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
• Float8 — tensors that arrive as float8_e4m3fn/float8_e5m2 (FSDP2, torchao) are stored bit-exact with no configuration. save_dtype="fp8" additionally quantizes fp32/bf16 down to one byte per element against a per-tensor scale — a quarter the size, four significant bits, so for archived copies rather than checkpoints you resume from
• 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 3.11-3.14 — 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)

Say which topology the manager is for. Under torchrun, "auto" takes it from the launcher:

torchrun --nproc_per_node=8 train.py

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

The ranks then share one store, through the explicit create_snapshot / save_rank / finalize_snapshot flow. If instead each rank writes to a directory of its own — one store per process, no coordination — then every one of them is single-rank and should say so:

mgr = CheckpointManager(f"./checkpoints/rank_{rank}", world_size=1, rank=0)

Until 0.0.9 the launcher's variables were adopted whenever nothing was stated. That is no longer the default: leaving it unsaid under a multi-rank launcher is an error naming both numbers and the ways forward. A single process is unaffected and still needs no configuration.

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

Two layers, and the line between them is the whole design. The Rust crate stores named tensors and has never heard of PyTorch; everything that knows what a state_dict is lives in the Python package on top. That is why Moonclip can sit under a runtime like Ravex without either one owning the other — and why import moonclip does not import torch.

src/ — the engine (Rust)

src/
├── lib.rs           # Crate root
├── coordinator/     # Snapshot lifecycle: create → save_rank → finalize, per rank
│   ├── mod.rs       #   The Coordinator facade and the Core behind it
│   ├── recovery.rs  #   Putting a store back together at open time
│   ├── saver.rs     #   The background thread a save is handed to
│   └── tests.rs     #   Reaches into Core and the packs; not an integration test
├── tensor.rs        # Per-tensor delta tracking and storage
├── cast.rs          # fp32 ↔ bf16/fp16/float8 casting, in parallel
├── delta.rs         # XOR delta computation, in parallel
├── shuffle.rs       # Byte-plane transpose, so a delta compresses
├── compression.rs   # Zstd, as concatenated frames across cores
├── pack.rs          # The pack file: data plus its own description, one write
├── manifest.rs      # Manifest v2 — per-rank, per-tensor, lineage
├── merger.rs        # Background consolidation of delta chains
├── inflight.rs      # Which snapshots a read holds, so a merge cannot delete them
├── storage.rs       # StorageBackend trait + LocalStorage (4KB aligned)
├── s3.rs            # S3-compatible storage (AWS SigV4, no SDK)
├── remote_sync.rs   # Batched sync to the remote backend
├── pool.rs          # Moonclip's private rayon pool — see Tuning
├── hash.rs          # xxHash3-128 integrity
├── profile.rs       # Opt-in phase timing (MOONCLIP_PROFILE)
├── python.rs        # PyO3 bindings — the only file that knows Python exists
└── error.rs         # Error types

python/moonclip/ — the PyTorch surface

python/moonclip/
├── __init__.py      # Re-exports; torch resolves lazily, never at import time
├── pytorch.py       # CheckpointManager — state dicts in, snapshots out
├── _env.py          # Reads torchrun's topology variables (detects; does not adopt)
└── *.pyi, py.typed  # Stubs, for both layers

And around them

As of 0.1.0 that is about 15.6k lines of Rust across 22 files and 1.4k of Python, covered by 222 crate tests, 19 more against a live MinIO, and 108 Python ones. Roughly half of the Rust is #[cfg(test)]: coordinator/ carries 2.2k lines of tests against 2.3k of code, which is why it is the one part of the crate laid out as a directory.

Development

cargo test                                      # Rust tests, no Python needed
maturin develop --release && pytest tests/ -v   # Python + PyTorch tests
cargo clippy --all-targets -- -D warnings       # what CI gates on

checks.yml runs clippy and cargo test on every branch push — one container, seconds. The full matrix (MinIO, the PyTorch adapter, CPython 3.11–3.14) waits for main, in ci.yml.

Both pin rust:1.97.1-bookworm, and rust-toolchain.toml pins the same version for a local build, so a red cargo clippy here means the gate is red too. That agreement is the point of the file: the two used to differ — CI on 1.90, development on 1.97 — and the crate spent a while green in CI and red locally on four findings that were not regressions, only lints the older clippy did not have.

The toolchain file is not the MSRV. rust-version in Cargo.toml says 1.83, which is what a consumer of the published crate needs; a rust-toolchain.toml applies only inside this directory and does not raise that floor. It does mean nothing verifies the 1.83 claim any more.

Note that the crate is deliberately not cargo fmt-clean: the gate is clippy, and running cargo fmt over it produces a diff nobody asked for.

License

Apache-2.0 — Minya AI