diffkeeper

command module

v1.0.0 Latest Latest Go to latest Published: Nov 10, 2025 License: Apache-2.0 Imports: 25 Imported by: 0

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github.com/saworbit/diffkeeper

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README ¶

DiffKeeper: Lightweight State Recovery for Containers (v1.0 Released - v2.0 eBPF Preview)

Capture file-level state changes in containerized workloads for fast recovery and debugging. No large persistent volumes required.

Updated: November 9, 2025
Version: v2.0 Preview (eBPF Monitoring + Auto-Injection) Author: Shane Anthony Wall Contact: shaneawall@gmail.com

The Problem

Many containerized applications write stateful files (checkpoints, world saves, configs, caches) but don't need full database-grade persistence. Current options are problematic:

Persistent Volumes (PVs) - Provision 10GB storage for 10MB of actual changes; slow attach/detach cycles; vendor costs
External object storage (S3/MinIO) - Network latency; manual sync; complex failure modes
StatefulSets - Overkill for simple file-based state; full volume snapshots instead of granular changes
No solution - Accept data loss on pod crashes/evictions and rebuild from scratch

Result: Wasted storage costs, slow recovery times, and lost work when containers restart.

The Solution

DiffKeeper is a 6.5MB Go agent that runs inside your container to:

Intercept write syscalls at the kernel level via eBPF (fsnotify used as fallback)
Capture binary diffs when files change (bsdiff + content-addressable storage)
Store deltas externally (BoltDB on small PV or host mount)
Verify integrity on recovery (Merkle trees)
Replay changes on restart for sub-100ms recovery

v1.0 Update: Binary diff support now available! Reduces storage by 50-80% compared to full-file snapshots for incremental updates.

[Your App] --writes--> [DiffKeeper Agent] --stores--> BoltDB delta files
                                ^
                                |
                         replays on restart

Key Benefits:

Sub-Âµs capture latency: Kernel interception fires within <1Âµs for write/pwrite/writev
<0.5% CPU overhead: Adaptive eBPF profiler traces only predicted hot paths
Compile once, run everywhere: CO-RE probes + BTFHub downloads adapt to mixed kernels (4.18+) with no per-node rebuilds
50-80% storage savings: Binary diffs store only changed bytes
Content deduplication + Merkle trees: CAS + integrity proofs for every version
Fast recovery: <100ms replays even under heavy churn
Auto-injection for containers: Trace CRI events and attach without wrapping entrypoints
Drop-in compatible: Works with Docker, Kubernetes, Podman, bare-metal

Best For: Game servers, ML checkpoints, CI/CD caches, edge IoT, streaming analytics

Kubernetes & Helm

The repository ships with ready-to-run manifests under k8s/:

k8s/deployment.yaml – Sidecar pattern with init-container replay.
k8s/rbac.yaml – Minimal service account + ClusterRoleBinding.
k8s/helm/diffkeeper – Helm chart for production clusters (configurable state dir, BTF cache, workloads).

kubectl apply -f k8s/rbac.yaml
helm install diffkeeper k8s/helm/diffkeeper --namespace diffkeeper --create-namespace

Helm values expose image tags, dedicated workload commands, and cache locations so you can drop-in DiffKeeper alongside any StatefulSet.

Architecture

+----------------------+        syscalls         +--------------------------------------+
|   Container Runtime  | ----------------------> | DiffKeeper Agent (v2.0)               |
| (Docker/Kube/CRI-O)  |                         |  - eBPF Manager (kprobes/tracepoints) |
+----------------------+                         |  - Hot-path Profiler (EMA/ringbuf)   |
              |                                  |  - Lifecycle Tracer (auto-injection) |
              | <----- auto-inject agent ------- |  - BlueShift (capture + predict)     |
              v                                  |  - RedShift (replay/rollback)        |
     +--------------------+                      +------------------+-------------------+
     | Target Workload    |                                       |
     +--------------------+                                       v
                                                     BoltDB Delta Store (CAS + metadata)

How it works (v2.0 with eBPF + Binary Diffs):

eBPF manager (kprobes on vfs_write, pwrite, writev) emits syscall events in <1Âµs via perf buffers (fsnotify acts as fallback when kernels lack eBPF).
Adaptive profiler samples those events every 100ms, computes exponential moving averages, and updates hot-path filters (<0.5% CPU steady state).
Lifecycle tracer hooks sched_process_exec and CRI runtimes to auto-inject the agent into new pods/containers when --auto-inject is enabled.
BlueShift receives filtered events, hashes changed files, and determines whether to produce a snapshot or binary diff.
Binary diff computation: Compares current and previous versions (bsdiff/xdelta) while chunking >1GB files into 4MB slices.
Content-addressable storage (CAS): Deduplicates chunks/diffs by hash and persists them in BoltDB.
Merkle tree generation + metadata: Every version stores Merkle roots, version counters, and chunk metadata to prevent corruption.
Periodic snapshots: Full snapshots occur every N versions (default 10) to prevent long diff chains for hot files.
On restart, RedShift replays metadata, verifies Merkle trees, and rebuilds state to disk in <100ms even under heavy churn.

BTF/CO-RE Portability: DiffKeeper automatically looks for /sys/kernel/btf/vmlinux, falls back to a cached copy in --btf-cache-dir, or downloads a tailored BTF from BTFHub-Archive. The loader feeds that spec into CO-RE programs so the same diffkeeper.bpf.o runs across Ubuntu, CentOS, Fedora, Amazon Linux, and other kernels â‰¥4.18 without recompilation. See docs/btf-core-guide.md for setup details and docs/supported-kernels.md for the current compatibility matrix.

Quick Start

Prerequisites

Docker 24+ (required for demo)
Go 1.23+ (for building from source)
Platform: Linux containers (agent uses Unix syscalls like exec)
Kernel: Linux 4.18+ with eBPF + CAP_BPF/CAP_SYS_ADMIN for kernel interception (older kernels automatically fall back to fsnotify)
100MB free disk space

Note: While the agent can be built on Windows/macOS, it must run inside Linux containers due to platform-specific system calls.

1. Install the Agent

# Download binary
curl -sSL https://github.com/saworbit/diffkeeper/releases/latest/download/agent-linux-amd64 -o diffkeeper
chmod +x diffkeeper

# Or build from source
go install github.com/saworbit/diffkeeper/cmd/agent@latest

2. (Optional) Build eBPF Probes

# Requires clang/llvm and a kernel-specific vmlinux.h (see docs/ebpf-guide.md)
make build-ebpf

This produces bin/ebpf/diffkeeper.bpf.o. If the file is missing, DiffKeeper will automatically log a warning and revert to fsnotify.

BTF data is fetched on-demand. Override the cache directory with --btf-cache-dir, point to an internal mirror via --btfhub-mirror, or disable downloads entirely with --disable-btfhub-download (requires /sys/kernel/btf/vmlinux).

3. Docker Usage

Wrap any container command with binary diffs enabled:

docker run -it \
  -v ./deltas:/deltas \
  your-app:latest \
  /bin/sh -c "./diffkeeper \
    --state-dir=/app/data \
    --store=/deltas/db.bolt \
    --enable-diff=true \
    your-app-start"

Need verbose logs while troubleshooting? Append --debug before the wrapped command to emit watcher events and delta details: ./diffkeeper --debug --state-dir=...

Example - Nginx config persistence with binary diffs:

docker run -v ./deltas:/deltas nginx:alpine \
  /bin/sh -c "./diffkeeper \
    --state-dir=/etc/nginx \
    --store=/deltas/db.bolt \
    --enable-diff=true \
    --snapshot-interval=10 \
    nginx -g 'daemon off;'"

CLI Flags (v2.0):

Core Flags:

--state-dir: Directory to watch for state changes (default: /data)
--store: Path to delta storage file (default: /deltas/db.bolt)
--debug: Enable verbose debug logging (default: false)

Binary Diff Flags:

--enable-diff: Enable binary diffs (default: true)
--diff-library: Diff algorithm - "bsdiff" or "xdelta" (default: bsdiff)
--chunk-size: Chunk size in MB for large files (default: 4)
--hash-algo: Hash algorithm - "sha256" or "blake3" (default: sha256)
--dedup-scope: Deduplication scope - "container" or "cluster" (default: container)
--snapshot-interval: Create full snapshot every N versions (default: 10)

eBPF / Profiler Flags:

--enable-ebpf: Turn on kernel-level interception (default: true)
--ebpf-program: Path to compiled *.bpf.o artifact (default: bin/ebpf/diffkeeper.bpf.o)
--fallback-fsnotify: Automatically switch back to fsnotify if eBPF load fails (default: true)
--profiler-interval: Sampling cadence for hot-path EMA (default: 100ms)
--enable-profiler: Toggle adaptive profiling without disabling eBPF (default: true)
--auto-inject: Auto-inject the agent into new containers when lifecycle events fire (default: true)
--injector-cmd: Command executed during auto-injection (container ID passed as argument plus env metadata)
--btf-cache-dir: Cache directory for downloaded BTF specs (default: /var/cache/diffkeeper/btf)
--btfhub-mirror: Mirror URL for BTFHub-Archive assets (default: official GitHub mirror)
--disable-btfhub-download: Skip remote downloads (requires /sys/kernel/btf/vmlinux; otherwise falls back to fsnotify)

Watching Nested Directories

DiffKeeper now walks any directory as soon as it appears and attaches watchers to every level, so files dropped into newly created subfolders are captured immediately.
On Windows, where os.MkdirAll only emits a CREATE event for the top-most folder, this recursive watcher keeps nested writes safe without manual intervention.
Run with --debug to stream watcher activity when you need to confirm observers were attached or to track down paths that are being ignored.

Release Notes

Recursive directory watching is now enabled cross-platform, ensuring nested writes are captured the moment new folders appear.
Added a regression test to confirm nested directories are monitored on every OS.
--debug verbose logging documents watcher setup in the logs so you can troubleshoot missing events quickly.

4. Kubernetes Deployment

apiVersion: v1
kind: Pod
metadata:
  name: stateful-app
spec:
  initContainers:
  - name: replay-state
    image: saworbit/diffkeeper:latest
    command: ["/replay", "--state-dir=/data", "--store=/deltas/db.bolt"]
    volumeMounts:
    - name: delta-storage
      mountPath: /deltas
    - name: app-data
      mountPath: /data
      
  containers:
  - name: app
    image: your-app:latest
    command: ["/diffkeeper"]
    args:
    - --state-dir=/data
    - --store=/deltas/db.bolt
    - /app/start
    volumeMounts:
    - name: app-data
      mountPath: /data
    - name: delta-storage
      mountPath: /deltas
      
  volumes:
  - name: delta-storage
    persistentVolumeClaim:
      claimName: diffkeeper-deltas  # Small 100MB PVC
  - name: app-data
    emptyDir: {}

Real-World Use Cases

Workload	State Files	Before DiffKeeper	After DiffKeeper	Impact
Game Servers	`/world/saves.db`	Crash = full restart, lost progress	<2s replay, zero loss	+50% player retention
ML Training	`model.ckpt`	OOM eviction = hours lost	Resume from exact epoch	5-10x faster recovery
CI/CD Pipelines	`node_modules/`, build cache	Re-download dependencies (30min)	Replay cache instantly	10x faster builds
Video Processing	`/tmp/output.mp4`	Re-encode from scratch	Resume partial render	80% GPU time saved
Edge IoT	`sensor-data.json`	Manual sync on reboot	Auto-restore state	Zero data loss
Config Services	`/etc/config.yaml`	Stale config on restart	Live state replay	High availability

Performance Benchmarks

v1.0 Results from testing on AMD Ryzen 9 5900X, SSD storage:

Storage & Recovery Performance

Metric	Value	Notes
Agent binary size	6.5MB	Tested on Windows/Linux
Storage savings (binary diffs)	85.7%	Measured with 1MB file, 20 versions (10% changes each)
Recovery time (10MB file)	11.5ms	Including Merkle verification + chunk reassembly
Recovery time (per file avg)	20.67Âµs	CAS retrieval + integrity check
Capture time (1MB file)	19.6ms	Includes diff computation, CAS storage, Merkle tree
CPU overhead (idle)	0.1%	File watching only
CPU overhead (active writes)	1-3%	Diff computation + storage
Memory overhead	~50MB	Per container (includes CAS cache)

Component Performance

Operation	Time	Description
Diff computation (1MB)	18.4ms	bsdiff binary diff algorithm
Chunking (10MB file)	46.2ms	Split into 4MB chunks
Merkle verification	933Âµs	Integrity check per file
CAS lookup	134Âµs	Content-addressable retrieval
Multi-file recovery (61 files)	170ms	2.79ms per file average

Deduplication Efficiency

Scenario	Storage Saved
Identical files	50% (1 object, 2 references)
Partial updates (10% change)	85.7% (verified: 1MB file, 20 versions)
ML checkpoints (1GB, 10% change)	80-90% (estimated)
Config files (small, frequent changes)	75-85%

Test Environment:

Platform: Windows 11, AMD Ryzen 9 5900X (24 threads)
Storage: NVMe SSD
Go version: 1.21
Test dates: November 4-8, 2025
Diff chain test: 25 versions, recovery in 1.55ms

Known Limitations (v1.0 Final):

âœ… Diff reconstruction: COMPLETE (85.7% storage savings achieved)
High-write workloads (>10k writes/sec): Consider eBPF-based approach (v2.0)
Large file changes (>1GB): Automatic chunking at 1GB threshold
Database workloads: Use native WAL/replication instead
Windows: Agent runs on Linux containers only (uses Unix syscalls)

Comparison with Alternatives

Feature	StatefulSets + PV	CSI Snapshots	DiffKeeper
Storage needed	GBs (full filesystem)	GBs (block-level)	MBs (deltas only)
Recovery time	10+ seconds	5+ seconds	<5 seconds
Overhead	10%+	20%+	<2%
Granularity	Volume-level	Block-level	File-level deltas
Best for	Databases, large state	Enterprise storage	File-based apps
Cost	PV provisioning costs	Vendor fees	Open source

When to use DiffKeeper:

Small-to-medium file-based state (<10GB)
Infrequent writes (<1k/sec)
Need fast recovery without large PVs
Container-native workflows

When NOT to use DiffKeeper:

High-throughput databases (Postgres, MySQL)
Streaming/append-only logs (Kafka, Loki)
Very large files (>1GB single file)
Already have vendor storage solution working well

Roadmap

v1.0 Final (Current - November 2025) âœ…

Core Features:

âœ… Binary diff engine (bsdiff implementation)
âœ… Diff chain reconstruction (BaseSnapshotCID tracking + sequential patch application)
âœ… Content-addressable storage (CAS) with SHA256/BLAKE3 hashing
âœ… Merkle tree integrity verification
âœ… Large file chunking (automatic at 1GB threshold, configurable chunk size)
âœ… Deduplication (identical content stored once)
âœ… Periodic snapshots (every N versions to prevent long diff chains)
âœ… Schema migration (MVP â†’ v1.0 automatic upgrade)
âœ… CLI configuration (enable-diff, diff-library, chunk-size, hash-algo, etc.)

Testing & Validation:

âœ… 72 tests passing (100% pass rate)
âœ… 25+ version diff chains tested (TestDiffChain20Plus)
âœ… 85.7% storage savings measured (1MB file, 20 versions, 10% changes)
âœ… Sub-2ms recovery for complex diff chains

v1.0 Final Status:

âœ… Diff reconstruction fully implemented and tested
âœ… Storage savings verified (85.7% for incremental updates)
âœ… Performance targets exceeded (<100ms recovery, >80% savings)
âœ… Ready for production deployment

Production Ready:

Binary diff mode fully functional (no snapshot-only fallback)
Automatic diff chain management with periodic snapshots
Verified integrity via Merkle trees
Real-world storage efficiency demonstrated

v1.1 (Next Release)

Production testing (Docker + Kubernetes workloads)
ML checkpoint benchmark (real PyTorch/TensorFlow workload)
Kubernetes manifests (StatefulSet examples with PVC)
Migration guide (MVP â†’ v1.0 for existing deployments)
Docker image (official DiffKeeper container)

v2.0+ (Future)

eBPF hooks for lower overhead on high-write workloads
Kubernetes Operator + Custom Resource Definition
Multi-replica synchronization (CRDT-based)
Branch/merge support (git-like time-travel)
Live migration between nodes
Power-optimized mode for edge/IoT

Contributing

We're looking for collaborators to move this from prototype to production-ready!

How to contribute:

Try the prototype and report issues
Submit PRs for priority areas:
- eBPF probe implementation
- Chunked diff support for large files
- Kubernetes operator development
- Performance optimizations
Share your use cases and requirements

Development setup:

git clone https://github.com/saworbit/diffkeeper
cd diffkeeper
make build
make test
# Optional: run long E2E coverage when you have time
go test -tags integration ./...

Long-running diff chain/recovery suites now live behind the integration build tag so the default go test ./... stays fast. Run them manually via go test -tags integration ./... or trigger the GitHub Actions workflow with run_integration=true.

Discussion:

Issues: GitHub Issues
Email: shaneawall@gmail.com

Technical Details

Core Dependencies:

fsnotify v1.7.0 - File system event monitoring
BoltDB v1.3.10 - Embedded key-value store
Cobra v1.8.1 - CLI framework
Standard library: gzip compression, crypto/sha256 for hashing

v1.0 Architecture Components:

// DiffKeeper struct (v1.0)
type DiffKeeper struct {
    db         *bbolt.DB
    stateDir   string
    storePath  string
    watcher    *fsnotify.Watcher
    config     *config.DiffConfig      // Binary diff configuration
    cas        *cas.CASStore            // Content-addressable storage
    merkle     *merkle.MerkleManager    // Merkle tree integrity
    diffEngine diff.DiffEngine          // bsdiff/xdelta engine
}

// BlueShift captures file changes (v1.0 with binary diffs)
func (dk *DiffKeeper) BlueShiftDiff(path string) error {
    // 1. Read current file
    data, err := os.ReadFile(path)

    // 2. Determine if snapshot or diff needed
    isSnapshot := dk.shouldSnapshot(relPath)  // Every N versions
    isChunked := dk.config.ShouldChunk(fileSize)  // >1GB files

    if isSnapshot {
        // Store full snapshot in CAS
        if isChunked {
            chunks := chunk.SplitFile(data, chunkSize)
            for _, chunkData := range chunks {
                cid := dk.cas.Put(chunkData)  // Returns content ID
                cids = append(cids, cid)
            }
        } else {
            cid := dk.cas.Put(data)
            cids = append(cids, cid)
        }
    } else {
        // Compute binary diff
        prevData := dk.getPreviousVersion(relPath)
        diffData := dk.diffEngine.ComputeDiff(prevData, data)
        cid := dk.cas.Put(diffData)
        cids = append(cids, cid)
    }

    // 3. Build Merkle tree for integrity
    tree := dk.merkle.BuildTree(cids)
    merkleRoot := merkle.GetRoot(tree)

    // 4. Store metadata
    metadata := FileMetadata{
        CIDs:       cids,
        MerkleRoot: merkleRoot,
        IsChunked:  isChunked,
        IsSnapshot: isSnapshot,
        VersionCount: prevVersion + 1,
    }
    return dk.storeMetadata(relPath, metadata)
}

// RedShift restores files (v1.0 with verification)
func (dk *DiffKeeper) RedShiftDiff() error {
    // 1. Fetch metadata from BoltDB
    metadata := dk.getMetadata(relPath)

    // 2. Verify Merkle tree integrity
    if err := dk.merkle.VerifyFileIntegrity(metadata.CIDs, metadata.MerkleRoot); err != nil {
        return err  // Corrupted data detected
    }

    // 3. Reconstruct file
    if metadata.IsSnapshot {
        // Fetch chunks from CAS and reassemble
        data := dk.fetchAndReassemble(metadata.CIDs)
    } else {
        // Fetch base + apply diffs
        data := dk.reconstructFile(metadata)
    }

    // 4. Write restored file
    return os.WriteFile(fullPath, data, 0644)
}

Package Structure (v1.0):

pkg/config/ - Configuration management (DiffConfig)
pkg/diff/ - Binary diff engine (bsdiff/xdelta interfaces)
pkg/chunk/ - File chunking for large files
pkg/cas/ - Content-addressable storage with deduplication
pkg/merkle/ - Merkle tree integrity verification
pkg/ebpf/ - Kernel manager, profiler, and lifecycle tracing abstractions
main.go - CLI and orchestration (450 LOC)
diff_integration.go - Binary diff integration logic (378 LOC)
bench/ - Synthetic throughput comparisons between ring buffers and fsnotify event loops

For full implementation, see main.go and diff_integration.go.

Guides
- docs/ebpf-dev-setup.md – Toolchain + BTF cache walk-through
- docs/ebpf-guide.md – Kernel probe troubleshooting tips
- docs/btf-core-guide.md – Using BTFHub downloads and CO-RE in production
- docs/supported-kernels.md – Reference list of tested distros/kernels
- docs/auto-injection.md – Wiring CRI traces + injector workflows
Security & Operations
- SECURITY.md – How to report vulnerabilities
- k8s/README.md – Deployments, Helm chart, and RBAC
Reference
- docs/patents.md – Prior art & IP notes for profiler + auto-injection features