feat: add QLoRA PDF pipeline and Gitea CI workflow
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- qlora_pdf_pipeline.py: 6-step QLoRA fine-tuning pipeline
  (S3 PDFs → prepare data → train → evaluate → push to Gitea → MLflow)
- .gitea/workflows/compile-upload.yaml: auto-compile and upload
  all pipelines to Kubeflow on push, with ntfy notifications
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2026-02-13 10:28:53 -05:00
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#!/usr/bin/env python3
"""
QLoRA Fine-Tuning Pipeline Kubeflow Pipelines SDK
Fetches PDFs from a Quobjects S3 bucket, extracts instruction-tuning
data, trains a QLoRA adapter on the Llama 3.1 70B base model using
the Strix Halo's 128 GB unified memory, evaluates it, and pushes the
adapter weights to a Gitea repository.
Usage:
pip install kfp==2.12.1
python qlora_pdf_pipeline.py
# Upload qlora_pdf_pipeline.yaml to Kubeflow Pipelines UI
Prerequisites in-cluster:
- Secret mlpipeline-minio-artifact (namespace kubeflow) for S3 creds
- Secret gitea-admin-secret (namespace gitea) for Gitea push
- Node khelben with amd.com/gpu and the ROCm PyTorch image
"""
from kfp import compiler, dsl
from typing import NamedTuple
# ──────────────────────────────────────────────────────────────
# 1. Fetch PDFs from Quobjects S3
# ──────────────────────────────────────────────────────────────
@dsl.component(
base_image="python:3.13-slim",
packages_to_install=["boto3"],
)
def fetch_pdfs_from_s3(
s3_endpoint: str,
s3_bucket: str,
s3_prefix: str,
aws_access_key_id: str,
aws_secret_access_key: str,
) -> NamedTuple("PDFOutput", [("pdf_dir", str), ("num_files", int)]):
"""Download all PDFs from a Quobjects S3 bucket."""
import os
import boto3
from botocore.client import Config
out_dir = "/tmp/pdfs"
os.makedirs(out_dir, exist_ok=True)
client = boto3.client(
"s3",
endpoint_url=f"http://{s3_endpoint}",
aws_access_key_id=aws_access_key_id,
aws_secret_access_key=aws_secret_access_key,
region_name="us-east-1",
config=Config(signature_version="s3v4"),
)
paginator = client.get_paginator("list_objects_v2")
count = 0
for page in paginator.paginate(Bucket=s3_bucket, Prefix=s3_prefix):
for obj in page.get("Contents", []):
key = obj["Key"]
if key.lower().endswith(".pdf"):
local_path = os.path.join(out_dir, os.path.basename(key))
print(f"Downloading: {key}{local_path}")
client.download_file(s3_bucket, key, local_path)
count += 1
print(f"Downloaded {count} PDFs to {out_dir}")
from collections import namedtuple
return namedtuple("PDFOutput", ["pdf_dir", "num_files"])(
pdf_dir=out_dir, num_files=count
)
# ──────────────────────────────────────────────────────────────
# 2. Extract text from PDFs → instruction-tuning dataset
# ──────────────────────────────────────────────────────────────
@dsl.component(
base_image="python:3.13-slim",
packages_to_install=["pymupdf"],
)
def prepare_training_data(
pdf_dir: str,
max_seq_length: int = 2048,
chunk_size: int = 512,
chunk_overlap: int = 64,
) -> NamedTuple("DataOutput", [("dataset_path", str), ("num_train", int), ("num_val", int)]):
"""Extract text from PDFs, chunk it, and format as instruction-tuning pairs."""
import json
import os
import fitz # PyMuPDF
out_dir = "/tmp/training_data"
os.makedirs(out_dir, exist_ok=True)
# 1. Extract text from all PDFs
all_chunks: list[dict] = []
for fname in sorted(os.listdir(pdf_dir)):
if not fname.lower().endswith(".pdf"):
continue
path = os.path.join(pdf_dir, fname)
print(f"Extracting: {fname}")
try:
doc = fitz.open(path)
full_text = ""
for page in doc:
full_text += page.get_text() + "\n"
doc.close()
except Exception as e:
print(f" SKIP ({e})")
continue
# 2. Chunk text with overlap
words = full_text.split()
for i in range(0, len(words), chunk_size - chunk_overlap):
chunk_words = words[i : i + chunk_size]
if len(chunk_words) < 50:
continue # skip tiny trailing chunks
chunk_text = " ".join(chunk_words)
all_chunks.append({"text": chunk_text, "source": fname})
print(f"Total chunks: {len(all_chunks)}")
if not all_chunks:
raise ValueError("No text extracted from PDFs — check your bucket")
# 3. Format as Llama 3 chat training pairs
# We create self-supervised pairs: model learns to continue/explain the content
samples = []
for chunk in all_chunks:
text = chunk["text"]
source = chunk["source"]
# Split chunk roughly in half for input/output
words = text.split()
mid = len(words) // 2
context = " ".join(words[:mid])
continuation = " ".join(words[mid:])
samples.append(
{
"messages": [
{
"role": "system",
"content": (
"You are a knowledgeable assistant. "
"Continue the information accurately and coherently."
),
},
{
"role": "user",
"content": f"Continue the following passage from {source}:\n\n{context}",
},
{"role": "assistant", "content": continuation},
]
}
)
# 4. Train/val split (90/10)
import random
random.seed(42)
random.shuffle(samples)
split = int(len(samples) * 0.9)
train = samples[:split]
val = samples[split:]
train_path = os.path.join(out_dir, "train.json")
val_path = os.path.join(out_dir, "val.json")
with open(train_path, "w") as f:
json.dump(train, f)
with open(val_path, "w") as f:
json.dump(val, f)
print(f"Train: {len(train)} samples, Val: {len(val)} samples")
from collections import namedtuple
return namedtuple("DataOutput", ["dataset_path", "num_train", "num_val"])(
dataset_path=out_dir, num_train=len(train), num_val=len(val)
)
# ──────────────────────────────────────────────────────────────
# 3. QLoRA training on Strix Halo (ROCm, 128 GB unified)
# ──────────────────────────────────────────────────────────────
@dsl.component(
# Use a ROCm base image with PyTorch + PEFT pre-installed.
# Falls back to pip-installing if not present.
base_image="python:3.13-slim",
packages_to_install=[
"torch",
"transformers",
"peft",
"datasets",
"accelerate",
"bitsandbytes",
"scipy",
"trl",
],
)
def train_qlora(
dataset_path: str,
base_model: str,
learning_rate: float = 2e-4,
num_epochs: int = 3,
batch_size: int = 2,
gradient_accumulation_steps: int = 8,
max_seq_length: int = 2048,
lora_r: int = 64,
lora_alpha: int = 16,
lora_dropout: float = 0.05,
) -> NamedTuple(
"TrainOutput",
[("adapter_path", str), ("train_loss", float), ("eval_loss", float)],
):
"""QLoRA fine-tune Llama 3.1 70B with 4-bit NF4 quantization."""
import json
import os
import torch
from datasets import Dataset
from peft import LoraConfig, get_peft_model, prepare_model_for_kbit_training
from transformers import (
AutoModelForCausalLM,
AutoTokenizer,
BitsAndBytesConfig,
TrainingArguments,
)
from trl import SFTTrainer
output_dir = "/tmp/qlora_output"
os.makedirs(output_dir, exist_ok=True)
# ── Load data ───────────────────────────────────────────
with open(os.path.join(dataset_path, "train.json")) as f:
train_data = json.load(f)
with open(os.path.join(dataset_path, "val.json")) as f:
val_data = json.load(f)
print(f"Loaded {len(train_data)} train / {len(val_data)} val samples")
# ── Tokenizer ───────────────────────────────────────────
print(f"Loading tokenizer: {base_model}")
tokenizer = AutoTokenizer.from_pretrained(base_model, trust_remote_code=True)
if tokenizer.pad_token is None:
tokenizer.pad_token = tokenizer.eos_token
tokenizer.padding_side = "right"
# ── Format with chat template ───────────────────────────
def format_chat(sample):
return {"text": tokenizer.apply_chat_template(
sample["messages"], tokenize=False, add_generation_prompt=False
)}
train_ds = Dataset.from_list(train_data).map(format_chat)
val_ds = Dataset.from_list(val_data).map(format_chat)
# ── 4-bit quantisation ──────────────────────────────────
bnb_config = BitsAndBytesConfig(
load_in_4bit=True,
bnb_4bit_quant_type="nf4",
bnb_4bit_compute_dtype=torch.bfloat16,
bnb_4bit_use_double_quant=True,
)
print(f"Loading model: {base_model} (4-bit NF4)")
model = AutoModelForCausalLM.from_pretrained(
base_model,
quantization_config=bnb_config,
device_map="auto",
trust_remote_code=True,
torch_dtype=torch.bfloat16,
)
model = prepare_model_for_kbit_training(model)
# ── LoRA config ─────────────────────────────────────────
lora_config = LoraConfig(
r=lora_r,
lora_alpha=lora_alpha,
target_modules=[
"q_proj", "k_proj", "v_proj", "o_proj",
"gate_proj", "up_proj", "down_proj",
],
lora_dropout=lora_dropout,
bias="none",
task_type="CAUSAL_LM",
)
model = get_peft_model(model, lora_config)
model.print_trainable_parameters()
# ── Training args ───────────────────────────────────────
training_args = TrainingArguments(
output_dir=os.path.join(output_dir, "checkpoints"),
num_train_epochs=num_epochs,
per_device_train_batch_size=batch_size,
per_device_eval_batch_size=batch_size,
gradient_accumulation_steps=gradient_accumulation_steps,
learning_rate=learning_rate,
bf16=True,
logging_steps=5,
eval_strategy="steps",
eval_steps=50,
save_strategy="steps",
save_steps=100,
save_total_limit=2,
load_best_model_at_end=True,
metric_for_best_model="eval_loss",
report_to="none",
warmup_ratio=0.03,
lr_scheduler_type="cosine",
optim="paged_adamw_8bit",
max_grad_norm=0.3,
group_by_length=True,
)
# ── SFTTrainer ──────────────────────────────────────────
trainer = SFTTrainer(
model=model,
args=training_args,
train_dataset=train_ds,
eval_dataset=val_ds,
tokenizer=tokenizer,
max_seq_length=max_seq_length,
dataset_text_field="text",
packing=True, # pack short samples for efficiency
)
print("Starting QLoRA training …")
result = trainer.train()
train_loss = result.training_loss
eval_result = trainer.evaluate()
eval_loss = eval_result.get("eval_loss", 0.0)
print(f"Train loss: {train_loss:.4f}, Eval loss: {eval_loss:.4f}")
# ── Save adapter ────────────────────────────────────────
adapter_path = os.path.join(output_dir, "adapter")
model.save_pretrained(adapter_path)
tokenizer.save_pretrained(adapter_path)
metadata = {
"base_model": base_model,
"lora_r": lora_r,
"lora_alpha": lora_alpha,
"lora_dropout": lora_dropout,
"learning_rate": learning_rate,
"num_epochs": num_epochs,
"batch_size": batch_size,
"gradient_accumulation_steps": gradient_accumulation_steps,
"max_seq_length": max_seq_length,
"train_samples": len(train_data),
"val_samples": len(val_data),
"train_loss": train_loss,
"eval_loss": eval_loss,
}
with open(os.path.join(adapter_path, "training_metadata.json"), "w") as f:
json.dump(metadata, f, indent=2)
print(f"Adapter saved to {adapter_path}")
from collections import namedtuple
return namedtuple("TrainOutput", ["adapter_path", "train_loss", "eval_loss"])(
adapter_path=adapter_path,
train_loss=train_loss,
eval_loss=eval_loss,
)
# ──────────────────────────────────────────────────────────────
# 4. Quick sanity evaluation
# ──────────────────────────────────────────────────────────────
@dsl.component(
base_image="python:3.13-slim",
packages_to_install=[
"torch", "transformers", "peft", "bitsandbytes", "accelerate", "scipy",
],
)
def evaluate_adapter(
adapter_path: str,
base_model: str,
) -> NamedTuple("EvalOutput", [("report", str), ("passed", bool)]):
"""Load the QLoRA adapter and run a few sanity-check prompts."""
import torch
from transformers import AutoModelForCausalLM, AutoTokenizer, BitsAndBytesConfig
from peft import PeftModel
bnb_config = BitsAndBytesConfig(
load_in_4bit=True,
bnb_4bit_quant_type="nf4",
bnb_4bit_compute_dtype=torch.bfloat16,
bnb_4bit_use_double_quant=True,
)
print(f"Loading base model {base_model}")
model = AutoModelForCausalLM.from_pretrained(
base_model,
quantization_config=bnb_config,
device_map="auto",
trust_remote_code=True,
torch_dtype=torch.bfloat16,
)
tokenizer = AutoTokenizer.from_pretrained(base_model, trust_remote_code=True)
print(f"Loading adapter from {adapter_path}")
model = PeftModel.from_pretrained(model, adapter_path)
model.eval()
test_prompts = [
"Summarise the key points from the training material.",
"What are the main topics covered in the source documents?",
"Explain the most important concept from the training data.",
]
lines = []
for prompt in test_prompts:
messages = [
{"role": "system", "content": "You are a helpful assistant."},
{"role": "user", "content": prompt},
]
input_text = tokenizer.apply_chat_template(
messages, tokenize=False, add_generation_prompt=True
)
inputs = tokenizer(input_text, return_tensors="pt").to(model.device)
with torch.no_grad():
out = model.generate(**inputs, max_new_tokens=128, temperature=0.7, do_sample=True)
response = tokenizer.decode(out[0][inputs["input_ids"].shape[1]:], skip_special_tokens=True)
lines.append(f"Q: {prompt}\nA: {response}\n")
print(lines[-1])
report = "\n".join(lines)
# Simple heuristic: did the model produce non-empty responses?
passed = all(len(l.split("A:")[1].strip()) > 10 for l in lines)
print(f"Evaluation passed: {passed}")
from collections import namedtuple
return namedtuple("EvalOutput", ["report", "passed"])(
report=report, passed=passed
)
# ──────────────────────────────────────────────────────────────
# 5. Push adapter to Gitea repo
# ──────────────────────────────────────────────────────────────
@dsl.component(
base_image="python:3.13-slim",
packages_to_install=["requests"],
)
def push_adapter_to_gitea(
adapter_path: str,
gitea_url: str,
gitea_owner: str,
gitea_repo: str,
gitea_username: str,
gitea_password: str,
branch: str = "main",
commit_message: str = "feat: add QLoRA adapter from PDF training pipeline",
) -> NamedTuple("PushOutput", [("repo_url", str), ("files_pushed", int)]):
"""Push the QLoRA adapter files to a Gitea repository via the API."""
import base64
import json
import os
import requests
api_base = f"{gitea_url}/api/v1"
auth = (gitea_username, gitea_password)
repo_api = f"{api_base}/repos/{gitea_owner}/{gitea_repo}"
# Check if repo exists, create if not
resp = requests.get(repo_api, auth=auth, timeout=30)
if resp.status_code == 404:
print(f"Creating repo {gitea_owner}/{gitea_repo}")
create_resp = requests.post(
f"{api_base}/orgs/{gitea_owner}/repos"
if gitea_owner != gitea_username
else f"{api_base}/user/repos",
auth=auth,
json={
"name": gitea_repo,
"description": "QLoRA adapters trained from PDF documents",
"private": False,
"auto_init": True,
},
timeout=30,
)
create_resp.raise_for_status()
print(f"Created: {create_resp.json().get('html_url')}")
# Collect all adapter files
files_to_push = []
for root, dirs, files in os.walk(adapter_path):
for fname in files:
fpath = os.path.join(root, fname)
rel_path = os.path.relpath(fpath, adapter_path)
with open(fpath, "rb") as f:
content = base64.b64encode(f.read()).decode("utf-8")
files_to_push.append({"path": rel_path, "content": content})
print(f"Pushing {len(files_to_push)} files to {gitea_owner}/{gitea_repo}")
# Push each file via Gitea contents API
pushed = 0
for item in files_to_push:
file_api = f"{repo_api}/contents/{item['path']}"
# Check if file already exists (need SHA for update)
existing = requests.get(file_api, auth=auth, params={"ref": branch}, timeout=30)
payload = {
"message": commit_message,
"content": item["content"],
"branch": branch,
}
if existing.status_code == 200:
payload["sha"] = existing.json()["sha"]
resp = requests.put(file_api, auth=auth, json=payload, timeout=60)
else:
resp = requests.post(file_api, auth=auth, json=payload, timeout=60)
if resp.status_code in (200, 201):
pushed += 1
print(f"{item['path']}")
else:
print(f"{item['path']}: {resp.status_code} {resp.text[:200]}")
repo_url = f"{gitea_url}/{gitea_owner}/{gitea_repo}"
print(f"Pushed {pushed}/{len(files_to_push)} files to {repo_url}")
from collections import namedtuple
return namedtuple("PushOutput", ["repo_url", "files_pushed"])(
repo_url=repo_url, files_pushed=pushed
)
# ──────────────────────────────────────────────────────────────
# 6. Log metrics to MLflow
# ──────────────────────────────────────────────────────────────
@dsl.component(
base_image="python:3.13-slim",
packages_to_install=["mlflow==2.22.0"],
)
def log_training_metrics(
base_model: str,
train_loss: float,
eval_loss: float,
num_train: int,
num_val: int,
num_pdfs: int,
lora_r: int,
lora_alpha: int,
learning_rate: float,
num_epochs: int,
repo_url: str,
mlflow_tracking_uri: str = "http://mlflow.mlflow.svc.cluster.local:80",
experiment_name: str = "qlora-pdf-training",
):
"""Log the full training run to MLflow."""
import mlflow
mlflow.set_tracking_uri(mlflow_tracking_uri)
mlflow.set_experiment(experiment_name)
with mlflow.start_run(run_name=f"qlora-{base_model.split('/')[-1]}"):
mlflow.log_params(
{
"base_model": base_model,
"lora_r": lora_r,
"lora_alpha": lora_alpha,
"learning_rate": learning_rate,
"num_epochs": num_epochs,
"num_pdfs": num_pdfs,
"data_source": "quobjects/training-data",
}
)
mlflow.log_metrics(
{
"train_loss": train_loss,
"eval_loss": eval_loss,
"train_samples": float(num_train),
"val_samples": float(num_val),
}
)
mlflow.set_tag("adapter_repo", repo_url)
# ──────────────────────────────────────────────────────────────
# Pipeline definition
# ──────────────────────────────────────────────────────────────
@dsl.pipeline(
name="QLoRA PDF Fine-Tuning",
description=(
"Fine-tune Llama 3.1 70B via QLoRA on PDFs from the Quobjects "
"training-data bucket. Pushes the adapter to Gitea and logs "
"metrics to MLflow."
),
)
def qlora_pdf_pipeline(
# ── S3 / Quobjects ──
s3_endpoint: str = "candlekeep.lab.daviestechlabs.io",
s3_bucket: str = "training-data",
s3_prefix: str = "",
aws_access_key_id: str = "",
aws_secret_access_key: str = "",
# ── Model ──
base_model: str = "meta-llama/Llama-3.1-70B-Instruct",
# ── Training hyper-params ──
learning_rate: float = 2e-4,
num_epochs: int = 3,
batch_size: int = 2,
gradient_accumulation_steps: int = 8,
max_seq_length: int = 2048,
lora_r: int = 64,
lora_alpha: int = 16,
lora_dropout: float = 0.05,
# ── Data prep ──
chunk_size: int = 512,
chunk_overlap: int = 64,
# ── Gitea ──
gitea_url: str = "http://gitea-http.gitea.svc.cluster.local:3000",
gitea_owner: str = "daviestechlabs",
gitea_repo: str = "qlora-adapters",
gitea_username: str = "",
gitea_password: str = "",
# ── MLflow ──
mlflow_tracking_uri: str = "http://mlflow.mlflow.svc.cluster.local:80",
):
# Step 1 — Fetch PDFs from S3
pdfs = fetch_pdfs_from_s3(
s3_endpoint=s3_endpoint,
s3_bucket=s3_bucket,
s3_prefix=s3_prefix,
aws_access_key_id=aws_access_key_id,
aws_secret_access_key=aws_secret_access_key,
)
# Step 2 — Extract text and build training dataset
data = prepare_training_data(
pdf_dir=pdfs.outputs["pdf_dir"],
max_seq_length=max_seq_length,
chunk_size=chunk_size,
chunk_overlap=chunk_overlap,
)
# Step 3 — QLoRA training (GPU-heavy)
trained = train_qlora(
dataset_path=data.outputs["dataset_path"],
base_model=base_model,
learning_rate=learning_rate,
num_epochs=num_epochs,
batch_size=batch_size,
gradient_accumulation_steps=gradient_accumulation_steps,
max_seq_length=max_seq_length,
lora_r=lora_r,
lora_alpha=lora_alpha,
lora_dropout=lora_dropout,
)
# Ask for a GPU on khelben
trained.set_accelerator_type("gpu")
trained.set_gpu_limit(1)
# Step 4 — Quick evaluation
evaluated = evaluate_adapter(
adapter_path=trained.outputs["adapter_path"],
base_model=base_model,
)
evaluated.set_accelerator_type("gpu")
evaluated.set_gpu_limit(1)
# Step 5 — Push adapter to Gitea
pushed = push_adapter_to_gitea(
adapter_path=trained.outputs["adapter_path"],
gitea_url=gitea_url,
gitea_owner=gitea_owner,
gitea_repo=gitea_repo,
gitea_username=gitea_username,
gitea_password=gitea_password,
)
# Step 6 — Log to MLflow
log_training_metrics(
base_model=base_model,
train_loss=trained.outputs["train_loss"],
eval_loss=trained.outputs["eval_loss"],
num_train=data.outputs["num_train"],
num_val=data.outputs["num_val"],
num_pdfs=pdfs.outputs["num_files"],
lora_r=lora_r,
lora_alpha=lora_alpha,
learning_rate=learning_rate,
num_epochs=num_epochs,
repo_url=pushed.outputs["repo_url"],
mlflow_tracking_uri=mlflow_tracking_uri,
)
# ──────────────────────────────────────────────────────────────
# Compile
# ──────────────────────────────────────────────────────────────
if __name__ == "__main__":
compiler.Compiler().compile(
pipeline_func=qlora_pdf_pipeline,
package_path="qlora_pdf_pipeline.yaml",
)
print("Compiled: qlora_pdf_pipeline.yaml")