import logging import argparse import boto3 import signal import os import sys import time import subprocess import hashlib import json import base64 import atexit import asyncio import aiohttp import datetime import tempfile import re from tqdm import tqdm from io import BytesIO from PIL import Image from pypdf import PdfReader from functools import partial from dataclasses import dataclass from typing import Optional from concurrent.futures import ProcessPoolExecutor from pdelfin.s3_utils import expand_s3_glob, get_s3_bytes, parse_s3_path, download_zstd_csv, upload_zstd_csv, download_directory from pdelfin.data.renderpdf import render_pdf_to_base64png from pdelfin.prompts import build_finetuning_prompt, PageResponse from pdelfin.prompts.anchor import get_anchor_text from pdelfin.check import check_poppler_version # Initialize logger logger = logging.getLogger(__name__) logger.setLevel(logging.DEBUG) file_handler = logging.FileHandler('beakerpipeline-debug.log', mode='a') file_handler.setLevel(logging.DEBUG) file_handler.setFormatter(logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')) # Add handlers to the logger logger.addHandler(file_handler) # Quiet logs from pypdf logging.getLogger("pypdf").setLevel(logging.ERROR) # Global s3 clients fo the whole script, we have two separate ones in case your workspace and your pdfs are in different accounts workspace_s3 = boto3.client('s3') pdf_s3 = boto3.client('s3') # Global variables for token statistics total_input_tokens = 0 total_output_tokens = 0 process_start_time = time.perf_counter() last_batch_time = process_start_time # Process pool for offloading cpu bound work, like calculating anchor texts process_pool = ProcessPoolExecutor() @dataclass(frozen=True) class PageResult: s3_path: str page_num: int response: PageResponse total_input_tokens: int total_output_tokens: int async def build_page_query(local_pdf_path: str, page: int, target_longest_image_dim: int, target_anchor_text_len: int, image_rotation: int=0) -> dict: MAX_TOKENS = 3000 assert image_rotation in [0, 90, 180, 270], "Invalid image rotation provided in build_page_query" # Allow the page rendering to process in the background while we get the anchor text (which blocks the main thread) image_base64 = asyncio.to_thread(render_pdf_to_base64png, local_pdf_path, page, target_longest_image_dim=target_longest_image_dim) # GET ANCHOR TEXT IS NOT THREAD SAFE!! Ahhhh..... don't try to do it # and it's also CPU bound, so it needs to run in a process pool loop = asyncio.get_running_loop() anchor_text = loop.run_in_executor(process_pool, partial(get_anchor_text, pdf_engine="pdfreport", target_length=target_anchor_text_len), local_pdf_path, page) image_base64, anchor_text = await asyncio.gather(image_base64, anchor_text) if image_rotation != 0: image_bytes = base64.b64decode(image_base64) with Image.open(BytesIO(image_bytes)) as img: rotated_img = img.rotate(-image_rotation, expand=True) # Save the rotated image to a bytes buffer buffered = BytesIO() rotated_img.save(buffered, format="PNG") # Encode the rotated image back to base64 image_base64 = base64.b64encode(buffered.getvalue()).decode('utf-8') return { "model": "Qwen/Qwen2-VL-7B-Instruct", "messages": [ { "role": "user", "content": [ {"type": "text", "text": build_finetuning_prompt(anchor_text)}, {"type": "image_url", "image_url": {"url": f"data:image/png;base64,{image_base64}"}} ], } ], "max_tokens": MAX_TOKENS, "temperature": 0.8 } def compute_workgroup_sha1(work_group: list[str]) -> str: sha1 = hashlib.sha1() # Ensure consistent ordering by sorting the list for pdf in sorted(work_group): sha1.update(pdf.encode('utf-8')) return sha1.hexdigest() async def populate_pdf_work_queue(args): index_file_s3_path = os.path.join(args.workspace, "pdf_index_list.csv.zstd") if args.pdfs.startswith("s3://"): logger.info(f"Expanding s3 glob at {args.pdfs}") all_pdfs = expand_s3_glob(pdf_s3, args.pdfs) elif os.path.exists(args.pdfs): logger.info(f"Loading file at {args.pdfs}") with open(args.pdfs, "r") as f: all_pdfs = list(filter(None, (line.strip() for line in tqdm(f, desc="Processing PDFs")))) else: raise ValueError("pdfs argument needs to be either an s3 glob search path, or a local file contains pdf paths (one per line)") all_pdfs = set(all_pdfs) logger.info(f"Found {len(all_pdfs):,} total pdf paths") existing_lines = download_zstd_csv(workspace_s3, index_file_s3_path) # Parse existing work items into groups existing_groups = {} for line in existing_lines: if line.strip(): parts = line.strip().split(",") group_hash = parts[0] group_pdfs = parts[1:] existing_groups[group_hash] = group_pdfs existing_pdf_set = set(pdf for group_pdfs in existing_groups.values() for pdf in group_pdfs) logger.info(f"Loaded {len(existing_pdf_set):,} existing pdf paths from the workspace") # Remove existing PDFs from all_pdfs new_pdfs = all_pdfs - existing_pdf_set logger.info(f"{len(new_pdfs):,} new pdf paths to add to the workspace") # Group the new PDFs into chunks of group_size # TODO: Figure out the group size automatically by sampling a few pdfs, and taking the mean/median number of pages, etc. new_groups = [] current_group = [] for pdf in sorted(new_pdfs): # Sort for consistency current_group.append(pdf) if len(current_group) == args.group_size: group_hash = compute_workgroup_sha1(current_group) new_groups.append((group_hash, current_group)) current_group = [] if current_group: group_hash = compute_workgroup_sha1(current_group) new_groups.append((group_hash, current_group)) logger.info(f"Created {len(new_groups):,} new work groups") # Combine existing groups with new groups combined_groups = existing_groups.copy() for group_hash, group_pdfs in new_groups: combined_groups[group_hash] = group_pdfs # Prepare lines to write back combined_lines = [",".join([group_hash] + group_pdfs) for group_hash, group_pdfs in combined_groups.items()] # Upload the combined work items back to S3 if new_groups: upload_zstd_csv(workspace_s3, index_file_s3_path, combined_lines) logger.info("Completed adding new PDFs.") async def load_pdf_work_queue(args) -> asyncio.Queue: index_file_s3_path = os.path.join(args.workspace, "pdf_index_list.csv.zstd") output_glob = f"{args.workspace}/dolma_documents/output_*.jsonl" # Define the two blocking I/O operations download_task = asyncio.to_thread(download_zstd_csv, workspace_s3, index_file_s3_path) expand_task = asyncio.to_thread(expand_s3_glob, workspace_s3, output_glob) # Run both tasks concurrently work_queue_lines, done_work_items = await asyncio.gather(download_task, expand_task) # Process the work queue lines work_queue = { parts[0]: parts[1:] for line in work_queue_lines if (parts := line.strip().split(",")) and line.strip() } # Extract done work hashes done_work_hashes = { os.path.basename(item)[len('output_'):-len('.jsonl')] for item in done_work_items if os.path.basename(item).startswith('output_') and os.path.basename(item).endswith('.jsonl') } # Determine remaining work remaining_work_hashes = set(work_queue) - done_work_hashes remaining_work_queue = { hash_: work_queue[hash_] for hash_ in remaining_work_hashes } # Populate the asyncio.Queue with remaining work queue = asyncio.Queue() for work, pdfs in remaining_work_queue.items(): await queue.put((work, pdfs)) return queue async def process_page(args, session: aiohttp.ClientSession, pdf_s3_path: str, pdf_local_path: str, page_num: int) -> PageResult: COMPLETION_URL = "http://localhost:30000/v1/chat/completions" MAX_RETRIES = 3 for attempt in range(1, MAX_RETRIES + 1): query = await build_page_query( pdf_local_path, page_num, args.target_longest_image_dim, args.target_anchor_text_len ) try: async with session.post(COMPLETION_URL, json=query) as response: response.raise_for_status() base_response_data = await response.json() model_response_json = json.loads(base_response_data["choices"][0]["message"]["content"]) page_response = PageResponse(**model_response_json) return PageResult( pdf_s3_path, page_num, page_response, total_input_tokens=base_response_data["usage"].get("prompt_tokens", 0), total_output_tokens=base_response_data["usage"].get("completion_tokens", 0) ) except aiohttp.ClientError as e: logger.warning(f"Client error on attempt {attempt} for {pdf_s3_path}-{page_num}:: {e}") except json.JSONDecodeError as e: logger.warning(f"JSON decode error on attempt {attempt} for {pdf_s3_path}-{page_num}: {e}") except Exception as e: logger.warning(f"Unexpected error on attempt {attempt} for {pdf_s3_path}-{page_num}:: {e}") if attempt >= MAX_RETRIES: logger.error(f"Failed to process {pdf_s3_path}-{page_num} after {MAX_RETRIES} attempts.") raise ValueError(f"Could not process {pdf_s3_path}-{page_num} after {MAX_RETRIES} attempts") async def process_pdf(args, pdf_s3_path: str): with tempfile.NamedTemporaryFile("wb+", suffix=".pdf") as tf: # TODO Switch to aioboto3 or something data = await asyncio.to_thread(lambda: get_s3_bytes(pdf_s3, pdf_s3_path)) tf.write(data) tf.flush() reader = PdfReader(tf.name) num_pages = reader.get_num_pages() # List to hold the tasks for processing each page page_tasks = [] async with aiohttp.ClientSession(timeout=aiohttp.ClientTimeout(total=3600), connector=aiohttp.TCPConnector(limit=10)) as session: for page_num in range(1, num_pages + 1): # Create a task for each page task = asyncio.create_task(process_page(args, session, pdf_s3_path, tf.name, page_num)) page_tasks.append(task) # Gather results from all page processing tasks try: page_results: list[PageResult] = await asyncio.gather(*page_tasks) except: logger.exception(f"Could not load page for {pdf_s3_path}, aborting document") return None # Build the document text and page spans document_text = "" pdf_page_spans = [] current_char_pos = 0 for index, page_result in enumerate(page_results): if page_result.response.natural_text is not None: content = page_result.response.natural_text + ("\n" if index == len(page_results) - 1 else "") else: content = "" start_pos = current_char_pos document_text += content current_char_pos = len(document_text) pdf_page_spans.append([start_pos, current_char_pos, page_result.page_num]) if not document_text: return None # Return None if the document text is empty # Build the Dolma document metadata = { "Source-File": pdf_s3_path, "pdf-total-pages": num_pages, "total-input-tokens": sum(page.total_input_tokens for page in page_results), "total-output-tokens": sum(page.total_output_tokens for page in page_results) } id_ = hashlib.sha1(document_text.encode()).hexdigest() dolma_doc = { "id": id_, "text": document_text, "source": "pdelfin", "added": datetime.datetime.now().strftime("%Y-%m-%d"), "created": datetime.datetime.now().strftime("%Y-%m-%d"), "metadata": metadata, "attributes": { "pdf_page_numbers": pdf_page_spans } } return dolma_doc async def worker(args, queue, semaphore): while True: [work_hash, pdfs] = await queue.get() try: # Wait until allowed to proceed await semaphore.acquire() dolma_docs = await asyncio.gather(*[process_pdf(args, pdf) for pdf in pdfs]) dolma_docs = [doc for doc in dolma_docs if doc is not None] # Write the Dolma documents to a local temporary file in JSONL format with tempfile.NamedTemporaryFile(mode='w+', delete=False) as tf: for doc in dolma_docs: tf.write(json.dumps(doc)) tf.write('\n') tf.flush() # Define the output S3 path using the work_hash output_s3_path = os.path.join(args.workspace, 'dolma_documents', f'output_{work_hash}.jsonl') bucket, key = parse_s3_path(output_s3_path) workspace_s3.upload_file(tf.name, bucket, key) # Sum up stats and report them since the last batch finished batch_input_tokens = sum(doc["metadata"]["total-input-tokens"] for doc in dolma_docs) batch_output_tokens = sum(doc["metadata"]["total-output-tokens"] for doc in dolma_docs) # Print statistics since process start global total_input_tokens, total_output_tokens, last_batch_time total_input_tokens += batch_input_tokens total_output_tokens += batch_output_tokens total_time = time.perf_counter() - process_start_time logger.info(f"Processing speed: input {total_input_tokens / total_time:.1f} tok/sec, output {total_output_tokens / total_time:.1f} tok/sec, total {(total_input_tokens + total_output_tokens) / total_time:.1f} tok/sec") # Update last batch time last_batch_time = time.perf_counter() except Exception as e: logger.exception(f"Exception occurred while processing work_hash {work_hash}: {e}") finally: queue.task_done() async def sglang_server_task(args, semaphore): model_cache_dir = os.path.join(os.path.expanduser('~'), '.cache', 'pdelfin', 'model') # TODO cache locally #download_directory(args.model, model_cache_dir) # Check the rope config and make sure it's got the proper key with open(os.path.join(model_cache_dir, "config.json"), "r") as cfin: config_data = json.load(cfin) if "rope_type" in config_data["rope_scaling"]: del config_data["rope_scaling"]["rope_type"] config_data["rope_scaling"]["type"] = "mrope" with open(os.path.join(model_cache_dir, "config.json"), "w") as cfout: json.dump(config_data, cfout) proc = await asyncio.create_subprocess_exec( "python3", "-m", "sglang.launch_server", "--model-path", model_cache_dir, "--chat-template", args.model_chat_template, "--context-length", str(args.model_max_context), stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE, ) # Make sure we kill this subprocess on exit def _kill_proc(): proc.terminate() atexit.register(_kill_proc) last_queue_req = None # To track transitions async def process_line(line): # Parse the line and update semaphore if necessary match = re.search(r'#running-req: (\d+), #queue-req: (\d+)', line) if match: logger.info(line) running_req = int(match.group(1)) queue_req = int(match.group(2)) nonlocal last_queue_req if last_queue_req is not None and last_queue_req != 0 and queue_req == 0: # Release the semaphore when queue_req transitions from non-zero to zero if semaphore.locked(): semaphore.release() logger.info("Semaphore released, allowing a worker to proceed.") last_queue_req = queue_req async def read_stream(stream): while True: line = await stream.readline() if not line: break line = line.decode('utf-8').rstrip() await process_line(line) # Start tasks to read stdout and stderr stdout_task = asyncio.create_task(read_stream(proc.stdout)) stderr_task = asyncio.create_task(read_stream(proc.stderr)) await proc.wait() await stdout_task await stderr_task async def sglang_server_ready(): max_attempts = 300 delay_sec = 1 url = 'http://localhost:30000/v1/models' for attempt in range(1, max_attempts + 1): try: async with aiohttp.ClientSession() as session: async with session.get(url) as response: if response.status == 200: logger.info("sglang server is ready.") return else: logger.info(f"Attempt {attempt}: Unexpected status code {response.status}") except Exception as e: logger.warning(f"Attempt {attempt}: {e}") await asyncio.sleep(delay_sec) raise Exception("sglang server did not become ready after waiting.") async def main(): parser = argparse.ArgumentParser(description='Manager for running millions of PDFs through a batch inference pipeline') parser.add_argument('workspace', help='The S3 path where work will be done e.g., s3://bucket/prefix/') parser.add_argument('--pdfs', help='Path to add pdfs stored in s3 to the workspace, can be a glob path s3://bucket/prefix/*.pdf or path to file containing list of pdf paths', default=None) parser.add_argument('--target_longest_image_dim', type=int, help='Dimension on longest side to use for rendering the pdf pages', default=1024) parser.add_argument('--target_anchor_text_len', type=int, help='Maximum amount of anchor text to use (characters)', default=6000) parser.add_argument('--workspace_profile', help='S3 configuration profile for accessing the workspace', default=None) parser.add_argument('--pdf_profile', help='S3 configuration profile for accessing the raw pdf documents', default=None) parser.add_argument('--group_size', type=int, default=20, help='Number of pdfs that will be part of each work item in the work queue.') parser.add_argument('--workers', type=int, default=3, help='Number of workers to run at a time') parser.add_argument('--model', help='List of paths where you can find the model to convert this pdf. You can specify several different paths here, and the script will try to use the one which is fastest to access', default=["weka://oe-data-default/jakep/Qwen_Qwen2-VL-7B-Instruct-e4ecf8-01JAH8GMWHTJ376S2N7ETXRXH4/best_bf16/", "gs://ai2-oe-data/jakep/experiments/qwen2vl-pdf/v1/models/jakep/Qwen_Qwen2-VL-7B-Instruct-e4ecf8-01JAH8GMWHTJ376S2N7ETXRXH4/checkpoint-9500/bf16/", "s3://ai2-oe-data/jakep/experiments/qwen2vl-pdf/v1/models/jakep/Qwen_Qwen2-VL-7B-Instruct-e4ecf8-01JAH8GMWHTJ376S2N7ETXRXH4/checkpoint-9500/bf16/"]) parser.add_argument('--model_max_context', type=int, default="8192", help="Maximum context length that the model was fine tuned under") parser.add_argument('--model_chat_template', type=str, default="qwen2-vl", help="Chat template to pass to sglang server") args = parser.parse_args() if args.workspace_profile: global workspace_s3 workspace_session = boto3.Session(profile_name=args.workspace_profile) workspace_s3 = workspace_session.client("s3") if args.pdf_profile: global pdf_s3 pdf_session = boto3.Session(profile_name=args.pdf_profile) pdf_s3 = pdf_session.client("s3") check_poppler_version() logger.info(f"Starting pipeline with PID {os.getpid()}") if args.pdfs: await populate_pdf_work_queue(args) # Create a semaphore to control worker access # We only allow one worker to move forward with requests, until the server has no more requests in its queue # This lets us get full utilization by having many workers, but also to be outputting dolma docs as soon as possible # As soon as one worker is no longer saturating the gpu, the next one can start sending requests semaphore = asyncio.Semaphore(1) sglang_server = asyncio.create_task(sglang_server_task(args, semaphore)) work_queue = await load_pdf_work_queue(args) logger.info(f"Work queue prepared with {work_queue.qsize()} items") await sglang_server_ready() # Create worker tasks to process the queue concurrently. worker_tasks = [] for i in range(args.workers): task = asyncio.create_task(worker(args, work_queue, semaphore)) worker_tasks.append(task) # Wait for the queue to be fully processed await work_queue.join() # Cancel our worker tasks. for task in worker_tasks: task.cancel() # Wait until all worker tasks are cancelled. await asyncio.gather(*worker_tasks, return_exceptions=True) # Wait for server to stop sglang_server.cancel() await sglang_server if __name__ == "__main__": asyncio.run(main()) # TODO # If there is a beaker flag, then your job is to trigger this script with N replicas on beaker # If not, then your job is to do the actual work # TODO # Possible future addon, in beaker, discover other nodes on this same job # Send them a message when you take a work item off the queue