mirror of
https://github.com/allenai/olmocr.git
synced 2025-06-27 04:00:02 +00:00
779 lines
31 KiB
Python
779 lines
31 KiB
Python
#!/usr/bin/env python3
|
||
"""
|
||
Tagging pipeline for Dolma JSONL datasets.
|
||
|
||
For each .jsonl, .jsonl.gz, or .jsonl.ztd file under the dataset/documents folder,
|
||
this script issues a model prompt completion
|
||
collects the yes/no answers, and writes corresponding Dolma attributes JSONL files under
|
||
scratch/attributes/, mirroring the input structure.
|
||
"""
|
||
import argparse
|
||
import asyncio
|
||
import atexit
|
||
import gzip
|
||
import json
|
||
import logging
|
||
import os
|
||
import random
|
||
import re
|
||
import sys
|
||
import time
|
||
from typing import Optional
|
||
from urllib.parse import urlparse
|
||
|
||
import boto3
|
||
import httpx
|
||
import zstandard as zstd
|
||
from huggingface_hub import snapshot_download
|
||
from pydantic import BaseModel, Field, ValidationError
|
||
|
||
from olmocr.check import check_torch_gpu_available
|
||
from olmocr.metrics import MetricsKeeper
|
||
from olmocr.s3_utils import (
|
||
download_directory,
|
||
expand_s3_glob,
|
||
get_s3_bytes_with_backoff,
|
||
parse_s3_path,
|
||
)
|
||
from olmocr.version import VERSION
|
||
from olmocr.work_queue import LocalWorkQueue, S3WorkQueue, WorkQueue
|
||
|
||
# Initialize logger
|
||
logger = logging.getLogger(__name__)
|
||
logger.setLevel(logging.DEBUG)
|
||
logger.propagate = False
|
||
|
||
server_logger = logging.getLogger("vllm")
|
||
server_logger.propagate = False
|
||
|
||
file_handler = logging.FileHandler("olmocr-pipeline-debug.log", mode="a")
|
||
file_handler.setLevel(logging.DEBUG)
|
||
file_handler.setFormatter(logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s"))
|
||
|
||
console_handler = logging.StreamHandler()
|
||
console_handler.setLevel(logging.INFO)
|
||
console_handler.setFormatter(logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s"))
|
||
|
||
# Add handlers to the logger
|
||
logger.addHandler(file_handler)
|
||
logger.addHandler(console_handler)
|
||
server_logger.addHandler(file_handler)
|
||
|
||
|
||
# Default port; overridden by --port
|
||
SERVER_PORT = 30024
|
||
|
||
# Global variables for token statistics
|
||
metrics = MetricsKeeper(window=60 * 5)
|
||
|
||
|
||
class PIIClassification(BaseModel):
|
||
primary_language: str = Field(..., description="Primary language as a two-letter code")
|
||
document_type: str = Field(..., description="Basic summary of document type classification")
|
||
is_resume_cv: Optional[bool] = Field(..., description="True if the document is a page from a resume or cv")
|
||
contains_pii: Optional[bool] = Field(..., description="True if document contains PII")
|
||
|
||
|
||
async def _process_single_page(page_text: str) -> PIIClassification:
|
||
"""Helper function to process a single document or page."""
|
||
text = page_text
|
||
|
||
query = {
|
||
"model": "google/gemma-3-4b-it",
|
||
"messages": [
|
||
{
|
||
"role": "user",
|
||
"content": [
|
||
{
|
||
"type": "text",
|
||
"text": (
|
||
f"{text}\n\n-----------\n"
|
||
"Given the text above, determine what type of document it is, and if it's a resume/CV. answer in JSON. The format of your json object should be {'primary_language': str, 'document_type': str, 'is_resume_cv': bool, 'contains_pii': bool}"
|
||
),
|
||
}
|
||
],
|
||
}
|
||
],
|
||
"max_tokens": 100,
|
||
"temperature": 0.0,
|
||
"response_format": {"type": "json_schema", "json_schema": {"name": "PIIClassification", "schema": PIIClassification.model_json_schema()}},
|
||
}
|
||
|
||
url = f"http://localhost:{SERVER_PORT}/v1/chat/completions"
|
||
|
||
# ---------- HTTP call ---------------------------------------------------
|
||
try:
|
||
status, body = await apost(url, json_data=query)
|
||
except Exception as e:
|
||
logger.warning(f"Server network error: {e!s}")
|
||
metrics.add_metrics(server_errors=1)
|
||
return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
|
||
|
||
metrics.add_metrics(server_requests=1)
|
||
|
||
if status != 200:
|
||
logger.warning(f"Server HTTP {status}: {body[:250]!r}")
|
||
metrics.add_metrics(server_errors=1)
|
||
return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
|
||
|
||
# ---------- Parse base JSON --------------------------------------------
|
||
try:
|
||
base = json.loads(body)
|
||
except json.JSONDecodeError:
|
||
logger.warning(f"Server response is not valid JSON: {body[:250]!r}")
|
||
metrics.add_metrics(server_errors=1)
|
||
return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
|
||
|
||
# Token accounting if available
|
||
if "usage" in base:
|
||
metrics.add_metrics(
|
||
server_input_tokens=base["usage"].get("prompt_tokens", 0),
|
||
server_output_tokens=base["usage"].get("completion_tokens", 0),
|
||
)
|
||
|
||
# ---------- Extract the model message ----------------------------------
|
||
try:
|
||
content = base["choices"][0]["message"].get("content")
|
||
except (KeyError, IndexError, AttributeError) as e:
|
||
logger.warning(f"Missing fields in Server response: {e!s}")
|
||
metrics.add_metrics(server_errors=1)
|
||
return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
|
||
|
||
if not isinstance(content, str):
|
||
logger.warning("Server `content` is not a string; treating as error.")
|
||
metrics.add_metrics(server_errors=1)
|
||
return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
|
||
|
||
try:
|
||
pii_classification: PIIClassification = PIIClassification.model_validate_json(content)
|
||
return pii_classification
|
||
except ValidationError as e:
|
||
logger.warning(f"Unable to parse pii classification object: {e!s}")
|
||
metrics.add_metrics(server_errors=1)
|
||
return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
|
||
|
||
|
||
# Manual simple implementation of HTTP Post
|
||
# It feels strange perhaps, but httpx and aiohttp are very complex beasts
|
||
# Ex. the sessionpool in httpcore has 4 different locks in it, and I've noticed
|
||
# that at the scale of 100M+ requests, that they deadlock in different strange ways
|
||
async def apost(url, json_data):
|
||
parsed_url = urlparse(url)
|
||
host = parsed_url.hostname
|
||
port = parsed_url.port or 80
|
||
path = parsed_url.path or "/"
|
||
|
||
writer = None
|
||
try:
|
||
reader, writer = await asyncio.open_connection(host, port)
|
||
|
||
json_payload = json.dumps(json_data)
|
||
request = (
|
||
f"POST {path} HTTP/1.1\r\n"
|
||
f"Host: {host}\r\n"
|
||
f"Content-Type: application/json\r\n"
|
||
f"Content-Length: {len(json_payload)}\r\n"
|
||
f"Connection: close\r\n\r\n"
|
||
f"{json_payload}"
|
||
)
|
||
writer.write(request.encode())
|
||
await writer.drain()
|
||
|
||
# Read status line
|
||
status_line = await reader.readline()
|
||
if not status_line:
|
||
raise ConnectionError("No response from server")
|
||
status_parts = status_line.decode().strip().split(" ", 2)
|
||
if len(status_parts) < 2:
|
||
raise ValueError(f"Malformed status line: {status_line.decode().strip()}")
|
||
status_code = int(status_parts[1])
|
||
|
||
# Read headers
|
||
headers = {}
|
||
while True:
|
||
line = await reader.readline()
|
||
if line in (b"\r\n", b"\n", b""):
|
||
break
|
||
key, _, value = line.decode().partition(":")
|
||
headers[key.strip().lower()] = value.strip()
|
||
|
||
# Read response body
|
||
if "content-length" in headers:
|
||
body_length = int(headers["content-length"])
|
||
response_body = await reader.readexactly(body_length)
|
||
else:
|
||
raise ConnectionError("Anything other than fixed content length responses are not implemented yet")
|
||
|
||
return status_code, response_body
|
||
except Exception as e:
|
||
# Pass through errors
|
||
raise e
|
||
finally:
|
||
# But just make sure to close the socket on your way out
|
||
if writer is not None:
|
||
try:
|
||
writer.close()
|
||
await writer.wait_closed()
|
||
except:
|
||
pass
|
||
|
||
|
||
async def process_dolma_document(args, dolma_doc, sem):
|
||
"""
|
||
Query model to detect PII, enforcing a JSON schema.
|
||
|
||
Resilient to:
|
||
• Transport / HTTP errors
|
||
• Missing or malformed fields in the response
|
||
• Non-string or None `content`
|
||
• Bad JSON in the model's answer
|
||
|
||
Always returns: (doc_id, contains_pii: bool, text_length: int)
|
||
"""
|
||
doc_id = dolma_doc.get("id")
|
||
text = dolma_doc.get("text", "") or ""
|
||
|
||
language_key_name = f"{args.model.replace('/', '_')}_language"
|
||
resume_cv_key_name = f"{args.model.replace('/', '_')}_is_resume_cv"
|
||
|
||
result_attributes = {resume_cv_key_name: [], language_key_name: []}
|
||
|
||
# If pdf_page_numbers is present, split the text and process each page separately
|
||
if "attributes" in dolma_doc and "pdf_page_numbers" in dolma_doc["attributes"]:
|
||
page_numbers = dolma_doc["attributes"]["pdf_page_numbers"]
|
||
|
||
logger.info(f"Document {doc_id} has {len(page_numbers)} pages, processing each individually")
|
||
|
||
# Filter pages down to actual real content
|
||
selected_page_numbers = [tuple(p) for p in page_numbers if p[0] < p[1]]
|
||
first_page_number = selected_page_numbers[0]
|
||
|
||
# Sample 3 pages max per document, but always include the first page, it's a good signal for CV classification
|
||
random.shuffle(selected_page_numbers)
|
||
selected_page_numbers = selected_page_numbers[:3]
|
||
|
||
if first_page_number not in selected_page_numbers:
|
||
selected_page_numbers[0] = first_page_number
|
||
|
||
for start_pos, end_pos, page_num in page_numbers:
|
||
if (start_pos, end_pos, page_num) in selected_page_numbers:
|
||
page_text = text[start_pos:end_pos]
|
||
|
||
# Process each page with the semaphore to limit concurrent requests
|
||
async with sem:
|
||
pii_class = await _process_single_page(page_text)
|
||
|
||
result_attributes[resume_cv_key_name].append([start_pos, end_pos, pii_class.is_resume_cv])
|
||
result_attributes[language_key_name].append([start_pos, end_pos, pii_class.primary_language])
|
||
else:
|
||
result_attributes[resume_cv_key_name].append([start_pos, end_pos, None])
|
||
result_attributes[language_key_name].append([start_pos, end_pos, None])
|
||
|
||
return result_attributes
|
||
else:
|
||
raise NotImplementedError("Missing code here, expecting this to be dolma docs made by olmocr....")
|
||
|
||
|
||
async def process_file(args, worker_id: int, file_uri: str):
|
||
"""
|
||
Download a JSONL file, query model per record, and collect attributes.
|
||
"""
|
||
# Fetch raw bytes (S3 or local)
|
||
if file_uri.startswith("s3://"):
|
||
raw = await asyncio.to_thread(get_s3_bytes_with_backoff, dataset_s3, file_uri)
|
||
else:
|
||
with open(file_uri, "rb") as f:
|
||
raw = f.read()
|
||
|
||
# Decompress if needed
|
||
if file_uri.endswith(".gz"):
|
||
file_bytes = gzip.decompress(raw)
|
||
elif file_uri.endswith(".ztd") or file_uri.endswith(".zst") or file_uri.endswith(".zstd"):
|
||
dctx = zstd.ZstdDecompressor()
|
||
file_bytes = dctx.decompress(raw, max_output_size=1_000_000_000)
|
||
else:
|
||
file_bytes = raw
|
||
|
||
lines = file_bytes.decode("utf-8").splitlines()
|
||
page_tasks = {}
|
||
|
||
# Send all records in parallel, max N queued at a time
|
||
sem = asyncio.Semaphore(args.parallel_requests)
|
||
|
||
async with asyncio.TaskGroup() as tg:
|
||
for line in lines:
|
||
dolma_doc = json.loads(line)
|
||
task = tg.create_task(process_dolma_document(args, dolma_doc, sem))
|
||
page_tasks[dolma_doc["id"]] = (task, dolma_doc)
|
||
|
||
logger.info(f"Finished taskgroup with {len(page_tasks)} items for {file_uri}")
|
||
|
||
# Collect results and build attributes
|
||
attributes = []
|
||
for doc_id, (task, dolma_doc) in page_tasks.items():
|
||
doc_attributes = task.result()
|
||
|
||
attributes.append({"id": doc_id, "attributes": doc_attributes})
|
||
|
||
return attributes
|
||
|
||
|
||
async def worker(args, work_queue: WorkQueue, semaphore: asyncio.Semaphore, worker_id: int):
|
||
"""
|
||
Pop work-items off the queue, run PII tagging, write the attributes file
|
||
next to the dataset (keeping the original compression), mark the item done,
|
||
and drop an empty sentinel file in <workspace>/results/.
|
||
"""
|
||
while True:
|
||
await semaphore.acquire()
|
||
work_item = await work_queue.get_work()
|
||
|
||
if work_item is None:
|
||
logger.info(f"Worker {worker_id} exiting – queue empty")
|
||
semaphore.release()
|
||
break
|
||
|
||
file_uri = work_item.work_paths[0]
|
||
logger.info(f"Worker {worker_id} processing {file_uri}")
|
||
|
||
try:
|
||
# ------------------------------------------------------------------
|
||
# Run the per-file pipeline
|
||
# ------------------------------------------------------------------
|
||
attributes = await process_file(args, worker_id, file_uri)
|
||
|
||
# 1. Build the relative path that mirrors documents/…
|
||
if file_uri.startswith("s3://"):
|
||
_, key = parse_s3_path(file_uri)
|
||
_, docs_prefix = parse_s3_path(args.dataset)
|
||
rel_path = key[len(os.path.join(docs_prefix, "documents/")) :]
|
||
else:
|
||
docs_root = os.path.join(args.dataset, "documents")
|
||
rel_path = os.path.relpath(file_uri, docs_root)
|
||
|
||
out_rel = os.path.join("attributes", args.attribute_name, rel_path)
|
||
out_jsonl = "\n".join(json.dumps(x) for x in attributes) + "\n"
|
||
|
||
# 2. Preserve compression type
|
||
if rel_path.endswith(".gz"):
|
||
payload = gzip.compress(out_jsonl.encode("utf-8"))
|
||
elif rel_path.endswith((".zst", ".ztd")):
|
||
payload = zstd.ZstdCompressor().compress(out_jsonl.encode("utf-8"))
|
||
else:
|
||
payload = out_jsonl.encode("utf-8")
|
||
|
||
# 3. Write to args.dataset (local or S3)
|
||
if args.dataset.startswith("s3://"):
|
||
bucket, prefix = parse_s3_path(args.dataset)
|
||
key = os.path.join(prefix, out_rel)
|
||
workspace_s3.put_object(Bucket=bucket, Key=key, Body=payload)
|
||
else:
|
||
out_path = os.path.join(args.dataset, out_rel)
|
||
os.makedirs(os.path.dirname(out_path), exist_ok=True)
|
||
with open(out_path, "wb") as fh:
|
||
fh.write(payload)
|
||
|
||
# 4. Mark queue item done
|
||
await work_queue.mark_done(work_item)
|
||
|
||
# 5. Drop empty sentinel file in <workspace>/results/
|
||
sentinel_rel = os.path.join("results", f"output_{work_item.hash}.jsonl")
|
||
if args.scratch.startswith("s3://"):
|
||
bkt, pfx = parse_s3_path(args.scratch)
|
||
key = os.path.join(pfx, sentinel_rel)
|
||
workspace_s3.put_object(Bucket=bkt, Key=key, Body=b"")
|
||
else:
|
||
sentinel_path = os.path.join(args.scratch, sentinel_rel)
|
||
os.makedirs(os.path.dirname(sentinel_path), exist_ok=True)
|
||
open(sentinel_path, "w").close()
|
||
|
||
except Exception as exc:
|
||
logger.exception(f"Worker {worker_id} exception: {exc!s}")
|
||
finally:
|
||
semaphore.release()
|
||
|
||
|
||
async def server_task(model_name_or_path, args, semaphore):
|
||
# Check GPU memory, lower mem devices need a bit less KV cache space because the VLM takes additional memory
|
||
# mem_fraction_arg = ["--mem-fraction-static", "0.80"]
|
||
|
||
cmd = [
|
||
"vllm",
|
||
"serve",
|
||
model_name_or_path,
|
||
"--port",
|
||
str(SERVER_PORT),
|
||
"--uvicorn-log-level",
|
||
"warning",
|
||
"--disable-log-requests",
|
||
]
|
||
|
||
proc = await asyncio.create_subprocess_exec(
|
||
*cmd,
|
||
stdout=asyncio.subprocess.PIPE,
|
||
stderr=asyncio.subprocess.PIPE,
|
||
)
|
||
|
||
# Ensure the subprocess is terminated on exit
|
||
def _kill_proc():
|
||
proc.terminate()
|
||
|
||
atexit.register(_kill_proc)
|
||
|
||
# Shared variables between tasks
|
||
last_running_req, last_queue_req = 0, 0
|
||
server_printed_ready_message = False
|
||
last_semaphore_release = time.time()
|
||
|
||
async def process_line(line):
|
||
nonlocal last_running_req, last_queue_req, last_semaphore_release, server_printed_ready_message
|
||
server_logger.info(line)
|
||
|
||
# if the server hasn't initialized yet, log all the lines to the main logger also, so that the user
|
||
# can see any warnings/errors more easily
|
||
if not server_printed_ready_message:
|
||
logger.info(line)
|
||
|
||
if not server_printed_ready_message and "The server is fired up and ready to roll!" in line:
|
||
server_printed_ready_message = True
|
||
last_semaphore_release = time.time()
|
||
|
||
match = re.search(r"Running: (\d+) reqs", line)
|
||
if match:
|
||
last_running_req = int(match.group(1))
|
||
|
||
match = re.search(r"Waiting: (\d+) reqs", line)
|
||
if match:
|
||
last_queue_req = int(match.group(1))
|
||
logger.info(f"running req: {last_running_req} queue req: {last_queue_req}")
|
||
|
||
async def read_stream(stream):
|
||
while True:
|
||
line = await stream.readline()
|
||
if not line:
|
||
break
|
||
try:
|
||
line = line.decode("utf-8").rstrip()
|
||
await process_line(line)
|
||
except Exception as ex:
|
||
logger.warning(f"Got {ex} when reading log line from inference server, skipping")
|
||
|
||
async def timeout_task():
|
||
nonlocal last_running_req, last_queue_req, last_semaphore_release
|
||
try:
|
||
while True:
|
||
await asyncio.sleep(1)
|
||
if server_printed_ready_message and last_queue_req == 0 and time.time() - last_semaphore_release > 30 and semaphore.locked():
|
||
semaphore.release()
|
||
last_semaphore_release = time.time()
|
||
logger.info("Semaphore released, allowing a worker to proceed.")
|
||
except asyncio.CancelledError:
|
||
pass # Clean up if the task is cancelled
|
||
|
||
# Start tasks to read stdout, stderr, and handle timeout logic
|
||
stdout_task = asyncio.create_task(read_stream(proc.stdout))
|
||
stderr_task = asyncio.create_task(read_stream(proc.stderr))
|
||
timeout_task = asyncio.create_task(timeout_task())
|
||
|
||
try:
|
||
await proc.wait()
|
||
except asyncio.CancelledError:
|
||
logger.info("Got cancellation request for server")
|
||
proc.terminate()
|
||
raise
|
||
|
||
timeout_task.cancel()
|
||
await asyncio.gather(stdout_task, stderr_task, timeout_task, return_exceptions=True)
|
||
|
||
|
||
async def server_host(model_name_or_path, args, semaphore):
|
||
MAX_RETRIES = 5
|
||
retry = 0
|
||
|
||
while retry < MAX_RETRIES:
|
||
await server_task(model_name_or_path, args, semaphore)
|
||
logger.warning("Server task ended")
|
||
retry += 1
|
||
|
||
if retry >= MAX_RETRIES:
|
||
logger.error(f"Ended up starting the server more than {retry} times, cancelling pipeline")
|
||
logger.error("")
|
||
logger.error("Please make sure vllm is installed according to the latest instructions for 0.8.4")
|
||
sys.exit(1)
|
||
|
||
|
||
async def check_server_ready():
|
||
max_attempts = 300
|
||
delay_sec = 1
|
||
url = f"http://localhost:{SERVER_PORT}/v1/models"
|
||
|
||
for attempt in range(1, max_attempts + 1):
|
||
try:
|
||
async with httpx.AsyncClient() as session:
|
||
response = await session.get(url)
|
||
|
||
if response.status_code == 200:
|
||
logger.info("server is ready.")
|
||
return
|
||
else:
|
||
logger.info(f"Attempt {attempt}: Unexpected status code {response.status_code}")
|
||
except Exception:
|
||
logger.warning(f"Attempt {attempt}: Please wait for model server to become ready...")
|
||
|
||
await asyncio.sleep(delay_sec)
|
||
|
||
raise Exception("model server did not become ready after waiting.")
|
||
|
||
|
||
async def download_model(model_name_or_path: str):
|
||
if model_name_or_path.startswith("s3://") or model_name_or_path.startswith("gs://") or model_name_or_path.startswith("weka://"):
|
||
logger.info(f"Downloading model directory from '{model_name_or_path}'")
|
||
model_cache_dir = os.path.join(os.path.expanduser("~"), ".cache", "olmocr", "model")
|
||
download_directory([model_name_or_path], model_cache_dir)
|
||
return model_cache_dir
|
||
elif os.path.isabs(model_name_or_path) and os.path.isdir(model_name_or_path):
|
||
logger.info(f"Using local model path at '{model_name_or_path}'")
|
||
return model_name_or_path
|
||
else:
|
||
logger.info(f"Downloading model with hugging face '{model_name_or_path}'")
|
||
snapshot_download(repo_id=model_name_or_path)
|
||
return model_name_or_path
|
||
|
||
|
||
async def metrics_reporter(work_queue):
|
||
while True:
|
||
# Leading newlines preserve table formatting in logs
|
||
logger.info(f"Queue remaining: {work_queue.size}")
|
||
logger.info("\n" + str(metrics))
|
||
await asyncio.sleep(10)
|
||
|
||
|
||
def submit_beaker_job(args):
|
||
from beaker import ( # type: ignore
|
||
Beaker,
|
||
Constraints,
|
||
EnvVar,
|
||
ExperimentSpec,
|
||
ImageSource,
|
||
Priority,
|
||
ResultSpec,
|
||
SecretNotFound,
|
||
TaskContext,
|
||
TaskResources,
|
||
TaskSpec,
|
||
)
|
||
|
||
b = Beaker.from_env(default_workspace=args.beaker_workspace)
|
||
account = b.account.whoami()
|
||
owner = account.name
|
||
beaker_image = f"jakep/olmocr-tagging-{VERSION}"
|
||
|
||
task_name = f"olmocr-{os.path.basename(args.dataset.rstrip('/'))}"
|
||
|
||
# Take out --beaker flag so the workers will just run things
|
||
args_list = [arg for arg in sys.argv[1:] if arg != "--beaker"]
|
||
|
||
# Take out the --pdfs [arg] or --pdfs=[arg], since the queue is populated locally
|
||
args_list = [arg for i, arg in enumerate(args_list) if not (arg.startswith("--pdfs") or (i > 0 and args_list[i - 1] == "--pdfs"))]
|
||
|
||
try:
|
||
b.secret.get(f"{owner}-WEKA_ACCESS_KEY_ID", args.beaker_workspace)
|
||
b.secret.get(f"{owner}-WEKA_SECRET_ACCESS_KEY", args.beaker_workspace)
|
||
b.secret.get(f"{owner}-AWS_CREDENTIALS_FILE", args.beaker_workspace)
|
||
except SecretNotFound:
|
||
print(
|
||
f"Expected beaker secrets for accessing Weka and S3 are not found. Are you okay to write those to your beaker workspace {args.beaker_workspace}? [y/n]"
|
||
)
|
||
|
||
if input().strip().lower() != "y":
|
||
print("Exiting...")
|
||
sys.exit(1)
|
||
|
||
b.secret.write(f"{owner}-WEKA_ACCESS_KEY_ID", os.environ.get("WEKA_ACCESS_KEY_ID", ""), args.beaker_workspace)
|
||
b.secret.write(f"{owner}-WEKA_SECRET_ACCESS_KEY", os.environ.get("WEKA_SECRET_ACCESS_KEY", ""), args.beaker_workspace)
|
||
b.secret.write(
|
||
f"{owner}-AWS_CREDENTIALS_FILE",
|
||
open(os.path.join(os.path.expanduser("~"), ".aws", "credentials")).read(),
|
||
args.beaker_workspace,
|
||
)
|
||
|
||
env_var_secrets = [
|
||
EnvVar(name="WEKA_ACCESS_KEY_ID", secret=f"{owner}-WEKA_ACCESS_KEY_ID"),
|
||
EnvVar(name="WEKA_SECRET_ACCESS_KEY", secret=f"{owner}-WEKA_SECRET_ACCESS_KEY"),
|
||
EnvVar(name="AWS_CREDENTIALS_FILE", secret=f"{owner}-AWS_CREDENTIALS_FILE"),
|
||
]
|
||
|
||
try:
|
||
b.secret.get("OLMOCR_PREVIEW_HF_TOKEN", args.beaker_workspace)
|
||
env_var_secrets.append(EnvVar(name="HF_TOKEN", secret="OLMOCR_PREVIEW_HF_TOKEN"))
|
||
except SecretNotFound:
|
||
pass
|
||
|
||
try:
|
||
b.secret.get("OE_DATA_GCS_SA_KEY", args.beaker_workspace)
|
||
env_var_secrets.append(EnvVar(name="GOOGLE_APPLICATION_CREDENTIALS_FILE", secret="OE_DATA_GCS_SA_KEY"))
|
||
except SecretNotFound:
|
||
print("Input the olmo-gcs SA key if you would like to load weights from gcs (end with a double newline):")
|
||
lines = []
|
||
prev_empty = False
|
||
for line in iter(input, None):
|
||
if not line and prev_empty:
|
||
break
|
||
prev_empty = not line
|
||
lines.append(line)
|
||
gcs_sa_key = "\n".join(lines[:-1]).strip() # Remove the last empty line
|
||
if gcs_sa_key:
|
||
b.secret.write("OE_DATA_GCS_SA_KEY", gcs_sa_key, args.beaker_workspace)
|
||
env_var_secrets.append(EnvVar(name="GOOGLE_APPLICATION_CREDENTIALS_FILE", secret="OE_DATA_GCS_SA_KEY"))
|
||
|
||
# Create the experiment spec
|
||
experiment_spec = ExperimentSpec(
|
||
budget="ai2/oe-data",
|
||
description=task_name,
|
||
tasks=[
|
||
TaskSpec(
|
||
name=task_name,
|
||
propagate_failure=False,
|
||
propagate_preemption=False,
|
||
replicas=args.beaker_gpus,
|
||
context=TaskContext(
|
||
priority=Priority(args.beaker_priority),
|
||
preemptible=True,
|
||
),
|
||
image=ImageSource(beaker=beaker_image),
|
||
command=["python", "scripts/tagging_pipeline.py"] + args_list,
|
||
env_vars=[EnvVar(name="BEAKER_JOB_NAME", value=task_name), EnvVar(name="OWNER", value=owner)] + env_var_secrets,
|
||
resources=TaskResources(gpu_count=1),
|
||
constraints=Constraints(cluster=args.beaker_cluster if isinstance(args.beaker_cluster, list) else [args.beaker_cluster]),
|
||
result=ResultSpec(path="/noop-results"),
|
||
)
|
||
],
|
||
)
|
||
|
||
experiment_data = b.experiment.create(spec=experiment_spec, workspace=args.beaker_workspace)
|
||
|
||
print(f"Experiment URL: https://beaker.org/ex/{experiment_data.id}")
|
||
|
||
|
||
async def main():
|
||
parser = argparse.ArgumentParser(description="Tagging pipeline for Dolma JSONL dataset")
|
||
parser.add_argument("dataset", help="Dolma dataset root (local or s3://) with documents/ folder")
|
||
parser.add_argument("scratch", help="Scratch workspace (local dir or s3://)")
|
||
parser.add_argument("--workers", type=int, default=4, help="Number of concurrent workers")
|
||
parser.add_argument("--parallel_requests", type=int, default=800, help="Max number of parallel requests to send to model")
|
||
parser.add_argument("--model", default="google/gemma-3-4b-it", help="Model path or name, hugging face or local path format")
|
||
parser.add_argument("--attribute_name", default="model_pii_tagging", help="Path to use for attribute naming")
|
||
|
||
# Beaker/job running stuff
|
||
parser.add_argument("--beaker", action="store_true", help="Submit this job to beaker instead of running locally")
|
||
parser.add_argument("--beaker_workspace", help="Beaker workspace to submit to", default="ai2/olmocr")
|
||
parser.add_argument(
|
||
"--beaker_cluster",
|
||
help="Beaker clusters you want to run on",
|
||
default=["ai2/jupiter-cirrascale-2", "ai2/ceres-cirrascale", "ai2/neptune-cirrascale", "ai2/saturn-cirrascale", "ai2/augusta-google-1"],
|
||
)
|
||
parser.add_argument("--beaker_gpus", type=int, default=1, help="Number of gpu replicas to run")
|
||
parser.add_argument("--beaker_priority", type=str, default="normal", help="Beaker priority level for the job")
|
||
|
||
parser.add_argument("--port", type=int, default=30024, help="Port for Model server")
|
||
args = parser.parse_args()
|
||
|
||
global SERVER_PORT, workspace_s3, dataset_s3
|
||
SERVER_PORT = args.port
|
||
workspace_s3 = boto3.client("s3")
|
||
dataset_s3 = boto3.client("s3")
|
||
|
||
# setup the job to work in beaker environment, load secrets, adjust logging, etc.
|
||
if "BEAKER_JOB_ID" in os.environ:
|
||
server_logger.addHandler(console_handler)
|
||
if "AWS_CREDENTIALS_FILE" in os.environ:
|
||
cred_path = os.path.join(os.path.expanduser("~"), ".aws", "credentials")
|
||
os.makedirs(os.path.dirname(cred_path), exist_ok=True)
|
||
with open(cred_path, "w") as f:
|
||
f.write(os.environ.get("AWS_CREDENTIALS_FILE"))
|
||
if "GOOGLE_APPLICATION_CREDENTIALS" in os.environ:
|
||
cred_path = os.path.join(os.path.expanduser("~"), ".gcs", "credentials")
|
||
os.makedirs(os.path.dirname(cred_path), exist_ok=True)
|
||
with open(cred_path, "w") as f:
|
||
f.write(os.environ.get("GOOGLE_APPLICATION_CREDENTIALS_FILE"))
|
||
os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = cred_path
|
||
workspace_s3 = boto3.client("s3")
|
||
dataset_s3 = boto3.client("s3")
|
||
|
||
# Wait a little bit so that not all beaker jobs in a task start at the same time and download the model at the same time
|
||
replica_count = int(os.environ.get("BEAKER_REPLICA_COUNT", "1"))
|
||
interval = 10 if (replica_count - 1) * 10 <= 240 else 240 / max(1, replica_count - 1)
|
||
sleep_time = int(int(os.environ.get("BEAKER_REPLICA_RANK", "0")) * interval)
|
||
logger.info(f"Beaker job sleeping for {sleep_time} seconds to stagger model downloads")
|
||
await asyncio.sleep(sleep_time)
|
||
|
||
# Initialize work queue
|
||
if args.scratch.startswith("s3://"):
|
||
work_queue = S3WorkQueue(workspace_s3, args.scratch)
|
||
else:
|
||
work_queue = LocalWorkQueue(args.scratch)
|
||
|
||
# Discover input files
|
||
files = set()
|
||
if args.dataset.startswith("s3://"):
|
||
pattern = args.dataset.rstrip("/") + "/documents/*.jsonl*"
|
||
matched = expand_s3_glob(dataset_s3, pattern)
|
||
files = set(matched.keys())
|
||
else:
|
||
docs_dir = os.path.join(args.dataset, "documents")
|
||
for root, _, fns in os.walk(docs_dir):
|
||
for fn in fns:
|
||
if fn.endswith((".jsonl", ".jsonl.gz", ".jsonl.ztd")):
|
||
files.add(os.path.join(root, fn))
|
||
|
||
# Populate the work queue if needed
|
||
await work_queue.populate_queue(list(files), items_per_group=1)
|
||
|
||
if args.beaker:
|
||
submit_beaker_job(args)
|
||
return
|
||
|
||
# If you get this far, then you are doing inference and need a GPU
|
||
check_torch_gpu_available()
|
||
|
||
logger.info(f"Starting pipeline with PID {os.getpid()}")
|
||
|
||
# Download the model before you do anything else
|
||
model_name_or_path = await download_model(args.model)
|
||
|
||
# Initialize the work queue
|
||
qsize = await work_queue.initialize_queue()
|
||
|
||
if qsize == 0:
|
||
logger.info("No work to do, exiting")
|
||
return
|
||
|
||
# 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)
|
||
|
||
model_server = asyncio.create_task(server_host(model_name_or_path, args, semaphore))
|
||
|
||
await check_server_ready()
|
||
|
||
metrics_task = asyncio.create_task(metrics_reporter(work_queue))
|
||
|
||
# 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_id=i))
|
||
worker_tasks.append(task)
|
||
|
||
# Wait for all worker tasks to finish
|
||
await asyncio.gather(*worker_tasks)
|
||
|
||
model_server.cancel()
|
||
metrics_task.cancel()
|
||
logger.info("Work done")
|
||
|
||
|
||
if __name__ == "__main__":
|
||
asyncio.run(main())
|