AlterLab-Academic-Skills alterlab-pytorch-lightning
Part of the AlterLab Academic Skills suite. Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.
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skills/data-science/alterlab-pytorch-lightning/SKILL.mdPyTorch 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.
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:
- Initialization -
and__init__()setup() - Training Loop -
training_step(batch, batch_idx) - 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:
- Download and process data (single-process)prepare_data()
- Create datasets and apply transforms (per-GPU)setup()
- Return training DataLoadertrain_dataloader()
- Return validation DataLoaderval_dataloader()
- Return test DataLoadertest_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)
- Neptune (NeptuneLogger)
- Comet (CometLogger)
- CSV (CSVLogger)
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
instead ofself.device.cuda() - Hyperparameter saving - Use
inself.save_hyperparameters()__init__() - Metric logging - Use
for automatic aggregation across devicesself.log() - Reproducibility - Use
andseed_everything()Trainer(deterministic=True) - Debugging - Use
to test with 1 batchTrainer(fast_dev_run=True)
Detailed documentation: Read
references/best_practices.md for common patterns and pitfalls.
Quick Workflow
-
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()) -
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) -
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:
- Complete LightningModule boilerplatetemplate_lightning_module.py
- Complete LightningDataModule boilerplatetemplate_datamodule.py
- Common Trainer configuration examplesquick_trainer_setup.py
references/
Detailed documentation for each PyTorch Lightning component:
- Comprehensive LightningModule guide (methods, hooks, properties)lightning_module.md
- Trainer configuration and parameterstrainer.md
- LightningDataModule patterns and methodsdata_module.md
- Built-in and custom callbackscallbacks.md
- Logger integrations and usagelogging.md
- DDP, FSDP, DeepSpeed comparison and setupdistributed_training.md
- Common patterns, tips, and pitfallsbest_practices.md