bench: reproducible Rust-vs-C sweep (sweep.py)

[cjfields]

Adds bench/sweep.py, a reproducible Rust-vs-C benchmark sweep, for #31 and in particular its x86/AVX2 measurements.

• Builds Rust's align_benchmark and C's at the pinned commit, both generic (as the differential harness builds it) and with -march=native. On x86 the native build runs C's AVX2 and AVX-512 kernels. build_c.sh gains C_NATIVE=1 for this; the harness is unchanged.

• Data: deterministic datasets with a fixed seed, so every machine aligns the same pairs. C's generate_dataset seeds from the clock. Sets:

  • 150 bp at 2%;
  • 1 kb at 5% and 20%;
  • 1 kb with long indels;
  • 10 kb at 5%;
  • 2 kb with random flanks.

• Configs: every metric × memory mode, ends-free/extension (including match < 0) and all five heuristics, about 300 in total.

• Records:

  • best-of-N alignment time;
  • max RSS, via wait4;
  • instructions: perf stat on Linux when permitted, time -l on macOS;
  • whether Rust's output matches generic C's.

• Writes target/bench-sweep/<host>/results.tsv and summary.md, with machine info, compiler versions and load.

• Arguments: Rust and C get their own argument forms. clap needs -g=-1,4,6,2, while C's getopt reads the = into a short option's value. The ad hoc sweep in Performance: high-memory mode slower and larger than C on long pairs; port-quirk optimizations #31 hit exactly this.

• Offline nodes: --offline runs cargo with --offline (run cargo fetch with network first) and requires a local ./WFA2-lib checkout that contains the pinned commit. The native builds (Rust target-cpu=native, C -march=native) go into per-host directories. Cargo doesn't track the CPU, so without this a binary built on a login node would be silently reused on a compute node.

• Without perf, instruction counts are left blank; times, memory and output checks still work.

Tested on macOS (M2 Pro) with --quick, including --offline and --no-build. (M2 Pro) The results agree with the #31 sweep. The Linux paths (perf, taskset, /proc/cpuinfo) are untested here; they fall back gracefully, and the summary says which instruction source was used.

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