inference.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Title     : maotao_inference.py.py
project   : minimind_RiboUTR
Created by: julse
Created on: 2025/10/23 16:49
des: TODO
"""

import sys
import os
import time
import pandas as pd
import numpy as np

import sys
import os
import time
import torch
import torch.distributed as dist
from model.tools import get_pretraining_args, find_unused_parameters
from contextlib import nullcontext
from train import sft_process_maotao, init_config, maotao


ddp = int(os.environ.get("RANK", -1)) != -1  # is this a ddp run?
print('Setting running environment')

def Logger(*content):
    if not ddp or dist.get_rank() == 0:
        print(*content)
def init_distributed_mode(ddp=True):
    print("init distributed mode,ddp=",ddp)

    if not ddp: return
    global ddp_local_rank, DEVICE
    dist.init_process_group(backend="nccl")
    ddp_rank = int(os.environ["RANK"])
    ddp_local_rank = int(os.environ["LOCAL_RANK"])
    ddp_world_size = int(os.environ["WORLD_SIZE"])
    DEVICE = f"cuda:{ddp_local_rank}"
    torch.cuda.set_device(DEVICE)

    print('init distributed mode, ddp_rank:', ddp_rank, 'ddp_local_rank:', ddp_local_rank, 'ddp_world_size:', ddp_world_size)
    return ddp_local_rank,DEVICE
def inference(args):
    sft = maotao()

    if args.predict:
        task = args.task
    else:
        task = 'AA2CDS_data'
    device_type = "cuda" if "cuda" in args.device else "cpu"
    ctx = nullcontext() if device_type == "cpu" else torch.cuda.amp.autocast()

    ddp_local_rank, DEVICE = 0, "cuda:0"
    if ddp:
        print('init distributed mode')
        ddp_local_rank, DEVICE = init_distributed_mode(ddp=ddp)
        args.device = torch.device(DEVICE)
    Logger('args.device:', args.device)
    Logger('setting args', args)
    max_seq_len = 1200
    args.seq_len = max_seq_len

    args.save_dir = os.path.join(args.out_dir)
    # os.system(f"rm -rf {args.save_dir}") # todo
    os.makedirs(args.save_dir, exist_ok=True)
    os.makedirs(args.out_dir, exist_ok=True)
    tokens_per_iter = args.batch_size * max_seq_len

    lm_config, tokenizer = init_config(args.arg_overrides['data'] + '/small_dict.txt', args.n_layers, max_seq_len)
    lm_config.use_moe = args.use_moe
    wandb_project = args.wandb_project

    '''3. benchmark downstream tasks'''
    prefix = 'TS'
    # with open(args.save_dir+'/benchmark_result.tsv','w') as f:
    #     f.write('Project\tModel\tTask\tSPR\tPR\tMSE\tRMSE\tR2\tckp\tepoch\n')
    epochs = args.epochs
    args.out_dir = os.path.abspath(args.out_dir)
    os.makedirs(args.out_dir, exist_ok=True)
    model_dir = args.out_dir  # 'exp_log/out_demo4/'
    model_dir = os.path.abspath(model_dir)
    data_dir = args.downstream_data_path  # 'dataset/downstreamV4/'
    Logger(f'model_dir:{model_dir}')

    os.makedirs(model_dir, exist_ok=True)
    args.save_dir = os.path.abspath(args.save_dir)
    args.downstream_data_path = os.path.abspath(args.downstream_data_path)
    # args.codon_table_path = 'maotao_file/codon_table/codon_usage_{species}.csv'
    Logger('args.downstream_data_path:', args.downstream_data_path)
    out_ckp = args.save_dir + f'/AA2CDS.pth'
    out_ckp = os.path.abspath(out_ckp)
    # os.system(f"rm -rf {out_ckp}")
    # in_ckp = model_dir + '/AA2CDS.pth'

    in_ckp = args.mlm_pretrained_model_path
    ckp, final_metrics, _ = sft_process_maotao(max_seq_len=max_seq_len, ctx=ctx, ddp=ddp,
                                                   ddp_local_rank=ddp_local_rank,
                                                   args=args, ckp=in_ckp, out_ckp=out_ckp,
                                                   lm_config=lm_config, tokenizer=tokenizer, Logger=Logger,task=task,
                                                   sft=sft,require_ckp=True)

if __name__ == '__main__':
    print('start', time.strftime('%Y-%m-%d %H:%M:%S', time.localtime()))
    start = time.time()


    parser = get_pretraining_args()
    args = parser.parse_args()


    # args.downstream_data_path = 'example/out/tmp/AA2CDS_data/' # TS.csv #
    args.downstream_data_path = 'maotao_file/' # TS.csv
    args.task='AA2CDS_data'
    args.predict =True
    args.mlm_pretrained_model_path = 'checkpoint/AA2CDS.pth'
    args.out_dir = 'example/out_TR_TS'

    inference(args)
    print('stop', time.strftime('%Y-%m-%d %H:%M:%S', time.localtime()))
    print('time', time.time() - start)