P9 (WIP): compiled kernels (rust/simurg-core, PyO3) with bit-identical pure-Python fallback

Rust ports of the hot paths found by profiling: fused per-locus GenCall calling
and scoring, BAF/LRR, libm maps with CPython math semantics, both nearest-neighbour
searches of the normalization fit, and the BPM LocusEntry parser. Address
coverage is memoised per IDAT layout. SIMURG_PURE_PYTHON=1 forces the pure paths.
On the Pi: genotype_sample 3.4 s -> 1.1 s, 36-sample GSA run 131 s -> 46 s, BPM
read 4x faster; 36 GSA + 6 Omni2.5 GTCs and QC tables byte-identical to the pure
path; tests/unit/test_core_kernels.py checks every kernel on edge cases.
bench/profile_genotype.py, bench/scaling.py, cloud task p9 (thread scaling).

scripts/cloud/tasks/p9.sh

@@ -0,0 +1,53 @@
+#!/bin/bash
+# Phase P9 performance gate on a 32-vCPU Graviton instance, GSE165845 GSA arrays (360 samples):
+#   1. build the compiled kernels (rust/simurg-core) into the venv;
+#   2. thread scaling 1 → 32 with the kernels (bench/scaling.py, per-sample phase from the run log);
+#   3. pure-Python reference at 1 and 32 threads on a subset, and byte-identity of all 360 GTCs (kernels vs pure).
+# Args: <unused data dir>  <results dir>. Run with OMNI=0.
+set -uo pipefail
+OUT=$2
+W=/work/p9; R=$OUT/p9; mkdir -p $W $R
+N=$(nproc)
+
+echo "=== build simurg-core $(date -u +%T) ==="
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --profile minimal > /dev/null 2>&1
+export PATH="$HOME/.cargo/bin:$PATH"
+rustc --version
+VIRTUAL_ENV=$PWD/.venv uv pip install -q ./rust/simurg-core || { echo "!! simurg-core build failed"; exit 1; }
+.venv/bin/python -c "from simurg._core import backend; print('backend', backend())"
+.venv/bin/python -m pytest tests/unit/test_core_kernels.py -q -p no:cacheprovider 2>&1 | tail -2
+
+echo "=== data $(date -u +%T) ==="
+GSA=https://webdata.illumina.com/downloads/productfiles/global-screening-array/v1-0
+mkdir -p $W/gsa && cd $W/gsa
+for z in infinium-global-screening-array-24-v1-0-c2-manifest-file-bpm-build38.zip \
+         infinium-global-screening-array-v1-0-c1-cluster-file.zip; do
+  curl -sSfL --retry 5 -O "$GSA/$z" && unzip -oq $z
+done
+cd - > /dev/null
+BPM=$W/gsa/GSA-24v1-0_C2.bpm; EGT=$W/gsa/GSA-24v1-0_C1_ClusterFile.egt
+.venv/bin/python scripts/p8/prepare.py --tsv scripts/p8/gse165845_samples.tsv --dl $W/geo --out $W/idats --workers 24 \
+  || exit 1
+
+echo "=== scaling with kernels $(date -u +%T) ==="
+.venv/bin/python bench/scaling.py --bpm $BPM --egt $EGT --idats $W/idats --out $W/rust \
+  --threads 1,2,4,8,16,$N 2>&1 | grep -v WARNING
+cp $W/rust/scaling.json $R/scaling_rust.json
+
+echo "=== pure Python reference $(date -u +%T) ==="
+.venv/bin/python bench/scaling.py --bpm $BPM --egt $EGT --idats $W/idats --out $W/python --threads 1 --samples 64 \
+  --pure-python 2>&1 | grep -v WARNING
+cp $W/python/scaling.json $R/scaling_python_t1.json
+.venv/bin/python bench/scaling.py --bpm $BPM --egt $EGT --idats $W/idats --out $W/python_all --threads $N \
+  --pure-python 2>&1 | grep -v WARNING
+cp $W/python_all/scaling.json $R/scaling_python_t$N.json
+
+echo "=== identity: 360 GTCs, kernels vs pure Python $(date -u +%T) ==="
+n=0; d=0
+for f in $(cd $W/rust/t$N && find samples -name '*.gtc'); do
+  n=$((n+1)); cmp -s $W/rust/t$N/$f $W/python_all/t$N/$f || { d=$((d+1)); echo "differs: $f"; }
+done
+s=$(cmp -s $W/rust/t$N/sample_summary.tsv $W/python_all/t$N/sample_summary.tsv && echo identical || echo DIFFERS)
+echo "{\"gtcs\": $n, \"differ\": $d, \"sample_summary\": \"$s\"}" | tee $R/identity.json
+lscpu | grep -i "model name\|^CPU(s)" > $R/cpu.txt; free -g >> $R/cpu.txt
+echo "=== task done $(date -u +%T) ==="