"""GCP Vertex AI Custom Job entrypoint — **evaluation** (not training). Mirrors gcp_entrypoint.py but: 1. Pulls dataset from HF Hub (same logic). 2. Pulls a trained checkpoint from //stage2/{best|last}/ into /workspace/run_pull//stage2//. 3. Pulls /configs/{model,train}_config.yaml (if present) so the model is rebuilt with the EXACT architecture used at training time. Falls back to the repo defaults when the snapshot is absent. 4. Patches the configs for the detected GPU (T4 → fp16+SDPA; L4/A100 → bf16+FA2 if flash-attn installed) and pins paths. 5. Pins run_id.txt to RUN_ID so evaluate.py writes under {output_dir}/{RUN_ID}/. 6. Execs `python -m evaluation.evaluate --checkpoint ... --run_id ... --task all --split test --output_dir /workspace/results`. Required env vars: HF_TOKEN — HuggingFace token (read code+data+runs, write runs) DATASET_NAME — 'IU-Xray' | 'MIMIC-CXR' | 'MIMIC-CXR_resized' RUN_ID — folder name on HF_RUNS_REPO to evaluate, e.g. 'MIMIC-CXR_resized_run_1' Optional env vars (defaults shown): HF_USER = hieu3636 HF_RUNS_REPO = hieu3636/cxr-vlm-runs CKPT_PICK = best # 'best' | 'last' (stage2 sub-folder) REPORT_MODE = # blank → use the run's saved snapshot IMAGE_MODE = # blank → use the run's saved snapshot TASK = all # 'all', one task, or comma list ('findings,vqa') SPLIT = test PNU_SOURCE = oracle # 'oracle' | 'predicted' (CheXpert classifier) CHEXPERT_CKPT_PATH = chexpert_classifier/chexpert_mimic_resized.pt # on HF_RUNS_REPO; predicted only BATCH_SIZE = # blank → from GPU profile MAX_NEW_TOKENS = 300 UPLOAD_RESULTS_TO_HF= 1 # set '0' to skip upload LLM_JUDGE = 0 # set '1' to enable VQA judge LLM_JUDGE_MODEL = gpt-4o-mini LLM_JUDGE_BASE_URL = # for OpenAI-compat endpoints LLM_JUDGE_MAX_SAMPLES= # cap samples for cost control WORK = /workspace """ from __future__ import annotations import os import shutil import subprocess import sys import tarfile import zipfile from pathlib import Path # Tame HF/transformers chatter so logs are readable in Cloud Logging. os.environ.setdefault("TOKENIZERS_PARALLELISM", "false") os.environ.setdefault("BITSANDBYTES_NOWELCOME", "1") os.environ.setdefault("HF_HUB_DISABLE_PROGRESS_BARS", "1") os.environ.setdefault("TRANSFORMERS_VERBOSITY", "warning") os.environ.setdefault("PYTHONUNBUFFERED", "1") os.environ.setdefault("CUDA_VISIBLE_DEVICES", "0") # tqdm flushes ≥ every 1s — keeps Cloud Logging looking alive during inference. os.environ.setdefault("TQDM_MININTERVAL", "1.0") def env(name: str, default: str | None = None, *, required: bool = False) -> str: val = os.environ.get(name, default) if required and not val: sys.exit(f"[gcp_eval_entrypoint] ERROR: required env var {name} not set") return val or "" # ── 1) Resolve config from env ──────────────────────────────────────────────── HF_TOKEN = env("HF_TOKEN", required=True) DATASET_NAME = env("DATASET_NAME", required=True) RUN_ID = env("RUN_ID", required=True) HF_USER = env("HF_USER", "hieu3636") HF_RUNS_REPO = env("HF_RUNS_REPO", "hieu3636/cxr-vlm-runs") CKPT_PICK = env("CKPT_PICK", "best") REPORT_MODE_OVERRIDE = env("REPORT_MODE", "") IMAGE_MODE_OVERRIDE = env("IMAGE_MODE", "") TASK = env("TASK", "all") SPLIT = env("SPLIT", "test") BATCH_SIZE_OVERRIDE = env("BATCH_SIZE", "") MAX_NEW_TOKENS = int(env("MAX_NEW_TOKENS", "300")) UPLOAD_RESULTS_TO_HF = env("UPLOAD_RESULTS_TO_HF", "1") not in ("0", "false", "False", "") LLM_JUDGE = env("LLM_JUDGE", "0") in ("1", "true", "True") LLM_JUDGE_MODEL = env("LLM_JUDGE_MODEL", "gpt-4o-mini") LLM_JUDGE_BASE_URL = env("LLM_JUDGE_BASE_URL", "") LLM_JUDGE_MAX_SAMPLES = env("LLM_JUDGE_MAX_SAMPLES", "") # PNU prompt-condition source — mirrors the notebook. 'oracle' = GT chex_* # labels from the JSON; 'predicted' = run the Stage-0 CheXpert classifier on # each image (needs CHEXPERT_CKPT_PATH on the runs repo). PNU_SOURCE = env("PNU_SOURCE", "oracle") CHEXPERT_CKPT_PATH = env("CHEXPERT_CKPT_PATH", "chexpert_classifier/chexpert_mimic_resized.pt") WORK = Path(env("WORK", "/workspace")) assert DATASET_NAME in ("IU-Xray", "MIMIC-CXR", "MIMIC-CXR_resized"), DATASET_NAME assert CKPT_PICK in ("best", "last"), CKPT_PICK # TASK may be 'all', a single task, or a comma-separated subset ('findings,vqa'). for _t in TASK.split(","): assert _t.strip() in ("all", "findings", "impression", "report", "vqa"), TASK assert PNU_SOURCE in ("oracle", "predicted"), PNU_SOURCE PROJECT = Path(__file__).resolve().parent.parent # /workspace/code DATA_SRC = WORK / "data" RUN_PULL_ROOT = WORK / "run_pull" RESULTS_DIR = WORK / "results" CKPT_ROOT = WORK / "ckpt_eval" for d in (DATA_SRC, RUN_PULL_ROOT, RESULTS_DIR, CKPT_ROOT): d.mkdir(parents=True, exist_ok=True) print(f"[gcp_eval] PROJECT = {PROJECT}") print(f"[gcp_eval] WORK = {WORK}") print(f"[gcp_eval] DATASET_NAME = {DATASET_NAME}") print(f"[gcp_eval] RUN_ID = {RUN_ID} (ckpt: stage2/{CKPT_PICK})") print(f"[gcp_eval] TASK = {TASK} SPLIT = {SPLIT}") print(f"[gcp_eval] UPLOAD_TO_HF = {UPLOAD_RESULTS_TO_HF}") # ── 2) Download dataset payload from HF Hub ─────────────────────────────────── from huggingface_hub import HfApi, hf_hub_download, snapshot_download # noqa: E402 if DATASET_NAME == "MIMIC-CXR_resized": mr_dir = DATA_SRC / "MIMIC-CXR_resized" mr_dir.mkdir(parents=True, exist_ok=True) files_dir = mr_dir / "files" manifests_present = all( (mr_dir / f).is_file() for f in ("manifest_train.csv", "manifest_val.csv", "manifest_test.csv") ) if manifests_present and files_dir.is_dir() and any(files_dir.glob("p*")): print(f"[gcp_eval] {mr_dir} already populated — skipping download.") else: api = HfApi(token=HF_TOKEN) all_files = api.list_repo_files( repo_id=f"{HF_USER}/cxr-vlm-data", repo_type="dataset" ) mr_files = [f for f in all_files if f.startswith("MIMIC-CXR_resized/")] tar_files = sorted(f for f in mr_files if f.endswith(".tar")) print(f"[gcp_eval] {len(tar_files)} tar shards on HF") snapshot_download( repo_id=f"{HF_USER}/cxr-vlm-data", repo_type="dataset", allow_patterns=[ "MIMIC-CXR_resized/*.csv", "MIMIC-CXR_resized/*.json", "MIMIC-CXR_resized/*.txt", "MIMIC-CXR_resized/vqa/**", ], token=HF_TOKEN, local_dir=str(DATA_SRC), ) for i, tf in enumerate(tar_files, 1): print(f"[gcp_eval] [{i}/{len(tar_files)}] {tf}", flush=True) tp = Path(hf_hub_download( repo_id=f"{HF_USER}/cxr-vlm-data", repo_type="dataset", filename=tf, token=HF_TOKEN, local_dir=str(DATA_SRC), )) with tarfile.open(tp) as t: t.extractall(mr_dir) tp.unlink(missing_ok=True) print(f"[gcp_eval] {mr_dir} ready.") DATA_ROOT_RESIZED = mr_dir else: zip_name = f"{DATASET_NAME}.zip" marker = DATA_SRC / DATASET_NAME if not marker.exists(): print(f"[gcp_eval] downloading {zip_name} ...") zpath = hf_hub_download( repo_id=f"{HF_USER}/cxr-vlm-data", filename=zip_name, repo_type="dataset", token=HF_TOKEN, local_dir=str(DATA_SRC), ) with zipfile.ZipFile(zpath) as zf: zf.extractall(DATA_SRC) try: os.remove(zpath) except OSError: pass else: print(f"[gcp_eval] {marker} already present — skipping download.") print(f"[gcp_eval] DATA_SRC contents: {sorted(os.listdir(DATA_SRC))}") # ── 3) Pull checkpoint + saved config snapshot from runs repo ──────────────── print(f"[gcp_eval] pulling {RUN_ID}/{{configs,stage2/{CKPT_PICK}}} from {HF_RUNS_REPO} …") snapshot_download( repo_id=HF_RUNS_REPO, repo_type="model", token=HF_TOKEN, allow_patterns=[ f"{RUN_ID}/configs/**", f"{RUN_ID}/run_meta.json", f"{RUN_ID}/stage2/{CKPT_PICK}/**", ], local_dir=str(RUN_PULL_ROOT), ) RUN_DIR_PULLED = RUN_PULL_ROOT / RUN_ID CKPT_DIR_PULLED = RUN_DIR_PULLED / "stage2" / CKPT_PICK PROJ_PT = CKPT_DIR_PULLED / "checkpoint_projection.pt" LORA_DIR = CKPT_DIR_PULLED / "checkpoint_lora" CHEXPERT_PT = CKPT_DIR_PULLED / "checkpoint_chexpert_classifier.pt" SAVED_CFG_DIR = RUN_DIR_PULLED / "configs" SAVED_TRAIN_CFG = SAVED_CFG_DIR / "train_config.yaml" SAVED_MODEL_CFG = SAVED_CFG_DIR / "model_config.yaml" assert PROJ_PT.is_file(), f"projection weights not found: {PROJ_PT}" assert (LORA_DIR / "adapter_config.json").is_file(), \ f"LoRA adapter_config.json missing in {LORA_DIR}" print(f"[gcp_eval] projection : {PROJ_PT} ({PROJ_PT.stat().st_size/1e6:.1f} MB)") print(f"[gcp_eval] lora : {LORA_DIR}/") print(f"[gcp_eval] chexpert : exists={CHEXPERT_PT.is_file()}") # CheXpert classifier checkpoint (separate location on the runs repo, outside # {RUN_ID}/). Only needed for PNU_SOURCE=predicted. CHEXPERT_LOCAL = None if PNU_SOURCE == "predicted": CHEXPERT_LOCAL = Path(hf_hub_download( repo_id=HF_RUNS_REPO, repo_type="model", filename=CHEXPERT_CKPT_PATH, token=HF_TOKEN, local_dir=str(RUN_PULL_ROOT), )) assert CHEXPERT_LOCAL.is_file(), \ f"CheXpert checkpoint not pulled: {CHEXPERT_LOCAL} " \ f"(expected {CHEXPERT_CKPT_PATH!r} on {HF_RUNS_REPO})." print(f"[gcp_eval] chexpert clf (predicted PNU): {CHEXPERT_LOCAL} " f"({CHEXPERT_LOCAL.stat().st_size/1e6:.2f} MB)") # ── 4) Build configs ───────────────────────────────────────────────────────── import torch # noqa: E402 from omegaconf import OmegaConf # noqa: E402 repo_train_cfg_path = PROJECT / "configs" / "train_config.yaml" repo_model_cfg_path = PROJECT / "configs" / "model_config.yaml" if SAVED_TRAIN_CFG.is_file(): train_cfg = OmegaConf.load(SAVED_TRAIN_CFG) print(f"[gcp_eval] train_cfg <- {SAVED_TRAIN_CFG}") else: train_cfg = OmegaConf.load(repo_train_cfg_path) print(f"[gcp_eval] train_cfg <- repo default (no snapshot)") if SAVED_MODEL_CFG.is_file(): model_cfg = OmegaConf.load(SAVED_MODEL_CFG) print(f"[gcp_eval] model_cfg <- {SAVED_MODEL_CFG}") else: model_cfg = OmegaConf.load(repo_model_cfg_path) print(f"[gcp_eval] model_cfg <- repo default (no snapshot)") # Optional report/image mode overrides — leave blank to use saved values. if REPORT_MODE_OVERRIDE: train_cfg.data.report_mode = REPORT_MODE_OVERRIDE if IMAGE_MODE_OVERRIDE: train_cfg.data.image_mode = IMAGE_MODE_OVERRIDE print(f"[gcp_eval] report_mode = {train_cfg.data.report_mode} image_mode = {train_cfg.data.image_mode}") # Dataset paths (mirror gcp_entrypoint.py) train_cfg.data.dataset_name = DATASET_NAME train_cfg.data.max_images_per_sample = int(getattr(train_cfg.data, "max_images_per_sample", 2)) out_dir = PROJECT / "data" / "data_files" out_dir.mkdir(parents=True, exist_ok=True) if DATASET_NAME == "MIMIC-CXR_resized": train_cfg.data.mimic_cxr_resized.root = str(DATA_ROOT_RESIZED) train_cfg.data.mimic_cxr_resized.manifest_dir = None train_cfg.data.mimic_cxr_resized.vqa_dir = None train_cfg.data.mimic_cxr_resized.reports_root = None train_cfg.data.mimic_cxr_resized.auto_build = True train_cfg.data.mimic_cxr_resized.instruct_json = str( out_dir / "mimic_cxr_resized_instruct.json") elif DATASET_NAME == "MIMIC-CXR": def _find_mimic_root(root: Path) -> Path: for cand in [root / "MIMIC-CXR", root]: if (cand / "train").exists() and (cand / "valid").exists() and (cand / "test").exists(): return cand for p in root.rglob("train"): if p.is_dir() and (p.parent / "valid").exists() and (p.parent / "test").exists(): return p.parent raise FileNotFoundError(f"MIMIC-CXR train/valid/test not found under {root}") cxr_root = _find_mimic_root(DATA_SRC) train_cfg.data.mimic_cxr_root = str(cxr_root) train_cfg.data.instruct_json = str(out_dir / "mimic_cxr_instruct_unified.json") train_cfg.data.mimic_auto_build = True _cx = sorted(DATA_SRC.rglob("*chexpert*.csv")) or sorted(DATA_SRC.rglob("*chexbert*.csv")) train_cfg.data.mimic_chexpert_csv = str(_cx[0]) if _cx else None _vqa = list(DATA_SRC.rglob("vqa")) train_cfg.data.mimic_vqa_root = str(_vqa[0]) if _vqa else None else: # IU-Xray iu_root = DATA_SRC / "IU-Xray" train_cfg.data.iu_xray.images_dir = str(iu_root / "images") train_cfg.data.iu_xray.labels_dir = str(iu_root / "labels") train_cfg.data.iu_xray.instruct_json = str(out_dir / "iu_xray_instruct.json") train_cfg.data.iu_xray.auto_build = True train_cfg.data.train_split = "train" train_cfg.data.val_split = "validate" train_cfg.data.test_split = "test" train_cfg.data.feature_cache_dir = None train_cfg.training.output_root = str(CKPT_ROOT) # ── GPU auto-profile (eval batch sizes — smaller than training because the KV # cache built during generation scales with batch × max_new_tokens). ── assert torch.cuda.is_available(), "CUDA not available in container" _props = torch.cuda.get_device_properties(0) _cap = (_props.major, _props.minor) _vram_gb = _props.total_memory / 1e9 _bf16_ok = torch.cuda.is_bf16_supported() _fa2_ok = _cap >= (8, 0) _flash_attn_installed = False if _fa2_ok: try: import flash_attn # noqa: F401 _flash_attn_installed = True except Exception: _flash_attn_installed = False if _vram_gb >= 70: _label, _eval_bs, _nw = "A100/H100 80GB", 16, 16 elif _vram_gb >= 35: _label, _eval_bs, _nw = "A100 40GB", 8, 12 elif _vram_gb >= 22: _label, _eval_bs, _nw = "3090 / L4 / A10 (24GB)", 4, 8 elif _vram_gb >= 14: _label, _eval_bs, _nw = "T4 / V100 (15-16GB)", 1, 2 else: _label, _eval_bs, _nw = f"unknown ({_vram_gb:.0f}GB)", 1, 2 if BATCH_SIZE_OVERRIDE: _eval_bs = int(BATCH_SIZE_OVERRIDE) print(f"[gcp_eval] BATCH_SIZE override -> {_eval_bs}") print(f"[gcp_eval] GPU: {_props.name} {_vram_gb:.1f}GB sm_{_cap[0]}{_cap[1]} " f"bf16={_bf16_ok} fa2={_fa2_ok} fa2_wheel={_flash_attn_installed}") print(f"[gcp_eval] -> profile {_label} eval_batch={_eval_bs}") train_cfg.training.per_device_train_batch_size = _eval_bs train_cfg.training.per_device_eval_batch_size = _eval_bs train_cfg.training.dataloader_num_workers = _nw train_cfg.training.fp16 = not _bf16_ok train_cfg.training.bf16 = bool(_bf16_ok) train_cfg.training.dataloader_pin_memory = True train_cfg.training.dataloader_persistent_workers = True model_cfg.llm.attn_implementation = ( "flash_attention_2" if (_fa2_ok and _flash_attn_installed) else "sdpa" ) model_cfg.llm.gradient_checkpointing = False # eval — no backward model_cfg.llm.torch_dtype = "bfloat16" if _bf16_ok else "float16" model_cfg.llm.bnb_4bit_compute_dtype = "bfloat16" if _bf16_ok else "float16" model_cfg.llm.bnb_4bit_quant_type = "nf4" model_cfg.llm.bnb_4bit_use_double_quant = True model_cfg.llm.load_in_8bit = False model_cfg.llm.load_in_4bit = True # CheXpert classifier. # PNU_SOURCE=predicted → enable + load the separately-pulled Stage-0 head. # PNU_SOURCE=oracle → only enable for the legacy case where the head was # saved inside the stage2 checkpoint; otherwise disabled # (oracle PNU comes from the JSON's GT chex_* labels). if PNU_SOURCE == "predicted": model_cfg.chexpert_classifier.enabled = True model_cfg.chexpert_classifier.checkpoint = str(CHEXPERT_LOCAL) print(f"[gcp_eval] PNU=predicted -> CheXpert classifier ENABLED, ckpt={CHEXPERT_LOCAL}") elif CHEXPERT_PT.is_file(): model_cfg.chexpert_classifier.enabled = True print("[gcp_eval] CheXpert classifier checkpoint found in stage2 -> enabled") else: model_cfg.chexpert_classifier.enabled = False print("[gcp_eval] PNU=oracle -> CheXpert classifier disabled (GT chex_* labels)") # HF Hub tracker train_cfg.wandb.enabled = False if UPLOAD_RESULTS_TO_HF: train_cfg.hf_hub.enabled = True train_cfg.hf_hub.repo_id = HF_RUNS_REPO train_cfg.hf_hub.token_env = "HF_TOKEN" train_cfg.hf_hub.private = True else: train_cfg.hf_hub.enabled = False train_cfg.hf_hub.run_state_file = str(CKPT_ROOT / "run_id.txt") # Pin run_id so resolve_run_id picks up exactly the one we're evaluating. (CKPT_ROOT / "run_id.txt").write_text(RUN_ID) print(f"[gcp_eval] pinned run_id = {RUN_ID}") # Save patched configs back into the project so evaluate.py reads them. OmegaConf.save(train_cfg, repo_train_cfg_path) OmegaConf.save(model_cfg, repo_model_cfg_path) print("[gcp_eval] configs patched.") # ── 5) Launch evaluation ───────────────────────────────────────────────────── cmd = [ "python", "-u", "-m", "evaluation.evaluate", "--model_config", str(repo_model_cfg_path), "--train_config", str(repo_train_cfg_path), # Pass the DIRECTORY, not the .pt file: load_checkpoint derives # checkpoint_projection.pt + checkpoint_lora/ from the dir. Passing the .pt # makes it look for checkpoint_projection_projection.pt → silently skips # BOTH projection and LoRA (evaluating raw, untrained Vicuna). "--checkpoint", str(CKPT_DIR_PULLED), "--run_id", RUN_ID, "--task", TASK, "--split", SPLIT, "--batch_size", str(_eval_bs), "--max_new_tokens", str(MAX_NEW_TOKENS), "--output_dir", str(RESULTS_DIR), "--pnu_source", PNU_SOURCE, "--device", "cuda", ] if not UPLOAD_RESULTS_TO_HF: cmd.append("--no_hf_upload") if LLM_JUDGE: cmd += ["--llm_judge", "--llm_judge_model", LLM_JUDGE_MODEL] if LLM_JUDGE_BASE_URL: cmd += ["--llm_judge_base_url", LLM_JUDGE_BASE_URL] if LLM_JUDGE_MAX_SAMPLES: cmd += ["--llm_judge_max_samples", LLM_JUDGE_MAX_SAMPLES] print(f"[gcp_eval] launching: {' '.join(cmd)}", flush=True) os.chdir(PROJECT) sys.exit(subprocess.call(cmd))