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skills/K-Dense-AI/scientific-agent-skills/pytorch-lightning

pytorch-lightning

Official1
K-Dense-AI/scientific-agent-skills·Data Science Tools·Audit passed·Snapshot 8a15c8b42546
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Summary

Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.

SKILL.md

PyTorch Lightning

Overview

PyTorch Lightning is a deep learning framework that organizes PyTorch code to eliminate boilerplate while maintaining full flexibility. Automate training workflows, multi-device orchestration, and implement best practices for neural network training and scaling across multiple GPUs/TPUs.

Current upstream: lightning 2.6.4 (PyPI, May 2026). Docs: lightning.ai/docs/pytorch/stable. Use import lightning as L (the pytorch-lightning package name still installs the same library).

Installation

uv pip install lightning

Optional extras:

uv pip install lightning[extra]    # loggers, strategies, etc.
uv pip install wandb mlflow        # specific loggers as needed

When to Use This Skill

This skill should be used when:

  • Building, training, or deploying neural networks using PyTorch Lightning
  • Organizing PyTorch code into LightningModules
  • Configuring Trainers for multi-GPU/TPU training
  • Implementing data pipelines with LightningDataModules
  • Working with callbacks, logging, and distributed training strategies (DDP, FSDP, DeepSpeed)
  • Structuring deep learning projects professionally

Core Capabilities

1. LightningModule - Model Definition

Organize PyTorch models into six logical sections:

  1. Initialization - __init__() and setup()
  2. Training Loop - training_step(batch, batch_idx)
  3. Validation Loop - validation_step(batch, batch_idx)
  • Test Loop - test_step(batch, batch_idx)
  • Prediction - predict_step(batch, batch_idx)
  • Optimizer Configuration - configure_optimizers()
  • Quick template reference: See scripts/template_lightning_module.py for a complete boilerplate.

    Detailed documentation: Read references/lightning_module.md for comprehensive method documentation, hooks, properties, and best practices.

    2. Trainer - Training Automation

    The Trainer automates the training loop, device management, gradient operations, and callbacks. Key features:

    • Multi-GPU/TPU support with strategy selection (DDP, FSDP, DeepSpeed)
    • Automatic mixed precision training
    • Gradient accumulation and clipping
    • Checkpointing and early stopping
    • Progress bars and logging

    Quick setup reference: See scripts/quick_trainer_setup.py for common Trainer configurations.

    Detailed documentation: Read references/trainer.md for all parameters, methods, and configuration options.

    3. LightningDataModule - Data Pipeline Organization

    Encapsulate all data processing steps in a reusable class:

    1. prepare_data() - Download and process data (single-process)
    2. setup() - Create datasets and apply transforms (per-GPU)
    3. train_dataloader() - Return training DataLoader
    4. val_dataloader() - Return validation DataLoader
    5. test_dataloader() - Return test DataLoader

    Quick template reference: See scripts/template_datamodule.py for a complete boilerplate.

    Detailed documentation: Read references/data_module.md for method details and usage patterns.

    4. Callbacks - Extensible Training Logic

    Add custom functionality at specific training hooks without modifying your LightningModule. Built-in callbacks include:

    • ModelCheckpoint - Save best/latest models
    • EarlyStopping - Stop when metrics plateau
    • LearningRateMonitor - Track LR scheduler changes
    • BatchSizeFinder - Auto-determine optimal batch size

    Detailed documentation: Read references/callbacks.md for built-in callbacks and custom callback creation.

    5. Logging - Experiment Tracking

    Integrate with multiple logging platforms:

    • TensorBoard (default)
    • Weights & Biases (WandbLogger)
    • MLflow (MLFlowLogger)
    • Comet (CometLogger)
    • CSV (CSVLogger)

    Note: NeptuneLogger was removed in lightning 2.6.4. Use W&B, MLflow, or TensorBoard instead.

    Log metrics using self.log("metric_name", value) in any LightningModule method.

    Detailed documentation: Read references/logging.md for logger setup and configuration.

    6. Distributed Training - Scale to Multiple Devices

    Choose the right strategy based on model size:

    • DDP - For models <500M parameters (ResNet, smaller transformers)
    • FSDP - For models 500M+ parameters (large transformers, recommended for Lightning users)
    • DeepSpeed - For cutting-edge features and fine-grained control

    Configure with: Trainer(strategy="ddp", accelerator="gpu", devices=4)

    Detailed documentation: Read references/distributed_training.md for strategy comparison and configuration.

    7. Best Practices

    • Device agnostic code - Use self.device instead of .cuda()
    • Hyperparameter saving - Use self.save_hyperparameters() in __init__()
    • Metric logging - Use self.log() for automatic aggregation across devices
    • Reproducibility - Use seed_everything() and Trainer(deterministic=True)
    • Debugging - Use Trainer(fast_dev_run=True) to test with 1 batch

    Detailed documentation: Read references/best_practices.md for common patterns and pitfalls.

    Quick Workflow

    1. Define model:

      class MyModel(L.LightningModule):
          def __init__(self):
              super().__init__()
              self.save_hyperparameters()
              self.model = YourNetwork()
      
          def training_step(self, batch, batch_idx):
              x, y = batch
              loss = F.cross_entropy(self.model(x), y)
              self.log("train_loss", loss)
              return loss
      
          def configure_optimizers(self):
              return torch.optim.Adam(self.parameters())
      
    2. Prepare data:

      # Option 1: Direct DataLoaders
      train_loader = DataLoader(train_dataset, batch_size=32)
      
      # Option 2: LightningDataModule (recommended for reusability)
      dm = MyDataModule(batch_size=32)
      
    3. Train:

      trainer = L.Trainer(max_epochs=10, accelerator="gpu", devices=2)
      trainer.fit(model, train_loader)  # or trainer.fit(model, datamodule=dm)
      

    Resources

    scripts/

    Executable Python templates for common PyTorch Lightning patterns:

    • template_lightning_module.py - Complete LightningModule boilerplate
    • template_datamodule.py - Complete LightningDataModule boilerplate
    • quick_trainer_setup.py - Common Trainer configuration examples

    references/

    Detailed documentation for each PyTorch Lightning component:

    • lightning_module.md - Comprehensive LightningModule guide (methods, hooks, properties)
    • trainer.md - Trainer configuration and parameters
    • data_module.md - LightningDataModule patterns and methods
    • callbacks.md - Built-in and custom callbacks
    • logging.md - Logger integrations and usage
    • distributed_training.md - DDP, FSDP, DeepSpeed comparison and setup
    • best_practices.md - Common patterns, tips, and pitfalls

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