embeds = self.llm_model.get_input_embeddings()(text_batch.input_ids)
        # inputs_embeds = torch.cat((prot_tokens, prompt_embeds, inputs_embeds), dim=1)
        # attention_mask = torch.cat([prot_mask, prompt_batch.attention_mask, text_batch.attention_mask], dim=1)
        
        # outputs = self.llm_model(
        #     inputs_embeds=inputs_embeds,
        #     attention_mask=attention_mask,
        #     return_dict=True,
        #     labels=targets,
        # )
        # loss = outputs.loss
        return loss

    # def forwardv2(self, batch):
    #     prot_batch, prompt_batch, text_batch = batch
    #     prot_embeds = self.plm(**prot_batch, return_dict=True)
    #     prot_embeds = prot_embeds.last_hidden_state
    #     if self.plm_tune == 'freeze':
    #         prot_embeds = prot_embeds.detach()
    #     prot_embeds = self.ln_layer(prot_embeds)
    #     device = prot_embeds.device
    #     query_tokens = self.query_tokens.expand(prot_embeds.shape[0], -1, -1)
    #     query_output = self.Qformer.bert(
    #         query_embeds=query_tokens,
    #         encoder_hidden_states=prot_embeds,
    #         encoder_attention_mask=prot_batch.attention_mask,
    #         return_dict=True,
    #     )
    #     prot_tokens = self.opt_proj(query_output.last_hidden_state)
    #     prot_mask = torch.ones(prot_tokens.shape[:2], dtype=text_batch.attention_mask.dtype, device=device)
    #     targets = text_batch.input_ids.masked_fill(text_batch.input_ids == self.llm_tokenizer.pad_token_id, -100)

    #     ### forward prefix
    #     prompt_embeds = self.llm_model.get_input_embeddings()(prompt_batch.input_ids)
    #     prefix_embeds = torch.cat([prot_tokens, prompt_embeds], dim=1)
    #     prefix_mask = torch.cat([prot_mask, prompt_batch.attention_mask], dim=1)
    #     prefix_output = self.llm_model.model(
    #         inputs_embeds=prefix_embeds,
    #         attention_mask=prefix_mask,
    #         use_cache=True,
    #         return_dict=True,
    #     )

    #     ## forward decoding
    #     if False:
    #         attention_mask = torch.cat([prot_mask, prompt_batch.attention_mask, text_batch.attention_mask], dim=1)
    #     else:
    #         attention_mask = text_batch.attention_mask
    #     print(prefix_output.past_key_values)
    #     outputs = self.llm_model(
    #         input_ids=text_batch.input_ids,
    #         attention_mask=attention_mask,
    #         past_key_values=prefix_output.past_key_values,
    #         return_dict=True,
    #         labels=targets,
    #     )
    #     loss = outputs.loss
    #     return loss
    
    @torch.no_grad()
    def generate(
        self,
        samples,
        do_sample=False,
        num_beams=5,
        max_length=128,
        min_length=1,
        top_p=0.9,
        repetition_penalty=1.0,
        length_penalty=1.0,
        num_captions=1,
        temperature=1,
    ):
        """
        Args:
            samples (dict): A dictionary containing the following keys:
                - image (torch.Tensor): A tensor of shape (batch_size, 3, H, W)
            num_beams (int): Number of beams for beam search. 1 means no beam search.
            max_length (int): The maximum length of the sequence to be generated.
            min_length (int): The minimum length of the sequence to be generated.
            top_p (float): The cumulative probability for nucleus sampling.
            repetition_penalty (float): The parameter for repetition penalty. 1.0 means no penalty.
            num_captions (int): Number of captions to be generated for each image.
        Returns:
            captions (list): A list of strings of length batch_size * num_captions.
        """
        # prot_batch = samples['prot_batch']
        # prompt_batch = samples['prompt_batch']
        
        # # with self.maybe_autocast():
        # prot_embeds = self.plm(**prot_batch, return_dict=True)
        # prot_embeds = self.ln_layer(prot_embeds.last_hidden_state)

        # query_tokens = self.query_tokens.expand(prot_embeds.shape[0], -1, -1)
        # query_output = self.Qformer.bert(
        #     query_embeds=query_tokens,
        #     encoder_hidden_states=prot_embeds,
        #     encoder_attention_mask=prot_batch['attention_mask'],
        #     return_dict=True,
        # )
        # prot_tokens = self.opt_proj(query_output.last_hidden_state)
        
        
        
        # # prompt_batch = samples['prompt_batch']
        # prompt_input_ids = prompt_batch['input_ids']           # shape: [B, L]
        # # for i, ids in enumerate(prompt_input_ids):
        # #     print(f"Prompt {i} token length: {len(ids)}")
        # decoded_texts = [self.llm_tokenizer.decode(ids, skip_special_tokens=True) for ids in prompt_input_ids]
        # # print("=========")
        # # print(decoded_texts)
        # #print(decoded_texts)
        # save_path = "decoded_prompts.json"

        # # 将 list 写入 JSON 文件
        # with open(save_path, 'w', encoding='utf-8') as f:
        #     json.dump(decoded_texts, f, ensure_ascii=False, indent=4)

        # prompt_attention_mask = prompt_batch['attention_mask']
        # prompt_embeds = self.llm_model.model.embed_tokens(prompt_input_ids)

        # inputs_embeds = torch.cat((prompt_embeds, prot_tokens), dim=1)

        # prot_attention_mask = torch.ones(prot_tokens.shape[:2], dtype=prompt_attention_mask.dtype, device=prompt_attention_mask.device)
        # #attention_mask = torch.cat([prot_attention_mask, prompt_attention_mask], dim=1) 
        # attention_mask = torch.cat([ prompt_attention_mask,prot_attention_mask], dim=1) 

        #==========================
        prot_batch = samples['prot_batch']
        prompt_batch = samples['prompt_batch']
        

        device = prompt_batch['input_ids'].device
        batch_size = prompt_batch['input_ids'].size(0)

        # === Step 1: 编码蛋白质 + QFormer ===
        prot_embeds = self.plm(**prot_batch, return_dict=True).last_hidden_state
        prot_embeds = self.ln_layer(prot_embeds)
        query_tokens = self.query_tokens.expand(prot_embeds.shape[0], -1, -1)
        query_output = self.Qformer.bert(
            query_embeds=query_tokens,
            encoder_hidden_states=prot_embeds,
            encoder_attention_mask=prot_batch['attention_mask'],
            return_dict=True,
        )
        prot_tokens = self.opt_proj(query_output.last_hidden_state)  # [B, L_qformer, D]

        # === Step 2: 编码 prompt 输入 ===
        prompt_input_ids = prompt_batch['input_ids']
        prompt_attention_mask = prompt_batch['attention_mask']
        prompt_embeds = self.llm_model.get_input_embeddings()(prompt_input_ids)

        # === Step 3: 获取 ChatML 特殊 token 的 embedding ===
        embedding_layer = self.llm_model.get_input_embeddings()

        def embed_special_str(token_str):
            # 先 tokenize，得到一系列 ID
            ids = self.llm_tokenizer(token_str, add_special_tokens=False).input_ids
            # 把它变成 [1, N] tensor
            ids_tensor = torch.tensor([ids], device=device)
            # 查 embedding 层：
            embs = embedding_layer(ids_tensor)  # shape [1, N, D]
            # Expand 到 batch 大小
            return embs.expand(batch_size, -1, -1)

        # 示例
        embed_im_start = embed_special_str("<|im_start|>user\nprotein sequence is: <protein>")   # 可能对应多个 sub-tokens
        embed_protein = embed_special_str("</protein>")
        embed_im_end   = embed_special_str("<|im_end|>\n")
        embed_assistant= embed_special_str("<|im_start|>assistant\n")


        # === Step 4: 拼接 Embeddings ===
        user_embeds = torch.cat([embed_im_start, prot_tokens, embed_protein, prompt_embeds, embed_im_end], dim=1)
        assistant_prefix = embed_assistant  # 模型从这里开始生成
        inputs_embeds = torch.cat([user_embeds, assistant_prefix], dim=1)

        # === Step 5: attention_mask ===
        user_mask = torch.ones(user_embeds.shape[:2], dtype=torch.long, device=device)
        assistant_mask = torch.ones((batch_size, embed_assistant.size(1)), dtype=torch.long, device=device)
        attention_mask = torch.cat([user_mask, assistant_mask], dim=1)
        
        outputs = self.llm_model.generate(
            inputs_embeds=inputs_embeds,
            attention_mask=attention_mask,
            do_sample=do_sample,
            top_p=top_p,
            temperature=temperature,
            num_beams=num_beams,
            max_new_tokens=max_length,
            min_length=min_length,
            # pad_token_id=self.pad_token_id,
            eos_token_id=self.eos_token_id,
            repetition_penalty=repetition_penalty,
            length_penalty=length_penalty,
            num_return_sequences=num_captions,
            use_cache=True,
            cache_implementation="hybrid"
        )
        output_text = self.llm_tokenizer.batch_decode(outputs, skip_special_tokens=True)
        output_text = [text.strip() for text in output_text]
        # print(output_text)
        return output_text