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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
30 lines
1.5 KiB
Markdown
30 lines
1.5 KiB
Markdown
# Memory-Limited Biosequence Iterator
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This Go function extends an `IBioSequence` iterator with memory-aware throttling to prevent excessive heap allocation during data processing.
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## Core Functionality
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- **`LimitMemory(fraction float64)`**
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Returns a new iterator that respects an upper bound on heap usage relative to total system memory.
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- **Memory Monitoring**
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Uses `runtime.ReadMemStats()` and `github.com/pbnjay/memory.TotalMemory()` to compute the current heap fraction (`Alloc / TotalMemory`) dynamically.
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- **Backpressure Mechanism**
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While the memory fraction exceeds `fraction`, the producer goroutine yields control (`runtime.Gosched()`) until sufficient memory becomes available.
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- **Logging**
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Warns via `obilog.Warnf` when:
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- Memory pressure persists (every ~1000 yields),
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- Or wait duration becomes unusually long (>10,000 yielding cycles).
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- **Concurrency Model**
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- A producer goroutine consumes from the original iterator and pushes items to `newIter`, pausing as needed.
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- A dedicated consumer goroutine calls `WaitAndClose()` to ensure graceful termination and resource cleanup.
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## Semantic Behavior
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- **Non-blocking consumer**: Downstream consumers are not stalled; they read from an internal buffered channel (`newIter`).
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- **Adaptive rate control**: The iterator automatically slows down when memory pressure rises, avoiding OOM conditions.
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- **Predictable resource use**: Ensures heap usage stays below the specified `fraction` (e.g., 0.5 → ≤ 50% of total RAM).
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