fetch_ml/native/README.md
Jeremie Fraeys 472590f831
docs: expand Research Trustworthiness section with detailed design rationale
Add comprehensive explanation of the reproducibility problem and fix:
- Document readdir filesystem-dependent ordering issue
- Explain std::sort fix for lexicographic ordering
- Clarify recursive traversal with cycle detection
- Document hidden file and special file exclusions
- Warn researchers about silent omissions and empty hash edge cases

This addresses the core concern that researchers need to understand
the hash is computed over sorted paths to trust cross-machine verification.
2026-02-21 13:38:25 -05:00

6.4 KiB

Native C++ Libraries

High-performance C++ libraries for critical system components.

Overview

This directory contains selective C++ optimizations for the highest-impact performance bottlenecks. Not all operations warrant C++ implementation - only those with clear orders-of-magnitude improvements.

Current Libraries

queue_index (Priority Queue Index)

  • Purpose: High-performance task queue with binary heap
  • Performance: 21,000x faster than JSON-based Go implementation
  • Memory: 99% allocation reduction
  • Security: CVE-2024-45339, CVE-2025-47290, CVE-2025-0838 mitigations applied
  • Status: Production ready

dataset_hash (SHA256 Hashing)

  • Purpose: SIMD-accelerated file hashing (ARMv8 crypto / Intel SHA-NI)
  • Performance: 78% syscall reduction, batch-first API
  • Memory: 99% less memory than Go implementation
  • Research: Deterministic sorted hashing, recursive directory traversal
  • Status: Production ready for research use

Security

CVE Mitigations Applied

CVE Description Mitigation
CVE-2024-45339 Symlink attack on temp files O_EXCL flag with retry-on-EEXIST
CVE-2025-47290 TOCTOU race in file open openat_nofollow() via path_sanitizer
CVE-2025-0838 Integer overflow in batch ops MAX_BATCH_SIZE = 10000 limit

Research Trustworthiness

Critical Design Decisions for Research Use:

For dataset hashing to be trustworthy in research, it must be reproducible. The original collect_files used readdir() which returns files in filesystem-dependent order — inode order on ext4, creation order on others, essentially random on network filesystems. This meant researchers hashing the same dataset on different machines would get different combined hashes for identical content, breaking cross-collaborator verification.

The fix: std::sort(paths.begin(), paths.end()) after collection ensures lexicographic ordering. The hash is computed over sorted file paths, making it reproducible across machines and time.

Behavior Summary:

  • Deterministic ordering: Files sorted lexicographically before hashing
  • Recursive traversal: Nested directories fully hashed (max depth 32 with cycle detection)
  • Reproducible: Same dataset produces identical hash across machines and filesystems

Documented Exclusions (intentional, not bugs):

  • Hidden files (names starting with .) are excluded — if your dataset has .data files or dotfiles that are part of the data, they will be silently skipped
  • Special files (symlinks, devices, sockets) are excluded — only regular files (S_ISREG) are hashed
  • Non-regular entries in subdirectories are silently skipped

These exclusions were conscious design choices for security (symlink attack prevention) and predictability. However, researchers must be aware: a dataset directory with only hidden files or non-regular files will produce an empty hash, not an error. Verify your dataset structure matches expectations.

Build Requirements

  • CMake 3.20+
  • C++20 compiler (GCC 11+, Clang 14+, or MSVC 2022+)
  • Go 1.25+ (for CGo integration)

Quick Start

# Build all native libraries
make native-build

# Run with native libraries enabled
FETCHML_NATIVE_LIBS=1 go run ./...

# Run benchmarks
FETCHML_NATIVE_LIBS=1 go test -bench=. ./tests/benchmarks/

Test Coverage

make native-test

8/8 tests passing:

  • storage_smoke - Basic storage operations
  • dataset_hash_smoke - Hashing correctness
  • storage_init_new_dir - Directory creation
  • parallel_hash_large_dir - 300+ file handling
  • queue_index_compact - Compaction operations
  • sha256_arm_kat - ARMv8 SHA256 verification
  • storage_symlink_resistance - CVE-2024-45339 verification
  • queue_index_batch_limit - CVE-2025-0838 verification

Build Options

# Debug build with AddressSanitizer
cd native/build && cmake .. -DCMAKE_BUILD_TYPE=Debug -DENABLE_ASAN=ON

# Release build (optimized)
cd native/build && cmake .. -DCMAKE_BUILD_TYPE=Release

# Build specific library
cd native/build && make queue_index

Architecture

Design Principles

  1. Selective optimization: Only 2 libraries out of 80+ profiled functions
  2. Batch-first APIs: Minimize CGo overhead (~100ns/call)
  3. Zero-allocation hot paths: Arena allocators, no malloc in critical sections
  4. C ABI for CGo: Simple C structs, no C++ exceptions across boundary
  5. Cross-platform: Runtime SIMD detection (ARMv8 / x86_64 SHA-NI)

CGo Integration

// #cgo LDFLAGS: -L${SRCDIR}/../../native/build -lqueue_index
// #include "../../native/queue_index/queue_index.h"
import "C"

Error Handling

  • C functions return -1 for errors, positive values for success
  • Use qi_last_error() / fh_last_error() for error messages
  • Go code checks rc < 0 not rc != 0

When to Add New C++ Libraries

DO implement when:

  • Profile shows >90% syscall overhead
  • Batch operations amortize CGo cost
  • SIMD can provide 3x+ speedup
  • Memory pressure is critical

DON'T implement when:

  • Speedup <2x (CGo overhead negates gains)
  • Single-file operations (per-call overhead too high)
  • Team <3 backend engineers (maintenance burden)
  • Complex error handling required

History

Implemented:

  • queue_index: Binary priority queue replacing JSON filesystem queue
  • dataset_hash: SIMD SHA256 for artifact verification

Deferred:

  • ⏸️ task_json_codec: 2-3x speedup not worth maintenance (small team)
  • ⏸️ artifact_scanner: Go filepath.Walk faster for typical workloads
  • ⏸️ streaming_io: Complexity exceeds benefit without io_uring

Maintenance

Build verification:

make native-build
FETCHML_NATIVE_LIBS=1 make test

Adding new library:

  1. Create subdirectory with CMakeLists.txt
  2. Implement C ABI in .h / .cpp files
  3. Add to root CMakeLists.txt
  4. Create Go bridge in internal/
  5. Add benchmarks in tests/benchmarks/
  6. Document in this README

Troubleshooting

Library not found:

  • Ensure native/build/lib*.dylib (macOS) or .so (Linux) exists
  • Check LD_LIBRARY_PATH or DYLD_LIBRARY_PATH

CGo undefined symbols:

  • Verify C function names match exactly (no name mangling)
  • Check #include paths are correct
  • Rebuild: make native-clean && make native-build

Performance regression:

  • Verify FETCHML_NATIVE_LIBS=1 is set
  • Check benchmark: go test -bench=BenchmarkQueue -v
  • Profile with: go test -bench=. -cpuprofile=cpu.prof