Checkpointing

Checkpointing lets you save and resume evolution runs without losing progress, and seed one experiment with the results of another. A long evolution run can take hours; checkpoints mean a crash or a configuration change does not cost you everything. Cross-phase seeding lets you chain experiments - evolve basic capabilities first, then build on them with different fitness pressure.

Checkpoint System

checkpoint {
    every: 100 generations    // save interval
    keep:  3                  // retained checkpoints
}

Fields

.quale Field	Config Field	Default	Description
every	CheckpointInterval	100	Generations between periodic checkpoint saves
keep	CheckpointKeep	3	Maximum number of checkpoint files to retain (older ones are deleted)

Contents

Each checkpoint (.quale-ckpt) contains:

• Full population (all genomes)
• Current generation number
• Best genome observed so far
• Generation history (fitness stats)
• Innovation tracker state (next node ID, next innovation number)
• Sensor and actuator name lists (for pathway analysis in quale inspect)

File Location

Checkpoints are saved to checkpoints/<run_name>/ relative to the current working directory. The run name is derived from the evolve block name, lowercased.

Note: Checkpoint pruning sorts filenames lexicographically (e.g., checkpoint_gen1000.quale-ckpt sorts before checkpoint_gen200.quale-ckpt). This can cause unexpected behavior when generation numbers differ in digit count, potentially pruning a more recent checkpoint instead of the oldest.

Note: There is an off-by-one in checkpoint generation numbering. The save trigger checks stats.Generation (set before the generation counter increments), but the filename uses ee.Generation (already incremented). So a checkpoint triggered at generation 100 is saved as checkpoint_gen101.quale-ckpt.

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Resuming

Use quale evolve --resume <path> to continue from a checkpoint. The checkpoint restores:

• Population
• Generation counter
• Best genome
• History
• Innovation tracker state

The evolution configuration (mutation rates, speciation settings, etc.) comes from the .quale file, not the checkpoint - so you can adjust parameters when resuming.

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Cross-Phase Seeding

evolve Phase2 {
    seed_from: Phase1
    // or: seed_from: "checkpoints/phase1_gen474.quale-ckpt"
    // ... all other fields ...
}

seed_from initializes the population from a prior experiment:

• When referencing an evolve block name (seed_from: Phase1), the runtime looks for the most recent checkpoint produced by that block
• When referencing a file path (seed_from: "checkpoints/...") , the runtime loads that specific checkpoint
• The generation counter and history are reset to zero
• No configuration is inherited - the evolve block is fully self-contained
• If the source population is smaller than the target population, additional genomes are created by mutating copies of the seed genomes

This enables multi-phase experiments where Phase 1 evolves basic capabilities and Phase 2 builds on them with different fitness pressure or world configuration.