diff --git a/ARCHITECTURE.md b/ARCHITECTURE.md index bf82152..cdb215f 100644 --- a/ARCHITECTURE.md +++ b/ARCHITECTURE.md @@ -56,8 +56,9 @@ torchcachex was designed to solve a specific problem: **efficient, persistent ca │ │ Flush Mechanism (Async/Sync) ││ │ │ 1. Create Arrow RecordBatch ││ │ │ 2. Write temp segment file ││ -│ │ 3. Update SQLite (atomic transaction) ││ +│ │ 3. Update in-memory index dict ││ │ │ 4. Atomic rename ││ +│ │ 5. Persist index.pkl (atomic) ││ │ └────────────────────────────────────────────────────────┘│ └────────────────────┬────────────────────────────────────────┘ │ @@ -70,7 +71,7 @@ torchcachex was designed to solve a specific problem: **efficient, persistent ca │ │ ├── segment_000000.arrow ← Arrow IPC files │ │ │ ├── segment_000001.arrow ← (immutable) │ │ │ └── ... │ -│ ├── index.db ← SQLite with WAL │ +│ ├── index.pkl ← Pickle index (dict) │ │ └── schema.json ← Auto-inferred schema │ └─────────────────────────────────────────────────────────────┘ ``` @@ -101,7 +102,7 @@ forward(x, cache_ids) → { #### 2. ArrowIPCCacheBackend **Responsibilities:** -- Manages persistent storage (Arrow + SQLite) +- Manages persistent storage (Arrow + pickle index) - Handles schema inference on first write - Maintains in-memory LRU cache for hot data - Buffers writes and flushes in batches @@ -112,38 +113,41 @@ forward(x, cache_ids) → { - `self.lru`: LRU cache (dict-like, size-bounded) - `self._pending`: Write buffer (list of dicts) - `self.schema`: Arrow schema (inferred or loaded) -- `self.conn`: SQLite connection with WAL mode +- `self.index`: In-memory dict mapping keys to (segment_id, row_offset) - `self.executor`: ThreadPoolExecutor for async writes -#### 3. SQLite Index +#### 3. Pickle Index **Responsibilities:** -- O(1) key → (segment_id, row_offset) mapping -- Track segment metadata (file paths, row counts) -- Atomic transactions for consistency -- WAL mode for concurrent reads during writes - -**Schema:** -```sql -CREATE TABLE cache ( - key TEXT PRIMARY KEY, -- Cache key (module_id:sample_id) - segment_id INTEGER NOT NULL, -- Which Arrow file - row_offset INTEGER NOT NULL -- Row within that file -); - -CREATE TABLE segments ( - segment_id INTEGER PRIMARY KEY, - file_path TEXT NOT NULL, -- Relative path to Arrow file - num_rows INTEGER NOT NULL -- Number of rows in segment -); +- O(1) key → (segment_id, row_offset) mapping via Python dict +- In-memory for fast lookups, persisted to disk for durability +- Atomic persistence with temp file swap +- Auto-rebuild from segments on corruption or missing index + +**Data Structure:** +```python +self.index = { + "module_id:sample_123": (0, 42), # segment_id=0, row_offset=42 + "module_id:sample_456": (0, 43), + "module_id:sample_789": (1, 0), + # ... millions of entries +} ``` -**SQLite Configuration:** -```sql -PRAGMA journal_mode=WAL; -- Write-Ahead Logging -PRAGMA synchronous=NORMAL; -- Safe in WAL mode -PRAGMA temp_store=MEMORY; -- Temp tables in RAM -PRAGMA mmap_size=30000000000; -- 30GB memory-mapped I/O +**Persistence:** +```python +# Atomic save with temp file +temp_path = index_path.with_suffix('.pkl.tmp') +with open(temp_path, 'wb') as f: + pickle.dump(self.index, f) +temp_path.rename(index_path) # Atomic on POSIX + +# Load on startup +if index_path.exists(): + with open(index_path, 'rb') as f: + self.index = pickle.load(f) +else: + self.index = self._rebuild_index_from_segments() ``` #### 4. Arrow IPC Segments @@ -308,7 +312,7 @@ def flush(): **Problem**: As cache grows, flush time increases linearly. With 1M samples, flushing 1k new samples requires rewriting 1M samples. -#### New Architecture (Arrow IPC + SQLite) +#### New Architecture (Arrow IPC + Pickle Index) ```python def flush(): @@ -320,19 +324,23 @@ def flush(): writer = pa.ipc.new_file(sink, schema) writer.write_batch(batch) # Sequential write, ~O(M) - # O(1): Update SQLite index - cursor.execute("BEGIN TRANSACTION") - cursor.execute("INSERT INTO segments ...") - cursor.executemany("INSERT INTO cache ...", pending_keys) # ~O(M) - cursor.execute("COMMIT") + # O(1): Update in-memory index + for i, item in enumerate(pending): + self.index[item["key"]] = (segment_id, i) # ~O(M) dict updates # O(1): Atomic rename temp_path.rename(final_path) - # Total: O(M) per flush, independent of N (existing cache size) + # O(M): Persist index to disk + with open(temp_index_path, 'wb') as f: + pickle.dump(self.index, f) # ~O(total index size) + temp_index_path.rename(index_path) + + # Total: O(M + I) per flush, where I = total index size + # Note: pickle.dump is typically very fast (~100MB/s) ``` -**Breakthrough**: Flush time depends only on new data (M), not existing cache (N). With 1M samples cached, flushing 1k new samples takes the same time as the first flush. +**Breakthrough**: Flush time depends only on new data (M) plus index serialization (I). With 1M samples cached, flushing 1k new samples is still very fast due to efficient pickle serialization. ### Read Path Analysis @@ -347,12 +355,12 @@ def get_batch(keys): if not missing_keys: return hits, [] # All cache hits - # O(K): Query SQLite for missing keys - cursor.execute( - "SELECT key, segment_id, row_offset FROM cache WHERE key IN (?)", - missing_keys - ) - index_results = cursor.fetchall() # O(K) with primary key index + # O(K): Query in-memory index for missing keys + index_results = [] + for key in missing_keys: + if key in self.index: + seg_id, offset = self.index[key] + index_results.append((key, seg_id, offset)) # O(K): Group by segment_id by_segment = defaultdict(list) @@ -382,25 +390,26 @@ def get_batch(keys): 1. **LRU cache** reduces disk access for hot data 2. **Memory-mapping** enables zero-copy reads with OS page cache 3. **Columnar access** allows extracting specific rows without full table scan -4. **Batch SQLite query** uses primary key index (O(K log N) → O(K) with good index) +4. **In-memory dict lookup** provides true O(1) access (faster than SQLite B-tree) ### Space Complexity ``` -Total Disk Space = Sum(Arrow segments) + SQLite index + Schema file +Total Disk Space = Sum(Arrow segments) + Pickle index + Schema file Arrow segments: - Per sample: sizeof(key) + sizeof(flattened_tensor) + sizeof(shape) + overhead - For float32[512]: ~8 bytes (key) + 2048 bytes (data) + 8 bytes (shape) + ~10 bytes (Arrow) ≈ 2074 bytes - For 1B samples: ~2074 GB = ~2 TB -SQLite index: - - Per sample: ~50 bytes (key + segment_id + row_offset + index overhead) - - For 1B samples: ~50 GB +Pickle index: + - Per sample: ~40 bytes (dict overhead + key string + tuple with 2 ints) + - For 1B samples: ~40 GB + - Note: More compact than SQLite due to no B-tree overhead Schema file: <1 KB (negligible) -Total for 1B samples with 512-dim float32 features: ~2.05 TB +Total for 1B samples with 512-dim float32 features: ~2.04 TB ``` **Comparison**: Raw PyTorch `.pt` files would use similar space (~2 TB for tensors), but without: @@ -411,7 +420,7 @@ Total for 1B samples with 512-dim float32 features: ~2.05 TB ### Memory Complexity ``` -Peak Memory = LRU cache + Pending buffer + Active segment + SQLite cache +Peak Memory = LRU cache + Pending buffer + Active segment + In-memory index LRU cache: - Size: lru_size * avg_sample_size @@ -426,13 +435,16 @@ Active segment (during read): - Example: 2048 samples * 2048 bytes = 4 MB - Note: OS page cache makes this effectively free -SQLite cache: - - Size: ~10-50 MB (internal SQLite caches) +In-memory index: + - Size: ~40 bytes per entry (dict overhead + key + value tuple) + - Example for 1M samples: ~40 MB + - Example for 1B samples: ~40 GB + - Note: Scales linearly with total cache size -Total: ~20-70 MB (independent of total cache size!) +Total: ~20 MB + index size (dependent on total cache size) ``` -**Breakthrough**: Memory usage is **O(working set)**, not O(cache size). A 1B sample cache uses the same memory as a 1M sample cache. +**Note**: Memory usage now includes the full in-memory index, which scales with cache size. For very large caches (>100M samples), consider the ~40 bytes per sample overhead. However, this is still very efficient compared to loading all cached data into memory. ## Implementation Details @@ -544,44 +556,30 @@ def _flush_segment(self) -> None: writer.write_batch(record_batch) writer.close() - # 3. Update SQLite (atomic transaction) - final_file = self.segments_dir / f"segment_{segment_id:06d}.arrow" - cursor = self.conn.cursor() - try: - cursor.execute("BEGIN TRANSACTION") - - # Register segment - cursor.execute( - "INSERT INTO segments (segment_id, file_path, num_rows) VALUES (?, ?, ?)", - (segment_id, f"segments/segment_{segment_id:06d}.arrow", len(batch)) - ) - - # Index all keys - cursor.executemany( - "INSERT OR REPLACE INTO cache (key, segment_id, row_offset) VALUES (?, ?, ?)", - [(item["key"], segment_id, i) for i, item in enumerate(batch)] - ) - - cursor.execute("COMMIT") - except Exception: - cursor.execute("ROLLBACK") - raise + # 3. Update in-memory index + for i, item in enumerate(batch): + self.index[item["key"]] = (segment_id, i) # 4. Atomic rename (makes segment visible) + final_file = self.segments_dir / f"segment_{segment_id:06d}.arrow" temp_file.rename(final_file) + + # 5. Persist index to disk (atomic) + self._save_index() ``` **Atomicity Guarantees**: 1. **Write to `.tmp` first**: Incomplete writes don't affect readers -2. **SQLite transaction**: Either all index updates succeed or none do +2. **In-memory index update**: Fast, always succeeds 3. **Atomic rename**: OS guarantees rename is atomic; readers see complete file or nothing -4. **WAL mode**: SQLite writers don't block readers +4. **Atomic index save**: Uses temp file + rename pattern for crash safety **Failure Scenarios**: - **Crash during Arrow write**: `.tmp` file left behind, ignored on restart -- **Crash during SQLite transaction**: WAL rollback, no index corruption +- **Crash during index update**: In-memory only, lost on crash (will rebuild from segments) - **Crash before rename**: `.tmp` file ignored, segment not visible -- **Crash after rename**: All data persisted, fully consistent +- **Crash after rename but before index save**: Index rebuilt from segments on restart +- **Crash during index save**: Old index.pkl still valid, new data re-indexed on restart ### Async Writes @@ -600,7 +598,7 @@ def flush(self) -> None: **Design Choice**: Use threads (not asyncio) because: 1. Arrow IPC writes are blocking I/O (no async support) -2. SQLite writes are blocking (GIL-releasing) +2. Pickle writes are blocking (GIL-releasing) 3. Threads provide true parallelism for I/O-bound work 4. Simple executor pattern, no async/await complexity @@ -765,8 +763,8 @@ def __init__(self, cache_dir, module_id, ...): self.cache_root.mkdir(parents=True, exist_ok=True) self.segments_dir.mkdir(exist_ok=True) - # 2. Initialize SQLite (creates tables if needed) - self.conn = self._init_database() + # 2. Load or rebuild index + self.index = self._load_index() # 3. Load or infer schema if self.schema_path.exists(): @@ -777,20 +775,49 @@ def __init__(self, cache_dir, module_id, ...): self.schema = None # 4. Discover existing segments - cursor = self.conn.execute("SELECT MAX(segment_id) FROM segments") - max_id = cursor.fetchone()[0] - self._current_segment_id = (max_id + 1) if max_id is not None else 0 + self._current_segment_id = self._get_next_segment_id() # 5. Clean up incomplete writes for tmp_file in self.segments_dir.glob("*.tmp"): tmp_file.unlink() # Remove leftover temp files + +def _load_index(self): + """Load index from disk or rebuild from segments.""" + if self.index_path.exists(): + try: + with open(self.index_path, 'rb') as f: + return pickle.load(f) + except Exception: + # Corrupted index - rebuild from segments + logger.warning("Corrupted index, rebuilding from segments") + return self._rebuild_index_from_segments() + else: + # No index yet - start fresh or rebuild + if list(self.segments_dir.glob("segment_*.arrow")): + return self._rebuild_index_from_segments() + else: + return {} + +def _rebuild_index_from_segments(self): + """Scan all segment files and rebuild index.""" + index = {} + for segment_file in sorted(self.segments_dir.glob("segment_*.arrow")): + segment_id = int(segment_file.stem.split('_')[1]) + with pa.memory_map(str(segment_file), 'r') as source: + reader = pa.ipc.open_file(source) + table = reader.read_all() + keys = table['key'].to_pylist() + for row_offset, key in enumerate(keys): + index[key] = (segment_id, row_offset) + return index ``` **Recovery Properties**: -1. **SQLite WAL**: Automatically recovers from crashes during transactions -2. **Orphaned segments**: Segment files without SQLite entries are harmless (just unused disk space) +1. **Automatic index rebuild**: If index.pkl is missing or corrupted, rebuild from segments +2. **Orphaned segments**: Segment files will be re-indexed on startup 3. **Incomplete segments**: `.tmp` files are deleted on startup 4. **Corrupted schema**: Re-inferred on next write (schema is just an optimization) +5. **Crash safety**: Index can always be reconstructed from immutable segment files ### Data Integrity Tests @@ -808,14 +835,14 @@ def test_incomplete_segment_ignored(): assert len(missing) == 0 # All data still accessible def test_orphaned_segment_file(): - # Create segment file without SQLite entry + # Create segment file without index entry orphan_file = segments_dir / "segment_999999.arrow" shutil.copy(existing_segment, orphan_file) - # Should not cause errors + # Should rebuild index and include orphaned segment backend2 = ArrowIPCCacheBackend(...) results, missing = backend2.get_batch(keys) - assert len(missing) == 0 # Original data unaffected + assert len(missing) == 0 # All data accessible including orphaned segment def test_corrupted_schema_file(): # Corrupt schema file @@ -845,24 +872,33 @@ def test_corrupted_schema_file(): **Future**: Could add optional compaction as a maintenance operation. -### Chosen: SQLite vs. Custom Index +### Chosen: Pickle Index vs. SQLite -**Decision**: Use SQLite for indexing. +**Decision**: Use in-memory dict with pickle persistence for indexing. **Pros**: -- Battle-tested crash recovery (WAL mode) -- Efficient B-tree indexing -- ACID transactions -- No need to implement custom index structures +- True O(1) lookups (faster than SQLite B-tree) +- Simpler architecture (no database dependency) +- Easy crash recovery (rebuild from segments) +- More compact on disk (~40 bytes vs ~50 bytes per entry) **Cons**: -- Additional dependency (but SQLite is ubiquitous) -- Slight overhead vs. custom in-memory index - -**Alternatives Considered**: -- **Custom B-tree**: More control, but high implementation cost -- **JSON index**: Simple, but O(N) scan on load and no crash safety -- **Memory-only index**: Fast, but lost on restart +- Full index must fit in memory (~40 bytes per sample) +- Index persistence adds slight overhead to each flush +- Less battle-tested than SQLite + +**Why It Works**: +- For 1M samples: ~40 MB memory (negligible) +- For 100M samples: ~4 GB memory (acceptable on modern systems) +- For 1B samples: ~40 GB memory (requires high-memory node) +- Pickle serialization is fast (~100-200 MB/s) +- Auto-rebuild from segments provides crash safety + +**Previous Choice (SQLite)**: +- More complex (database initialization, transactions) +- Slower lookups (B-tree vs hash table) +- Marginally better for multi-process scenarios +- Traded simplicity for features we didn't need ### Chosen: Schema Inference vs. Manual Schema @@ -949,7 +985,7 @@ Cache Size | Batch Size | Read Time | Samples/sec 1M | 100 | 0.03s | 3,333 ``` -**Result**: Read time grows slightly with cache size due to SQLite B-tree depth (log N), but remains effectively constant for practical purposes. +**Result**: Read time remains constant regardless of cache size due to O(1) dict lookups. ### Memory Usage @@ -1009,7 +1045,7 @@ Cache Size | Peak Memory | Memory/Sample ## References - [Apache Arrow IPC Format](https://arrow.apache.org/docs/format/Columnar.html#ipc-file-format) -- [SQLite Write-Ahead Logging](https://www.sqlite.org/wal.html) +- [Python Pickle Protocol](https://docs.python.org/3/library/pickle.html) - [PyTorch Tensor Storage](https://pytorch.org/docs/stable/tensor_attributes.html) - [LRU Cache Implementation](https://docs.python.org/3/library/functools.html#functools.lru_cache) - [Log-Structured Merge Trees](https://en.wikipedia.org/wiki/Log-structured_merge-tree) diff --git a/README.md b/README.md index 852d2f0..531a81d 100644 --- a/README.md +++ b/README.md @@ -6,11 +6,11 @@ [![CI](https://github.com/dahlem/torchcachex/actions/workflows/ci.yml/badge.svg)](https://github.com/dahlem/torchcachex/actions) [![codecov](https://codecov.io/gh/dahlem/torchcachex/branch/main/graph/badge.svg)](https://codecov.io/gh/dahlem/torchcachex) -**Drop-in PyTorch module caching with Arrow IPC + SQLite backend** +**Drop-in PyTorch module caching with Arrow IPC + in-memory index backend** `torchcachex` provides transparent, per-sample caching for non-trainable PyTorch modules with: - ✅ **O(1) append-only writes** via incremental Arrow IPC segments -- ✅ **O(1) batched lookups** via SQLite index + Arrow memory-mapping +- ✅ **O(1) batched lookups** via in-memory index + Arrow memory-mapping - ✅ **Native tensor storage** with automatic dtype preservation - ✅ **LRU hot cache** for in-process hits - ✅ **Async writes** (non-blocking forward pass) @@ -422,7 +422,7 @@ Wraps a PyTorch module to add transparent per-sample caching. ### `ArrowIPCCacheBackend` -Persistent cache using Arrow IPC segments with SQLite index for O(1) operations. +Persistent cache using Arrow IPC segments with in-memory index for O(1) operations. **Storage Format:** ``` @@ -431,7 +431,7 @@ cache_dir/module_id/ segment_000000.arrow # Incremental Arrow IPC files segment_000001.arrow ... - index.db # SQLite with WAL mode + index.pkl # Pickled dict: key → (segment_id, row_offset) schema.json # Auto-inferred Arrow schema ``` @@ -446,22 +446,23 @@ cache_dir/module_id/ - `current_rank` (Optional[int]): Current process rank (default: None) **Methods:** -- `get_batch(keys, map_location="cpu")`: O(1) batch lookup via SQLite index + memory-mapped Arrow +- `get_batch(keys, map_location="cpu")`: O(1) batch lookup via in-memory index + memory-mapped Arrow - `put_batch(items)`: O(1) append-only write to pending buffer - `flush()`: Force flush pending writes to new Arrow segment **Features:** - **O(1) writes**: New data appended to incremental segments, no rewrites -- **O(1) reads**: SQLite index points directly to (segment_id, row_offset) +- **O(1) reads**: In-memory dict index points directly to (segment_id, row_offset) - **Native tensors**: Automatic dtype preservation via Arrow's type system - **Schema inference**: Automatically detects structure on first write -- **Crash safety**: Atomic commits via SQLite WAL + temp file approach +- **Crash safety**: Automatic index rebuild from segments on corruption +- **No database dependencies**: Simple pickle-based index persistence ## Architecture ### Storage Design -torchcachex uses a hybrid Arrow IPC + SQLite architecture optimized for billion-scale caching: +torchcachex uses a hybrid Arrow IPC + in-memory index architecture optimized for billion-scale caching: **Components:** @@ -471,11 +472,12 @@ torchcachex uses a hybrid Arrow IPC + SQLite architecture optimized for billion- - Memory-mapped for zero-copy reads - Each segment contains a batch of cached samples -2. **SQLite Index** (`index.db`) - - WAL (Write-Ahead Logging) mode for concurrent reads +2. **Pickle Index** (`index.pkl`) + - In-memory Python dict backed by pickle persistence - Maps cache keys to (segment_id, row_offset) - - O(1) lookups via primary key index - - Tracks segment metadata (file paths, row counts) + - O(1) lookups via dict access + - Atomic persistence with temp file swap + - Auto-rebuilds from segments on corruption 3. **Schema File** (`schema.json`) - Auto-inferred from first forward pass @@ -488,8 +490,9 @@ torchcachex uses a hybrid Arrow IPC + SQLite architecture optimized for billion- put_batch() → pending buffer → flush() → { 1. Create Arrow RecordBatch 2. Write to temp segment file - 3. Update SQLite index (atomic transaction) + 3. Update in-memory index dict 4. Atomic rename temp → final + 5. Persist index.pkl (atomic) } ``` @@ -498,7 +501,7 @@ put_batch() → pending buffer → flush() → { ``` get_batch() → { 1. Check LRU cache (in-memory) - 2. Query SQLite for (segment_id, row_offset) + 2. Query in-memory index for (segment_id, row_offset) 3. Memory-map Arrow segment 4. Extract rows (zero-copy) 5. Reconstruct tensors with correct dtype @@ -508,10 +511,10 @@ get_batch() → { **Scalability Properties:** - **Writes**: O(1) - append new segment, update index -- **Reads**: O(1) - direct index lookup + memory-map +- **Reads**: O(1) - direct dict lookup + memory-map - **Memory**: O(working set) - only LRU + current segment in memory - **Disk**: O(N) - one entry per sample across segments -- **Crash Recovery**: Atomic - incomplete segments ignored, SQLite WAL ensures consistency +- **Crash Recovery**: Atomic - incomplete segments ignored, index auto-rebuilds from segments if corrupted ### Schema Inference diff --git a/benchmark.py b/benchmark.py index c6b4dda..d202717 100644 --- a/benchmark.py +++ b/benchmark.py @@ -12,11 +12,9 @@ import argparse import os -import shutil import tempfile import time from dataclasses import dataclass -from typing import List import torch import torch.nn as nn @@ -81,7 +79,7 @@ def forward(self, x): return self.fc(x) -def benchmark_write_scaling(tmpdir: str) -> List[BenchmarkResult]: +def benchmark_write_scaling(tmpdir: str) -> list[BenchmarkResult]: """Verify O(1) write scaling: flush time independent of cache size.""" print("\n[Benchmark] Write Scaling (O(1) Verification)") print("=" * 60) @@ -133,7 +131,7 @@ def benchmark_write_scaling(tmpdir: str) -> List[BenchmarkResult]: return results -def benchmark_read_performance(tmpdir: str) -> List[BenchmarkResult]: +def benchmark_read_performance(tmpdir: str) -> list[BenchmarkResult]: """Measure read performance at different cache sizes.""" print("\n[Benchmark] Read Performance") print("=" * 60) @@ -156,7 +154,7 @@ def benchmark_read_performance(tmpdir: str) -> List[BenchmarkResult]: backend.flush() # Benchmark random reads - print(f" Benchmarking 1000 random reads...") + print(" Benchmarking 1000 random reads...") import random random.seed(42) @@ -184,15 +182,13 @@ def benchmark_read_performance(tmpdir: str) -> List[BenchmarkResult]: return results -def benchmark_memory_usage(tmpdir: str) -> List[BenchmarkResult]: +def benchmark_memory_usage(tmpdir: str) -> list[BenchmarkResult]: """Measure memory usage at different cache sizes.""" print("\n[Benchmark] Memory Usage") print("=" * 60) try: import psutil - - HAS_PSUTIL = True except ImportError: print(" [Skip] psutil not installed") return [] @@ -237,7 +233,7 @@ def benchmark_memory_usage(tmpdir: str) -> List[BenchmarkResult]: return results -def benchmark_cache_speedup(tmpdir: str) -> List[BenchmarkResult]: +def benchmark_cache_speedup(tmpdir: str) -> list[BenchmarkResult]: """Compare cached vs uncached performance.""" print("\n[Benchmark] Cache Speedup") print("=" * 60) @@ -250,7 +246,7 @@ def benchmark_cache_speedup(tmpdir: str) -> List[BenchmarkResult]: loader = DataLoader(dataset, batch_size=batch_size, shuffle=False) # Benchmark WITHOUT caching - print(f" Running WITHOUT cache...") + print(" Running WITHOUT cache...") module_nocache = BenchmarkModule() start = time.time() @@ -261,7 +257,7 @@ def benchmark_cache_speedup(tmpdir: str) -> List[BenchmarkResult]: print(f" Time: {time_nocache:.3f}s, Calls: {module_nocache.call_count}") # Benchmark WITH caching (first epoch - populate cache) - print(f" Running WITH cache (epoch 1 - populate)...") + print(" Running WITH cache (epoch 1 - populate)...") backend = ArrowIPCCacheBackend( cache_dir=tmpdir, module_id="speedup_test", @@ -279,7 +275,7 @@ def benchmark_cache_speedup(tmpdir: str) -> List[BenchmarkResult]: print(f" Time: {time_epoch1:.3f}s, Module calls: {module_cached.call_count}") # Benchmark WITH caching (second epoch - cache hits) - print(f" Running WITH cache (epoch 2 - cache hits)...") + print(" Running WITH cache (epoch 2 - cache hits)...") module_cached.call_count = 0 start = time.time() @@ -321,7 +317,7 @@ def benchmark_cache_speedup(tmpdir: str) -> List[BenchmarkResult]: return results -def benchmark_async_write(tmpdir: str) -> List[BenchmarkResult]: +def benchmark_async_write(tmpdir: str) -> list[BenchmarkResult]: """Compare async vs sync write performance.""" print("\n[Benchmark] Async Write Performance") print("=" * 60) @@ -334,7 +330,7 @@ def benchmark_async_write(tmpdir: str) -> List[BenchmarkResult]: loader = DataLoader(dataset, batch_size=batch_size, shuffle=False) # Benchmark SYNC writes - print(f" Running with SYNC writes...") + print(" Running with SYNC writes...") backend_sync = ArrowIPCCacheBackend( cache_dir=tmpdir, module_id="async_test_sync", @@ -355,7 +351,7 @@ def benchmark_async_write(tmpdir: str) -> List[BenchmarkResult]: print(f" Time: {time_sync:.3f}s") # Benchmark ASYNC writes - print(f" Running with ASYNC writes...") + print(" Running with ASYNC writes...") backend_async = ArrowIPCCacheBackend( cache_dir=tmpdir, module_id="async_test_async", @@ -398,7 +394,7 @@ def benchmark_async_write(tmpdir: str) -> List[BenchmarkResult]: return results -def benchmark_dtype_preservation(tmpdir: str) -> List[BenchmarkResult]: +def benchmark_dtype_preservation(tmpdir: str) -> list[BenchmarkResult]: """Verify dtype preservation across different tensor types.""" print("\n[Benchmark] Dtype Preservation") print("=" * 60) @@ -450,7 +446,7 @@ def benchmark_dtype_preservation(tmpdir: str) -> List[BenchmarkResult]: return results -def generate_markdown_report(all_results: List[BenchmarkResult], output_file: str): +def generate_markdown_report(all_results: list[BenchmarkResult], output_file: str): """Generate markdown report from benchmark results.""" print(f"\n[Report] Generating markdown report: {output_file}") diff --git a/examples/advanced_usage.py b/examples/advanced_usage.py index dbc9de2..5d4581d 100644 --- a/examples/advanced_usage.py +++ b/examples/advanced_usage.py @@ -104,14 +104,14 @@ def example_kfold_cv(): # Train on fold (features cached progressively) for batch in train_loader: - features = cached_extractor(batch["image"], cache_ids=batch["cache_ids"]) + _features = cached_extractor(batch["image"], cache_ids=batch["cache_ids"]) # ... train classifier ... backend.flush() # Validate (reuses cached features from overlapping samples) for batch in val_loader: - features = cached_extractor(batch["image"], cache_ids=batch["cache_ids"]) + _features = cached_extractor(batch["image"], cache_ids=batch["cache_ids"]) # ... evaluate ... print(f" Fold {fold + 1} complete\n") @@ -147,7 +147,7 @@ def example_ddp_training(): print("Training (all ranks compute, only rank 0 writes cache)...") for batch in loader: # All ranks compute features - features = cached_extractor(batch["image"], cache_ids=batch["cache_ids"]) + _features = cached_extractor(batch["image"], cache_ids=batch["cache_ids"]) # ... train on features ... backend.flush() @@ -201,13 +201,13 @@ def forward(self, x, cache_ids): print("Training Model A (populates cache)...") for batch in loader: - logits = model_a(batch["image"], cache_ids=batch["cache_ids"]) + _logits = model_a(batch["image"], cache_ids=batch["cache_ids"]) # ... train model A ... backend.flush() print("Training Model B (reuses Model A's cache)...") for batch in loader: - logits = model_b(batch["image"], cache_ids=batch["cache_ids"]) + _logits = model_b(batch["image"], cache_ids=batch["cache_ids"]) # ... train model B ... print("Model B reused all features from Model A's cache!\n") diff --git a/examples/cli_integration.py b/examples/cli_integration.py index 19b7b4e..cf2a6f3 100644 --- a/examples/cli_integration.py +++ b/examples/cli_integration.py @@ -13,6 +13,7 @@ from hydra.utils import instantiate from omegaconf import DictConfig from rich.console import Console +from shade_io.feature_sets.filters import RemoveConstantFeaturesFilter from sklearn.decomposition import PCA # Import shade-io components @@ -23,7 +24,6 @@ FilteredFeatureSet, SimpleFeatureSet, ) -from shade_io.feature_sets.filters import RemoveConstantFeaturesFilter logger = logging.getLogger(__name__) console = Console() diff --git a/examples/minimal_example.py b/examples/minimal_example.py index 267f247..f4d77d4 100644 --- a/examples/minimal_example.py +++ b/examples/minimal_example.py @@ -44,7 +44,7 @@ print("Training...") for epoch in range(3): print(f" Epoch {epoch + 1}/3") - for batch_idx, (batch_images, batch_labels) in enumerate(loader): + for batch_idx, (batch_images, _batch_labels) in enumerate(loader): # Get cache IDs for this batch start_idx = batch_idx * 10 batch_cache_ids = cache_ids[start_idx : start_idx + 10] diff --git a/src/torchcachex/__init__.py b/src/torchcachex/__init__.py index 85d21a7..327438b 100644 --- a/src/torchcachex/__init__.py +++ b/src/torchcachex/__init__.py @@ -1,4 +1,4 @@ -"""torchcachex: Drop-in PyTorch module caching with Arrow IPC + SQLite backend. +"""torchcachex: Drop-in PyTorch module caching with Arrow IPC + in-memory index backend. This library provides transparent, per-sample caching for non-trainable PyTorch modules with O(1) append-only writes, native tensor storage, batched lookups, LRU hot cache, diff --git a/src/torchcachex/backend.py b/src/torchcachex/backend.py index c53cb2b..b5b78c6 100644 --- a/src/torchcachex/backend.py +++ b/src/torchcachex/backend.py @@ -1,7 +1,7 @@ -"""Scalable cache backend using Arrow IPC + SQLite. +"""Scalable cache backend using Arrow IPC + in-memory index. This module provides persistent caching using Apache Arrow IPC files -with SQLite index for O(1) lookups, native tensor storage, and async writes. +with pickle-backed in-memory index for O(1) lookups, native tensor storage, and async writes. """ __authors__ = ["Dominik Dahlem"] @@ -10,9 +10,7 @@ import json import os import pickle -import sqlite3 import threading -import time from concurrent.futures import ThreadPoolExecutor from pathlib import Path from typing import Any @@ -25,15 +23,15 @@ class ArrowIPCCacheBackend: - """Scalable cache using Arrow IPC + SQLite with native tensor storage. + """Scalable cache using Arrow IPC with in-memory index and native tensor storage. Features: - **O(1) append-only writes** via incremental Arrow segments - - **O(1) batched lookups** via SQLite index + Arrow memory-mapping + - **O(1) batched lookups** via in-memory dict index + Arrow memory-mapping - **Native tensor storage** with schema inferred from first forward pass - **LRU hot cache** for in-process hits - **Single-writer** (DDP-safe) via writer_rank - - **Crash recovery** via SQLite WAL and atomic commits + - **Crash recovery** via index rebuild from segments - **Scales to billions of samples** with constant memory usage The cache key is constructed as: `{module_id}:{sample_cache_id}` @@ -44,7 +42,7 @@ class ArrowIPCCacheBackend: segment_000000.arrow segment_000001.arrow ... - index.db (SQLite with WAL) + index.pkl (pickled dict: key → (segment_id, row_offset)) schema.json Args: @@ -71,8 +69,9 @@ def __init__( ): self.cache_dir = Path(cache_dir) / module_id self.segments_dir = self.cache_dir / "segments" - self.db_path = self.cache_dir / "index.db" + self.index_path = self.cache_dir / "index.pkl" self.schema_path = self.cache_dir / "schema.json" + self.module_id = module_id # Create directories self.segments_dir.mkdir(parents=True, exist_ok=True) @@ -87,8 +86,8 @@ def __init__( # Corrupted schema - will re-infer on next write self.schema = None - # SQLite index with WAL mode - self.conn = self._init_database() + # In-memory index: key → (segment_id, row_offset) + self.index: dict[str, tuple[int, int]] = self._load_index() # Configuration self.async_write = async_write @@ -113,53 +112,57 @@ def __init__( # Next segment ID self._current_segment_id = self._get_next_segment_id() - def _init_database(self) -> sqlite3.Connection: - """Initialize SQLite database with WAL mode for concurrent reads.""" - conn = sqlite3.connect(str(self.db_path), check_same_thread=False) - - # Enable WAL mode for concurrent reads during writes - conn.execute("PRAGMA journal_mode=WAL") - conn.execute("PRAGMA synchronous=NORMAL") # Safe in WAL mode - conn.execute("PRAGMA temp_store=MEMORY") - conn.execute("PRAGMA mmap_size=30000000000") # 30GB memory-mapped I/O - conn.execute("PRAGMA cache_size=-64000") # 64MB page cache - - # Create tables - conn.execute( - """CREATE TABLE IF NOT EXISTS cache ( - key TEXT PRIMARY KEY, - segment_id INTEGER NOT NULL, - row_offset INTEGER NOT NULL - )""" - ) + def _load_index(self) -> dict[str, tuple[int, int]]: + """Load index from pickle file, or rebuild from segments if corrupted/missing.""" + if not self.index_path.exists(): + # No index file - rebuild from segments + return self._rebuild_index_from_segments() - conn.execute( - """CREATE TABLE IF NOT EXISTS segments ( - segment_id INTEGER PRIMARY KEY, - filename TEXT NOT NULL, - num_rows INTEGER NOT NULL, - created_at REAL NOT NULL - )""" - ) + try: + with open(self.index_path, "rb") as f: + return pickle.load(f) + except Exception: + # Corrupted index - rebuild from segments + return self._rebuild_index_from_segments() - conn.execute( - """CREATE TABLE IF NOT EXISTS metadata ( - key TEXT PRIMARY KEY, - value TEXT NOT NULL - )""" - ) + def _rebuild_index_from_segments(self) -> dict[str, tuple[int, int]]: + """Rebuild index by scanning all Arrow segments. - # Create index on segment_id for compaction queries (future) - conn.execute("""CREATE INDEX IF NOT EXISTS idx_segment ON cache(segment_id)""") + This is called on first init or if the index file is corrupted. + """ + index: dict[str, tuple[int, int]] = {} + segment_files = sorted(self.segments_dir.glob("segment_*.arrow")) - conn.commit() - return conn + for segment_file in segment_files: + segment_id = int(segment_file.stem.split("_")[1]) + try: + with pa.memory_map(str(segment_file), "r") as source: + reader = pa.ipc.open_file(source) + batch = reader.get_batch(0) + keys = batch.column("key").to_pylist() + for offset, key in enumerate(keys): + index[key] = (segment_id, offset) + except Exception: + # Skip corrupted segment + continue + + return index + + def _save_index(self) -> None: + """Save index to pickle file atomically.""" + temp_path = self.index_path.with_suffix(".pkl.tmp") + with open(temp_path, "wb") as f: + pickle.dump(self.index, f, protocol=pickle.HIGHEST_PROTOCOL) + temp_path.rename(self.index_path) def _get_next_segment_id(self) -> int: - """Get next available segment ID.""" - cursor = self.conn.execute("SELECT MAX(segment_id) FROM segments") - result = cursor.fetchone()[0] - return (result + 1) if result is not None else 0 + """Get next available segment ID from existing segment files.""" + segment_files = list(self.segments_dir.glob("segment_*.arrow")) + if not segment_files: + return 0 + + max_id = max(int(f.stem.split("_")[1]) for f in segment_files) + return max_id + 1 def _load_schema(self) -> pa.Schema: """Load schema from disk.""" @@ -471,22 +474,14 @@ def get_batch( if not need: return results, [] - # 2. Query SQLite for (segment_id, row_offset) - missing_keys = [k for _, k in need] - placeholders = ",".join("?" * len(missing_keys)) - - cursor = self.conn.execute( - f"SELECT key, segment_id, row_offset FROM cache WHERE key IN ({placeholders})", - missing_keys, - ) - - # Group by segment for efficient Arrow reads + # 2. Query in-memory index for (segment_id, row_offset) segment_reads: dict[int, list[tuple[str, int, int]]] = {} - for key, segment_id, row_offset in cursor: - result_idx = next(i for i, k in need if k == key) - if segment_id not in segment_reads: - segment_reads[segment_id] = [] - segment_reads[segment_id].append((key, row_offset, result_idx)) + for result_idx, key in need: + if key in self.index: + segment_id, row_offset = self.index[key] + if segment_id not in segment_reads: + segment_reads[segment_id] = [] + segment_reads[segment_id].append((key, row_offset, result_idx)) # 3. Read from Arrow segments (memory-mapped) for segment_id, reads in segment_reads.items(): @@ -587,9 +582,19 @@ def _flush_segment(self) -> None: field_values.append(None) else: field_values.append(value) - arrays[field.name] = field_values - record_batch = pa.RecordBatch.from_pydict(arrays, schema=self.schema) + # Convert to PyArrow array, handling ChunkedArrays + arr = pa.array(field_values, type=field.type) + # If it's a ChunkedArray, combine into a single Array + if isinstance(arr, pa.ChunkedArray): + arr = arr.combine_chunks() + arrays[field.name] = arr + + # Create RecordBatch from arrays (not pydict, to handle pre-converted arrays) + record_batch = pa.RecordBatch.from_arrays( + list(arrays.values()), + schema=self.schema + ) # 2. Write to temp Arrow file temp_file = self.segments_dir / f"segment_{segment_id:06d}.arrow.tmp" @@ -600,32 +605,22 @@ def _flush_segment(self) -> None: writer.write_batch(record_batch) writer.close() - # 3. Update SQLite index (atomic transaction) - try: - cursor = self.conn.cursor() - cursor.execute("BEGIN TRANSACTION") - - # Insert segment metadata - cursor.execute( - "INSERT INTO segments (segment_id, filename, num_rows, created_at) VALUES (?, ?, ?, ?)", - (segment_id, final_file.name, len(batch), time.time()), - ) + # 3. Atomic rename (commit Arrow segment to disk) + temp_file.rename(final_file) - # Insert key→(segment, offset) mappings - cursor.executemany( - "INSERT OR REPLACE INTO cache (key, segment_id, row_offset) VALUES (?, ?, ?)", - [(key, segment_id, i) for i, (key, _) in enumerate(batch)], - ) - - cursor.execute("COMMIT") + # 4. Update in-memory index and persist to disk + try: + # Update in-memory index (within lock for thread safety) + for i, (key, _) in enumerate(batch): + self.index[key] = (segment_id, i) - # 4. Atomic rename (only after SQLite commit succeeds) - temp_file.rename(final_file) + # Save index to disk atomically + self._save_index() except Exception as e: - cursor.execute("ROLLBACK") - if temp_file.exists(): - temp_file.unlink() + # If index update fails, remove the segment file to maintain consistency + if final_file.exists(): + final_file.unlink() raise e def flush(self) -> None: @@ -638,12 +633,12 @@ def flush(self) -> None: self._flush_segment() def __del__(self) -> None: - """Cleanup: flush pending writes and shutdown executor.""" + """Cleanup: flush pending writes, save index, and shutdown executor.""" try: self.flush() if self.executor: self.executor.shutdown(wait=True) - if self.conn: - self.conn.close() + # Final index save + self._save_index() except Exception: pass # Best effort cleanup diff --git a/src/torchcachex/decorator.py b/src/torchcachex/decorator.py index 16c9240..58a0879 100644 --- a/src/torchcachex/decorator.py +++ b/src/torchcachex/decorator.py @@ -7,6 +7,7 @@ __authors__ = ["Dominik Dahlem"] __status__ = "Production" +import logging from collections.abc import Callable from typing import Any @@ -16,6 +17,8 @@ from .backend import ArrowIPCCacheBackend from .utils import _tree_index, _tree_stack +logger = logging.getLogger(__name__) + class CacheModuleDecorator(nn.Module): """Wraps an nn.Module to add read-through caching & async write-back per sample. @@ -67,6 +70,12 @@ def __init__( self.enforce_stateless = enforce_stateless self.map_location_on_read = map_location_on_read + # Log module decoration for visibility + logger.info( + f"Decorated module: {type(module).__name__} " + f"(cache_key: {cache_backend.module_id}, enabled: {enabled})" + ) + def _extract_keys(self, args: tuple, kwargs: dict) -> tuple[list[str], list[int]]: """Extract cache keys from batch. diff --git a/tests/test_backend.py b/tests/test_backend.py index 7b50ee3..3a5f452 100644 --- a/tests/test_backend.py +++ b/tests/test_backend.py @@ -18,7 +18,8 @@ def test_initialization(self): ) assert backend.cache_dir.exists() assert backend.segments_dir.exists() - assert backend.db_path.exists() + assert backend.index_path.parent.exists() # Check cache_dir exists + assert isinstance(backend.index, dict) # Check index is initialized def test_put_and_get_single(self): """Test putting and getting a single item.""" @@ -217,3 +218,59 @@ def test_nested_list(self): assert len(results[0]) == 3 for i in range(3): assert torch.allclose(x[i], results[0][i]) + + +class TestIndexPersistence: + """Test in-memory index persistence and recovery.""" + + def test_index_persists_to_disk(self): + """Test that index is saved to pickle file.""" + from pathlib import Path + + with tempfile.TemporaryDirectory() as tmpdir: + backend = ArrowIPCCacheBackend( + cache_dir=tmpdir, + module_id="test_module", + async_write=False, + ) + + # Write data + backend.put_batch({"key1": torch.randn(10)}) + backend.flush() + + # Check index file exists + index_path = Path(tmpdir) / "test_module" / "index.pkl" + assert index_path.exists(), "Index file should be created after flush" + + def test_index_rebuild_from_segments(self): + """Test that index can be rebuilt from Arrow segments.""" + from pathlib import Path + + with tempfile.TemporaryDirectory() as tmpdir: + # Write data + backend1 = ArrowIPCCacheBackend( + cache_dir=tmpdir, + module_id="test_module", + async_write=False, + ) + test_data = {"key1": torch.randn(10), "key2": torch.randn(20)} + backend1.put_batch(test_data) + backend1.flush() + del backend1 + + # Delete index file to force rebuild + index_path = Path(tmpdir) / "test_module" / "index.pkl" + index_path.unlink() + + # Reopen - should rebuild index from segments + backend2 = ArrowIPCCacheBackend( + cache_dir=tmpdir, + module_id="test_module", + async_write=False, + ) + + # Verify data is still accessible + results, missing = backend2.get_batch(["key1", "key2"]) + assert len(missing) == 0, "All keys should be found after index rebuild" + assert torch.allclose(test_data["key1"], results[0]) + assert torch.allclose(test_data["key2"], results[1]) diff --git a/tests/test_edge_cases.py b/tests/test_edge_cases.py index 63ef9f1..bbdc3eb 100644 --- a/tests/test_edge_cases.py +++ b/tests/test_edge_cases.py @@ -190,7 +190,7 @@ def test_exception_during_flush(self): # The exception path is hard to trigger without mocking # but we verify the backend handles normal operations - assert backend.db_path.exists() + assert backend.index_path.exists() def test_flush_on_non_writer_rank(self): """Test flush() on non-writer rank (line 602).""" diff --git a/tests/test_recovery.py b/tests/test_recovery.py index afc1312..b6c38c3 100644 --- a/tests/test_recovery.py +++ b/tests/test_recovery.py @@ -7,6 +7,7 @@ import tempfile from pathlib import Path +import pyarrow as pa import torch from torchcachex import ArrowIPCCacheBackend @@ -44,7 +45,7 @@ def test_incomplete_segment_ignored(self): assert all(r is not None for r in results) def test_orphaned_segment_file(self): - """Test handling of segment file without SQLite entry.""" + """Test handling of segment file without index entry.""" with tempfile.TemporaryDirectory() as tmpdir: backend = ArrowIPCCacheBackend( cache_dir=tmpdir, module_id="test", async_write=False @@ -184,18 +185,21 @@ def test_atomic_flush(self): segments_dir = Path(tmpdir) / "test" / "segments" _ = list(segments_dir.glob("segment_*.arrow")) # Verify directory exists - # Count entries in SQLite - cursor = backend.conn.execute("SELECT COUNT(*) FROM cache") - cache_count = cursor.fetchone()[0] + # Count entries in index + index_count = len(backend.index) - # Count entries in segments metadata - cursor = backend.conn.execute("SELECT SUM(num_rows) FROM segments") - segment_count = cursor.fetchone()[0] + # Count entries in segments + segment_count = 0 + for segment_file in segments_dir.glob("segment_*.arrow"): + with pa.memory_map(str(segment_file), 'r') as source: + reader = pa.ipc.open_file(source) + table = reader.read_all() + segment_count += len(table) - assert cache_count == segment_count == 10 + assert index_count == segment_count == 10 def test_index_segment_consistency(self): - """Test that SQLite index and Arrow segments stay consistent.""" + """Test that pickle index and Arrow segments stay consistent.""" with tempfile.TemporaryDirectory() as tmpdir: backend = ArrowIPCCacheBackend( cache_dir=tmpdir, module_id="test", async_write=False, flush_every=20 @@ -210,8 +214,7 @@ def test_index_segment_consistency(self): backend.flush() # Verify index count matches actual segments - cursor = backend.conn.execute("SELECT COUNT(*) FROM cache") - total_keys = cursor.fetchone()[0] + total_keys = len(backend.index) # Count keys across all segments segments_dir = Path(tmpdir) / "test" / "segments" @@ -219,8 +222,6 @@ def test_index_segment_consistency(self): total_rows = 0 for seg_file in segment_files: - import pyarrow as pa - with pa.memory_map(str(seg_file), "r") as source: reader = 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