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linux-aarch64 CPython ships without PGO (cross-compiled build skips --enable-optimizations); interpreter-bound code measurably slower on Graviton

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4/5
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3-5 giorni
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38/100
Tipo di issue
Funzionalità
Chiarezza
Abbastanza chiara
Stato di attività
Attiva
Stack tecnologico
aws, linux, python, shell
Ambito
build-system, developer-experience, performance

Direzione di ricerca

Start with recipe/build_base.sh around the conditional that adds --with-lto and --enable-optimizations, and inspect how _OPTIMIZED and CONDA_BUILD_CROSS_COMPILATION are set. Trace the generated CONFIG_ARGS for native arm64 and cross-compiled builds, then evaluate native arm64 CI or an emulated profile step. Done means identifying a supported PGO/LTO build path and verifying the resulting configure arguments and interpreter performance.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Observation. sysconfig.get_config_var("CONFIG_ARGS") for conda-forge CPython 3.12.13, linux-aarch64 (built Mar 5 2026, GCC 14.3.0) contains --build=x86_64-conda-linux-gnu --host=aarch64-conda-linux-gnu and neither --enable-optimizations nor --with-lto. CPython 3.12.11, linux-64 (Jun 4 2025) has --enable-optimizations --with-lto=full.

Why. recipe/build_base.sh on main, around L281–285:

if [[ ${_OPTIMIZED} == yes ]]; then
  _common_configure_args+=(--with-lto=full)
  if [[ "$CONDA_BUILD_CROSS_COMPILATION" != "1" ]]; then
    _common_configure_args+=(--enable-optimizations)

linux-aarch64 is cross-compiled, so PGO is always skipped there. I haven't traced why --with-lto is also missing from the 3.12.13 aarch64 build's CONFIG_ARGS.

Measured impact (confounded, stated as such). We ran the same pure-Python inner loop (MAGeCK's count: gzip line reading plus dict lookups) on the same bytes on AWS, in each platform's conda-forge interpreter:

Graviton4 (aarch64, no PGO) Intel Xeon 6975P-C (x86, PGO+LTO) AMD EPYC 9R45 (x86, PGO+LTO)
gzip lines/s 2.56 M 3.85 M 5.02 M
guide lookups/s 0.60 M 1.19 M 1.60 M

This mixes core differences, a patch-version difference, and the build difference, so it doesn't isolate PGO's share. (PGO+LTO speedups on interpreter-bound code are commonly cited as 10–20%; I haven't measured that here.) On Graviton, arm64 has no published PGO build to compare against at all, since it's skipped by construction.

Question. Is a native (non-cross) linux-aarch64 build with PGO feasible now that native arm64 CI runners exist, or is there a way to run the profile step under emulation? Every Python-heavy bioinformatics or science tool on linux-aarch64 inherits this.

Found while verifying real workloads on AWS for scientific-codes-cookbook (measurements/mageck-real).

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