Moonclip

Stop losing checkpoints. Start training fearlessly.

Moonclip is a checkpoint engine for ML training, written in Rust with Python bindings. It tracks per-tensor deltas, skips unchanged weights entirely, and compresses the rest, so a save blocks the training loop for tens of milliseconds and the checkpoint on disk is about half the size.

Against torch.save on dense pre-training — the least favourable case, where Adam changes every parameter at every step and there is nothing to skip — that is 1.6-3.0× faster and 1.9× smaller. The gap widens on fine-tuning, LoRA and adapters, where most tensors are identical between two checkpoints.

A moonclip is the ring that holds a full circle of rounds so a revolver reloads in one motion, instead of one chamber at a time. That is the idea here: your whole training state goes down and comes back in a single movement, not tensor by tensor.

Three lines in your training loop. That's it.

from moonclip import CheckpointManager

mgr = CheckpointManager("./checkpoints", save_dtype="bf16")
start_step = mgr.resume(model=model, optimizer=optimizer, scheduler=scheduler)

for step in range(start_step, 100_000):
    loss = train_step(model, batch)

    if step % 500 == 0:
        mgr.save(step=step, model=model, optimizer=optimizer,
                 metadata={"loss": f"{loss:.4f}"})

Why

Every ML engineer has lost a training run. The spot instance dies, the node crashes, the disk fills up — and your last checkpoint was 2 hours ago. So you save more often, but now checkpointing is the bottleneck: a 3B model in bf16 is ~5.5 GB per save, and torch.save blocks your training loop every time.

Moonclip fixes this at the storage layer. Instead of dumping the full state dict every time, it diffs against the previous checkpoint at the tensor level: unchanged tensors → zero I/O, changed tensors → XOR delta + zstd compression. The result is saves that are both faster and smaller.

Inspired by DECK (Meta, PVLDB 2025).

Benchmarks

MiniGPT 41.7M params, fp32 model + full AdamW optimizer state (~540 MB per checkpoint), 10 saves, CPU (bench/benchmark_checkpoints.py):

* safetensors saves the model only — no optimizer state, ~3× less data per checkpoint.

Saves are asynchronous by default: save() returns as soon as the tensor data has been copied, while hashing, delta detection, zstd compression and the disk write run on a background thread and overlap with training. Call flush() when you need the checkpoint on disk — as of 0.0.6 that means fsynced, not merely written; loads and list_snapshots() wait for pending saves automatically. Pass async_save=False for fully synchronous saves.

Resume integrity verified: max weight diff 0.0 after save → load.

Features

• Async background saves — save() returns in milliseconds; compression and I/O overlap with training (disable with async_save=False)
• Per-tensor delta tracking — unchanged tensors are skipped entirely (zero I/O), changed tensors use XOR delta compression; a cheap sampled density check bails out early when everything changed
• Parallel zstd — large tensors are compressed/decompressed as concatenated zstd frames across all cores
• Rust-native dtype casting — save_dtype="bf16" casts fp32→bf16 in parallel Rust threads before compression, auto-uncasts on load
• 4KB page-aligned writes — eliminates SSD write amplification, extends drive lifespan
• Rank-aware distributed saves — each rank saves its own shard independently, auto-detects torchrun env vars
• Hierarchical delta merging — background thread consolidates deltas to keep load times fast
• S3 backend — local SSD as primary (fast), batched sync to S3/MinIO/R2 in background
• xxHash3-128 integrity checks — every tensor verified on read, corruption detected immediately
• Auto-resume — mgr.resume() loads the latest checkpoint if it exists, returns the next step

Installation

pip install moonclip

Wheels are built for Linux x86_64 (manylinux_2_28), CPython 3.9-3.14 — the platform training actually runs on. No Rust toolchain needed there; the extension is compiled. What changed between versions is in CHANGELOG.md.

On any other platform (Windows, macOS, aarch64) pip finds no wheel and stops. Build it yourself instead, which needs a Rust toolchain:

pip install git+https://codeberg.org/JHNMACHINE/moonclip.git

# On a cloud instance without Rust (Vast.ai, RunPod, Lambda, …)
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
source $HOME/.cargo/env
pip install git+https://codeberg.org/JHNMACHINE/moonclip.git

Build from source

git clone https://codeberg.org/JHNMACHINE/moonclip.git
cd moonclip
pip install maturin
maturin develop --release

S3 Backend

Checkpoint to local SSD for speed, sync to S3-compatible storage for durability:

mgr = CheckpointManager(
    "./checkpoints",
    save_dtype="bf16",
    s3_bucket="my-bucket",
    s3_access_key="...",
    s3_secret_key="...",
    s3_endpoint="http://localhost:9000",   # MinIO / R2 / B2
    s3_path_style=True,
    sync_every_n_saves=5,
)

Multi-GPU (FSDP / DDP)

Moonclip auto-detects torchrun environment variables. No configuration needed:

torchrun --nproc_per_node=8 train.py

mgr = CheckpointManager("./checkpoints")
# mgr.rank == 3, mgr.world_size == 8  (auto-detected)
start_step = mgr.resume(model=model, optimizer=optimizer)

Tuning

Three environment variables, none required:

The parallel work runs in a pool of Moonclip's own, not rayon's global one, so it neither claims every core on the machine nor competes with your application's par_iter. On a node running several ranks the default splits the cores between them — LOCAL_WORLD_SIZE is what torchrun sets — so eight ranks on 128 cores take 16 threads each rather than 128 apiece.

Set MOONCLIP_THREADS when that guess is wrong for your box: the machine is Moonclip's alone (give it every core), or the ranks do not all checkpoint at the same time.

Architecture

src/
├── cast.rs          # Rust-native fp32↔bf16/fp16 casting (rayon parallel)
├── coordinator.rs   # Rank-aware snapshot lifecycle
├── tensor.rs        # Per-tensor delta tracking and storage
├── manifest.rs      # Manifest v2: per-rank, per-tensor, lineage
├── compression.rs   # Zstd compression (parallel frames)
├── delta.rs         # XOR delta computation (rayon parallel)
├── shuffle.rs       # Byte-plane transpose before compressing a delta
├── pack.rs          # One pack file per rank, with a recovery descriptor
├── merger.rs        # Background delta merging
├── remote_sync.rs   # Batched S3 sync
├── s3.rs            # S3-compatible storage (AWS SigV4)
├── storage.rs       # StorageBackend trait + LocalStorage (4KB aligned)
├── pool.rs          # The private rayon pool (see Tuning)
├── profile.rs       # Opt-in phase timing (MOONCLIP_PROFILE)
├── hash.rs          # xxHash3-128 integrity
├── python.rs        # PyO3 bindings
└── error.rs         # Error types

Development

cargo test                          # Rust tests
maturin develop --release && pytest tests/ -v   # Python + PyTorch tests

License

Apache-2.0 — Minya AI