fix+perf: eliminate data races & replace all synchronization with Highway futex (zero mutex, wall -7%, sys -51%)#684

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KimYannn wants to merge 21 commits intoOpenGene:masterfrom

KimYannn:refactor/cpp23-threading

Commits on Apr 13, 2026

fix: eliminate data race on mNextSeq in pwrite path
Hermes
committed

Commits on Apr 14, 2026

fix: make SPSC head pointer atomic to eliminate producer/consumer race
Hermes
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fix: make ReadPool counters atomic and SPSC produced/consumed atomic
Hermes
committed

Commits on Apr 16, 2026

build: switch to C++23 with GCC 15 (conda-forge toolchain)

Kim Yann
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Kim Yann
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refactor(5): replace cerr with std::println in PE/SE reporting blocks

Kim Yann
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Kim Yann
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refactor(4): replace mFinishedThreads atomic counter with std::latch

Kim Yann
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Kim Yann
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refactor(3): replace raw thread* with std::jthread + std::optional, remove manual join/delete

Kim Yann
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Kim Yann
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refactor(2): replace usleep(100) busy-wait with std::counting_semaphore in writer output loop

Kim Yann
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Kim Yann
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refactor(1): replace mutex+CV backpressure polling with atomic::wait/notify_all

Kim Yann
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Kim Yann
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fix(2): revert counting_semaphore, use yield() — semaphore release/acquire mismatch with N-producer round-robin

Kim Yann
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Kim Yann
committed

Commits on Apr 17, 2026

perf: replace yield() with hwy::BlockUntilDifferent/WakeAll futex

Kim Yann
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Kim Yann
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fix: restore CXX ?= g++ in Makefile (remove hardcoded local toolchain path)

Kim Yann
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Kim Yann
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refactor: downgrade C++20/23 to C++11 for Apple Clang compatibility

Kim Yann
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Kim Yann
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fix: writer thread deadlock with BlockUntilDifferent

Kim Yann
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Kim Yann
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perf: replace pwrite ring sleep_for(1µs) spin with Highway futex

Kim Yann
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Kim Yann
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perf: replace bgzf mutex+condvar with Highway futex

Kim Yann
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Kim Yann
committed

Commits on Apr 23, 2026

fix: eliminate data races in writer thread

KimYannn
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charmcrush
committed

Commits on Apr 24, 2026

fix: break reader/worker/writer circular deadlock and close lost-wakeup races

KimYannn
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claude
committed

Commits on Apr 29, 2026

Commits on May 2, 2026

fix(spsc): eliminate all TSan-confirmed data races in SPSC queue

KimYannn
and
claude
committed