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README: note on the Skylake JCC erratum build flag #50

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cjfields merged 2 commits into from
Oct 16, 2026
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README: note on the Skylake JCC erratum build flag #50

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08fc3f0
* Reword and organize the Skylake section for specific optimizations
cjfields Oct 16, 2026
261f94a
Fix typo and a trailing space
cjfields Oct 16, 2026
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Expand Up @@ -63,6 +63,26 @@ RUSTFLAGS="-C target-cpu=native" cargo build --release
cargo test
```

### Chip-specific optimizations

On Skylake-family Intel CPUs (6th–10th generation Core, Skylake-SP and
Cascade Lake Xeon), the microcode fix for the
[JCC erratum](https://www.intel.com/content/www/us/en/content-details/841076/intel-mitigations-for-jump-conditional-code-erratum.html)
makes run time depend on code alignment. On a Xeon Gold 6150, building with
LLVM's mitigation made edit, indel, gap-linear and X-drop/Z-drop alignments
7–17% faster, but gap-affine 4% slower; output is unchanged:

```bash
RUSTFLAGS="-C target-cpu=native -C llvm-args=-x86-branches-within-32B-boundaries" cargo build --release
```

Other CPUs don't need it. For example: on an AMD EPYC 7713 (Zen 3) it was
neutral to 7% slower. `RUSTFLAGS` applies to the whole build, so a crate that
depends on wfa2lib-rs sets it in its own build. To reference specific
measurements, see HPCBio/wfa2lib-rs#31.

### Tests, Parity, Performance, and CI

The integration tests (`tests/test_vs_reference.rs`) and the C-parity script
(`tests/wfa_utest.sh`) compare against the reference outputs shipped with the
C library, so they expect a [WFA2-lib](https://github.com/Marco-Sola-Lab/WFA2-lib)
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