ma-agents 3.4.6 → 3.4.8

package/.opencode/skills/ml-experiment/SKILL.md

@@ -0,0 +1,74 @@
+---
+name: ml-experiment
+description: ML Experiment - Execute training, hyperparameter optimization, and log all runs to the tracking tool
+---
+
+# ML Stage 6 - Experiment Execution
+
+Execute the training pipeline as specified in the locked TechSpec. Log everything. Touch nothing outside the HPO space.
+
+## Instructions
+
+### 1. Load Context
+- Read `_bmad-output/planning-artifacts/ml-techspec.md` — MUST be LOCKED. If not, STOP.
+- Read `_bmad-output/planning-artifacts/ml-architecture.md`
+- Note the fixed random seed, feature set, and validation strategy — do not deviate
+
+### 2. Write Training Script
+If `scripts/train.py` does not exist, generate it following the TechSpec exactly:
+- Load data from TechSpec data contract paths
+- Apply preprocessing pipeline (from ml-architecture)
+- Create train/val split using TechSpec validation strategy and fixed seed
+- Instantiate tracking run (wandb.init / mlflow.start_run / local log)
+- Log all TechSpec fixed params as run config
+- Run baseline model first — log its metrics
+- Run candidate model with fixed hyperparameters — log metrics
+- If HPO is specified: run HPO trials, log each trial
+- Select best model; log final metrics against ALL TechSpec acceptance criteria
+- Save model artifact to `_bmad-output/implementation-artifacts/models/`
+- Log pass/fail for each acceptance criterion explicitly
+
+Use `assets/` templates if they exist (e.g. `assets/train_template.py`).
+
+### 3. Execute Baseline
+Run baseline first — always:
+
+    uv run python scripts/train.py --mode baseline
+
+Log baseline metrics. The candidate model must beat this.
+
+### 4. Execute Candidate Model
+
+    uv run python scripts/train.py --mode candidate
+
+### 5. Execute HPO (if specified in TechSpec)
+Run hyperparameter optimization within the HPO space defined in TechSpec:
+
+    uv run python scripts/train.py --mode hpo
+
+Log all trials. Select best params by primary metric on validation set only.
+
+### 6. Write Experiment Log
+Write `_bmad-output/implementation-artifacts/experiment-log.md` with:
+- **Run IDs**: Tracking tool run IDs or local log paths
+- **Baseline Results**: metrics for each acceptance criterion
+- **Best Model Results**: metrics for each acceptance criterion
+- **Best Hyperparameters**: final selected values
+- **Acceptance Criteria Status**: PASS / FAIL for each criterion from TechSpec
+- **Training Time**: wall-clock time
+- **Model Artifact Path**: path to saved model
+
+### 7. Surface Dilemmas & Commit Gate
+
+Before presenting and **before any git commit**:
+
+- Identify every execution decision where two or more options existed (early stopping patience, batch size, resampling applied or not, model variant selected, etc.)
+- Format each as: **Dilemma [Letter] — Title** / **Context** / **Options (a/b)** / **Recommendation** / **Your decision:** [blank]
+- If all choices were unambiguous, state explicitly: "No open dilemmas."
+- **Do NOT commit the experiment log or model artifacts until the user has reviewed and approved.**
+
+### 8. Confirm and Advance
+- Present experiment log summary
+- State clearly: "Primary criterion ([metric] >= [threshold]): PASS / FAIL"
+- On approval: commit artifacts, then say "Proceed to **Stage 7 — /ml-analysis** to evaluate results against the TechSpec contract."
+- STOP and WAIT for user confirmation

package/.opencode/skills/ml-experiment/assets/advanced_trainer_configs.py

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+"""
+advanced_trainer_configs.py — BMAD DL Lifecycle
+(Adapted from K-Dense claude-scientific-skills/pytorch-lightning/quick_trainer_setup.py)
+
+10 ready-to-use Lightning Trainer configurations for different training scenarios.
+Each function is self-contained — copy the one you need into your training script.
+
+Configurations:
+  1.  basic_trainer()              — Quick prototyping, CPU/auto hardware
+  2.  debug_trainer()              — Fast dev run, anomaly detection
+  3.  single_gpu_trainer()         — Production single GPU with checkpointing + logging
+  4.  multi_gpu_ddp_trainer()      — Multi-GPU with DDP (models < 500M params)
+  5.  large_model_fsdp_trainer()   — FSDP for large models (500M+ params)
+  6.  deepspeed_trainer()          — DeepSpeed for very large models (10B+)
+  7.  hparam_search_trainer()      — Lightweight for hyperparameter sweeps
+  8.  overfit_test_trainer()       — Overfit on N batches to verify model capacity
+  9.  cluster_time_limited_trainer()— SLURM/cluster jobs with wall-clock limit
+  10. reproducible_trainer()       — Deterministic, full-precision for publications
+
+Usage in your training script:
+    from assets.advanced_trainer_configs import single_gpu_trainer
+    trainer = single_gpu_trainer(max_epochs=50, experiment_name="run_001")
+    trainer.fit(model, datamodule)
+    trainer.test(model, datamodule)
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+try:
+    import lightning as L
+    from lightning.pytorch.callbacks import (
+        ModelCheckpoint, EarlyStopping, LearningRateMonitor,
+        DeviceStatsMonitor, RichProgressBar,
+    )
+    from lightning.pytorch import loggers as pl_loggers
+    from lightning.pytorch.strategies import DDPStrategy, FSDPStrategy
+    LIGHTNING_PKG = "lightning"
+except ImportError:
+    try:
+        import pytorch_lightning as L
+        from pytorch_lightning.callbacks import (
+            ModelCheckpoint, EarlyStopping, LearningRateMonitor,
+        )
+        from pytorch_lightning import loggers as pl_loggers
+        from pytorch_lightning.strategies import DDPStrategy, FSDPStrategy
+        RichProgressBar = DeviceStatsMonitor = None
+        LIGHTNING_PKG = "pytorch_lightning"
+    except ImportError:
+        raise ImportError("Install: pip install lightning")
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 1. BASIC TRAINER — Quick prototyping
+# ══════════════════════════════════════════════════════════════════════════════
+
+def basic_trainer(max_epochs: int = 10) -> "L.Trainer":
+    """
+    Minimal trainer for quick prototyping.
+    Auto-selects GPU/CPU, minimal logging.
+    """
+    return L.Trainer(
+        max_epochs=max_epochs,
+        accelerator="auto",
+        devices="auto",
+        enable_progress_bar=True,
+        logger=True,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 2. DEBUG TRAINER — Fast dev run + anomaly detection
+# ══════════════════════════════════════════════════════════════════════════════
+
+def debug_trainer() -> "L.Trainer":
+    """
+    Debug trainer: runs 1 batch through train/val/test to find bugs fast.
+    Enables gradient anomaly detection (NaN/Inf catching).
+    """
+    return L.Trainer(
+        fast_dev_run=True,
+        accelerator="cpu",
+        detect_anomaly=True,
+        log_every_n_steps=1,
+        enable_progress_bar=True,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 3. SINGLE GPU TRAINER — Production single GPU
+# ══════════════════════════════════════════════════════════════════════════════
+
+def single_gpu_trainer(
+    max_epochs: int = 100,
+    experiment_name: str = "experiment",
+    version: str | None = None,
+    log_dir: str | Path = "logs/",
+    monitor: str = "val/loss",
+    monitor_mode: str = "min",
+    patience: int = 10,
+) -> "L.Trainer":
+    """
+    Production-ready single GPU trainer.
+    Features: mixed precision, checkpointing (top-3 + last), early stopping,
+              LR monitor, CSV + TensorBoard loggers.
+    """
+    log_dir = Path(log_dir)
+    ckpt_dir = log_dir / "checkpoints" / experiment_name
+
+    callbacks = [
+        ModelCheckpoint(
+            dirpath=ckpt_dir,
+            filename=f"{experiment_name}-{{epoch:02d}}-{{{monitor}:.4f}}",
+            monitor=monitor, mode=monitor_mode,
+            save_top_k=3, save_last=True, verbose=True,
+        ),
+        EarlyStopping(monitor=monitor, mode=monitor_mode, patience=patience, verbose=True),
+        LearningRateMonitor(logging_interval="epoch"),
+    ]
+    if RichProgressBar is not None:
+        callbacks.append(RichProgressBar())
+
+    # TensorBoard required — version= prevents fold/run log collision
+    loggers = [
+        pl_loggers.TensorBoardLogger(save_dir=str(log_dir), name=experiment_name, version=version),
+        pl_loggers.CSVLogger(save_dir=str(log_dir), name=experiment_name, version=version),
+    ]
+    log_path = Path(log_dir) / experiment_name / (version or "version_0")
+    print(f"GPU: {__import__('torch').cuda.get_device_name(0) if __import__('torch').cuda.is_available() else 'WARNING: No GPU detected'}")
+    print(f"Logs → {log_path}/   run: tensorboard --logdir={log_dir}")
+
+    return L.Trainer(
+        max_epochs=max_epochs,
+        accelerator="gpu", devices=1,
+        precision="16-mixed",
+        gradient_clip_val=1.0,
+        callbacks=callbacks, logger=loggers,
+        log_every_n_steps=10,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 4. MULTI-GPU DDP TRAINER — Distributed Data Parallel
+# ══════════════════════════════════════════════════════════════════════════════
+
+def multi_gpu_ddp_trainer(
+    max_epochs: int = 100,
+    num_gpus: int = 4,
+    experiment_name: str = "experiment",
+    log_dir: str | Path = "logs/",
+    monitor: str = "val/loss",
+    monitor_mode: str = "min",
+) -> "L.Trainer":
+    """
+    Multi-GPU training with DDP strategy.
+    Best for: standard DL models < 500M parameters.
+    Syncs batch norm across GPUs automatically.
+    """
+    log_dir = Path(log_dir)
+    ckpt_dir = log_dir / "checkpoints" / experiment_name
+
+    callbacks = [
+        ModelCheckpoint(
+            dirpath=ckpt_dir,
+            filename=f"{experiment_name}-{{epoch:02d}}-{{{monitor}:.4f}}",
+            monitor=monitor, mode=monitor_mode,
+            save_top_k=3, save_last=True,
+        ),
+        EarlyStopping(monitor=monitor, mode=monitor_mode, patience=10),
+        LearningRateMonitor(logging_interval="step"),
+    ]
+
+    loggers = [pl_loggers.CSVLogger(save_dir=str(log_dir), name=experiment_name)]
+
+    return L.Trainer(
+        max_epochs=max_epochs,
+        accelerator="gpu", devices=num_gpus,
+        strategy=DDPStrategy(
+            find_unused_parameters=False,
+            gradient_as_bucket_view=True,
+        ),
+        precision="16-mixed",
+        gradient_clip_val=1.0,
+        sync_batchnorm=True,
+        callbacks=callbacks, logger=loggers,
+        log_every_n_steps=50,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 5. LARGE MODEL FSDP TRAINER — Fully Sharded Data Parallel
+# ══════════════════════════════════════════════════════════════════════════════
+
+def large_model_fsdp_trainer(
+    max_epochs: int = 100,
+    num_gpus: int = 8,
+    experiment_name: str = "large_model",
+    log_dir: str | Path = "logs/",
+    cpu_offload: bool = False,
+) -> "L.Trainer":
+    """
+    FSDP trainer for large models (500M+ parameters).
+    Shards model weights across GPUs — each GPU holds a fraction of params.
+    Set cpu_offload=True if you run out of GPU memory even with FSDP.
+    Requires BF16 capable hardware (A100/H100).
+    """
+    import torch.nn as nn
+    log_dir = Path(log_dir)
+    ckpt_dir = log_dir / "checkpoints" / experiment_name
+
+    callbacks = [
+        ModelCheckpoint(
+            dirpath=ckpt_dir,
+            filename=f"{experiment_name}-{{epoch:02d}}-{{val_loss:.4f}}",
+            monitor="val/loss", mode="min",
+            save_top_k=3, save_last=True,
+        ),
+        LearningRateMonitor(logging_interval="step"),
+    ]
+
+    loggers = [pl_loggers.CSVLogger(save_dir=str(log_dir), name=experiment_name)]
+
+    return L.Trainer(
+        max_epochs=max_epochs,
+        accelerator="gpu", devices=num_gpus,
+        strategy=FSDPStrategy(
+            sharding_strategy="FULL_SHARD",
+            activation_checkpointing_policy={
+                nn.TransformerEncoderLayer,
+                nn.TransformerDecoderLayer,
+            },
+            cpu_offload=cpu_offload,
+        ),
+        precision="bf16-mixed",
+        gradient_clip_val=1.0,
+        accumulate_grad_batches=4,
+        callbacks=callbacks, logger=loggers,
+        log_every_n_steps=10,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 6. DEEPSPEED TRAINER — Very large models (10B+)
+# ══════════════════════════════════════════════════════════════════════════════
+
+def deepspeed_trainer(
+    max_epochs: int = 100,
+    num_gpus: int = 8,
+    stage: int = 3,
+    experiment_name: str = "xlarge_model",
+    log_dir: str | Path = "logs/",
+) -> "L.Trainer":
+    """
+    DeepSpeed trainer for very large models (>10B parameters).
+    Stage 3 shards optimizer states, gradients, AND parameters across GPUs.
+    Requires: pip install deepspeed
+    """
+    log_dir = Path(log_dir)
+    ckpt_dir = log_dir / "checkpoints" / experiment_name
+
+    callbacks = [
+        ModelCheckpoint(
+            dirpath=ckpt_dir, save_top_k=3, save_last=True,
+            every_n_train_steps=1000,
+        ),
+        LearningRateMonitor(logging_interval="step"),
+    ]
+    loggers = [pl_loggers.CSVLogger(save_dir=str(log_dir), name=experiment_name)]
+
+    return L.Trainer(
+        max_epochs=max_epochs,
+        accelerator="gpu", devices=num_gpus,
+        strategy=f"deepspeed_stage_{stage}",
+        precision="16-mixed",
+        gradient_clip_val=1.0,
+        accumulate_grad_batches=4,
+        callbacks=callbacks, logger=loggers,
+        log_every_n_steps=10,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 7. HYPERPARAMETER SEARCH TRAINER — Lightweight sweep runner
+# ══════════════════════════════════════════════════════════════════════════════
+
+def hparam_search_trainer(max_epochs: int = 20) -> "L.Trainer":
+    """
+    Lightweight trainer for hyperparameter sweeps (Optuna, Ray Tune, W&B Sweeps).
+    No checkpointing, no heavy logging, uses 50% of batches for speed.
+    """
+    return L.Trainer(
+        max_epochs=max_epochs,
+        accelerator="auto", devices=1,
+        enable_checkpointing=False,
+        logger=False,
+        enable_progress_bar=False,
+        limit_train_batches=0.5,
+        limit_val_batches=0.5,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 8. OVERFIT TEST TRAINER — Verify model capacity
+# ══════════════════════════════════════════════════════════════════════════════
+
+def overfit_test_trainer(num_batches: int = 10, max_epochs: int = 100) -> "L.Trainer":
+    """
+    Overfit on a tiny subset to verify the model CAN learn.
+    If it can't overfit on 10 batches, there's a model/optimizer bug.
+    """
+    return L.Trainer(
+        max_epochs=max_epochs,
+        accelerator="auto", devices=1,
+        overfit_batches=num_batches,
+        log_every_n_steps=1,
+        enable_progress_bar=True,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 9. CLUSTER TIME-LIMITED TRAINER — SLURM/HPC wall-clock aware
+# ══════════════════════════════════════════════════════════════════════════════
+
+def cluster_time_limited_trainer(
+    max_time_hours: float = 23.5,
+    max_epochs: int = 1000,
+    checkpoint_dir: str | Path = "checkpoints/",
+) -> "L.Trainer":
+    """
+    Time-aware trainer for SLURM/HPC jobs.
+    Saves last checkpoint automatically when time limit approaches.
+    Resume from last.ckpt on re-submission.
+
+    Usage:
+        trainer = cluster_time_limited_trainer(max_time_hours=23.5)
+        trainer.fit(model, dm, ckpt_path="checkpoints/last.ckpt")  # resumes if exists
+    """
+    from datetime import timedelta
+    checkpoint_dir = Path(checkpoint_dir)
+
+    callbacks = [
+        ModelCheckpoint(
+            dirpath=checkpoint_dir,
+            save_top_k=3, save_last=True,
+            every_n_epochs=5, verbose=False,
+        ),
+    ]
+    if RichProgressBar is not None:
+        callbacks.append(RichProgressBar())
+
+    return L.Trainer(
+        max_epochs=max_epochs,
+        max_time=timedelta(hours=max_time_hours),
+        accelerator="gpu", devices="auto",
+        callbacks=callbacks,
+        log_every_n_steps=50,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# 10. REPRODUCIBLE TRAINER — Deterministic results for publications
+# ══════════════════════════════════════════════════════════════════════════════
+
+def reproducible_trainer(
+    seed: int = 42,
+    max_epochs: int = 100,
+    experiment_name: str = "reproducible",
+    log_dir: str | Path = "logs/",
+) -> "L.Trainer":
+    """
+    Fully deterministic trainer for reproducible research.
+    Uses full FP32 precision, deterministic CUDA ops.
+    NOTE: Slower than mixed precision — only use for final publication runs.
+    """
+    L.seed_everything(seed, workers=True)
+    log_dir = Path(log_dir)
+
+    callbacks = [
+        ModelCheckpoint(
+            dirpath=log_dir / "checkpoints" / experiment_name,
+            filename=f"{experiment_name}-{{epoch:02d}}-{{val_loss:.4f}}",
+            monitor="val/loss", mode="min",
+            save_top_k=3, save_last=True,
+        ),
+        LearningRateMonitor(logging_interval="epoch"),
+    ]
+    loggers = [
+        pl_loggers.CSVLogger(save_dir=str(log_dir), name=experiment_name),
+    ]
+
+    return L.Trainer(
+        max_epochs=max_epochs,
+        accelerator="gpu", devices=1,
+        precision="32-true",
+        deterministic=True,
+        benchmark=False,
+        callbacks=callbacks, logger=loggers,
+        log_every_n_steps=50,
+    )
+
+
+# ══════════════════════════════════════════════════════════════════════════════
+# Quick selection guide
+# ══════════════════════════════════════════════════════════════════════════════
+
+if __name__ == "__main__":
+    print("""
+Advanced Trainer Configurations — BMAD DL Lifecycle
+(Adapted from K-Dense AI claude-scientific-skills)
+
+╔══════════════════════╦═════════════════════════════════════════════════╗
+║ Scenario             ║ Use                                             ║
+╠══════════════════════╬═════════════════════════════════════════════════╣
+║ Quick test           ║ basic_trainer()                                 ║
+║ Find bugs            ║ debug_trainer()                                 ║
+║ Verify model learns  ║ overfit_test_trainer()                          ║
+║ Hparam sweep         ║ hparam_search_trainer()                         ║
+║ Production 1 GPU     ║ single_gpu_trainer()                            ║
+║ Production N GPUs    ║ multi_gpu_ddp_trainer(num_gpus=4)               ║
+║ Large model (500M+)  ║ large_model_fsdp_trainer(num_gpus=8)            ║
+║ Very large (10B+)    ║ deepspeed_trainer(num_gpus=8, stage=3)          ║
+║ SLURM cluster        ║ cluster_time_limited_trainer(max_time_hours=23) ║
+║ Publication result   ║ reproducible_trainer(seed=42)                   ║
+╚══════════════════════╩═════════════════════════════════════════════════╝
+
+After training, analyze with:
+    python3 scripts/parse_training_logs.py logs/<exp>/version_0/metrics.csv docs/prd/01_PRD.md
+    python3 scripts/plot_training_curves.py logs/<exp>/version_0/metrics.csv
+""")