Setting b_sanitize=thread breaks for projects that have Fortran dependencies

[ngoldbaum]

Describe the bug

If you try to build a project like SciPy that has a meson build system and Fortran dependencies using gfortran with b_sanitize=thread, you will eventually see an error like:

  ERROR: Linker gfortran does not support sanitizer arguments ['-fsanitize=thread']

To Reproduce
Build SciPy from source using a sanitizer. On my Mac, I can trigger the error with this command inside a source checkout of the SciPy repository:

$ CC=/opt/homebrew/opt/llvm/bin/clang CXX=/opt/homebrew/opt/llvm/bin/clang++ PKG_CONFIG_PATH="/opt/homebrew/opt/openblas/lib/pkgconfig" python -m pip install -v . -C'setup-args=-Db_sanitize=thread'

After installing llvm, gfortran, and openblas via homebrew.

Details

  Running command Preparing metadata (pyproject.toml)
  + meson setup /Users/goldbaum/Documents/scipy /Users/goldbaum/Documents/scipy/.mesonpy-vh4wyhe9 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md -Db_sanitize=thread --native-file=/Users/goldbaum/Documents/scipy/.mesonpy-vh4wyhe9/meson-python-native-file.ini
  The Meson build system
  Version: 1.10.0
  Source dir: /Users/goldbaum/Documents/scipy
  Build dir: /Users/goldbaum/Documents/scipy/.mesonpy-vh4wyhe9
  Build type: native build
  Project name: scipy
  Project version: 1.17.0.dev0+git20250716.6ed0250
  C compiler for the host machine: /opt/homebrew/opt/llvm/bin/clang (clang 21.1.7 "Homebrew clang version 21.1.7")
  C linker for the host machine: /opt/homebrew/opt/llvm/bin/clang ld64 1230.1
  C++ compiler for the host machine: /opt/homebrew/opt/llvm/bin/clang++ (clang 21.1.7 "Homebrew clang version 21.1.7")
  C++ linker for the host machine: /opt/homebrew/opt/llvm/bin/clang++ ld64 1230.1
  Cython compiler for the host machine: cython (cython 3.2.2)
  Host machine cpu family: aarch64
  Host machine cpu: aarch64
  Program python found: YES (/Users/goldbaum/.pyenv/versions/3.14.2/bin/python)
  Found pkg-config: YES (/opt/homebrew/bin/pkg-config) 2.5.1
  Run-time dependency python found: YES 3.14
  Program cython found: YES (/private/var/folders/nk/yds4mlh97kg9qdq745g715rw0000gn/T/pip-build-env-02uwx2qw/overlay/bin/cython)
  Compiler for C supports arguments -Wno-unused-but-set-variable: YES
  Compiler for C supports arguments -Wno-unused-function: YES
  Compiler for C supports arguments -Wno-conversion: YES
  Compiler for C supports arguments -Wno-misleading-indentation: YES
  Library m found: YES
  Fortran compiler for the host machine: gfortran (gcc 15.2.0 "GNU Fortran (Homebrew GCC 15.2.0) 15.2.0")
  Fortran linker for the host machine: gfortran ld64 1230.1
  ../meson.build:94: WARNING: Consider using the built-in option for language standard version instead of using "-std=legacy".
  Compiler for Fortran supports arguments -Wno-conversion: YES
  Compiler for C supports link arguments -Wl,-dead_strip: YES
  Checking if "-Wl,--version-script" links: NO
  Program tools/generate_f2pymod.py found: YES (/Users/goldbaum/.pyenv/versions/3.14.2/bin/python /Users/goldbaum/Documents/scipy/tools/generate_f2pymod.py)
  Program scipy/_build_utils/tempita.py found: YES (/Users/goldbaum/.pyenv/versions/3.14.2/bin/python /Users/goldbaum/Documents/scipy/scipy/_build_utils/tempita.py)
  Program pythran found: YES 0.18.1 0.18.1 (/private/var/folders/nk/yds4mlh97kg9qdq745g715rw0000gn/T/pip-build-env-02uwx2qw/overlay/bin/pythran)
  Found pkg-config: YES (/opt/homebrew/bin/pkg-config) 2.5.1
  WARNING: Found CMake '/Users/goldbaum/.pyenv/versions/3.14.2/bin/cmake' but couldn't run it
  Found CMake: NO
  Run-time dependency xsimd found: NO (tried pkgconfig, framework and cmake)

  Executing subproject xsf

  xsf| Project name: xsf
  xsf| Project version: 0.1.0
  xsf| C++ compiler for the host machine: /opt/homebrew/opt/llvm/bin/clang++ (clang 21.1.7 "Homebrew clang version 21.1.7")
  xsf| C++ linker for the host machine: /opt/homebrew/opt/llvm/bin/clang++ ld64 1230.1
  xsf| Build targets in project: 0
  xsf| Subproject xsf finished.


  Executing subproject boost_math

  boost_math| Project name: boost-math
  boost_math| Project version: 1.88.0
  boost_math| Build targets in project: 0
  boost_math| Subproject boost_math finished.


  Executing subproject qhull_r

  qhull_r| Project name: qhull_r
  qhull_r| Project version: 8.0.2
  qhull_r| C compiler for the host machine: /opt/homebrew/opt/llvm/bin/clang (clang 21.1.7 "Homebrew clang version 21.1.7")
  qhull_r| C linker for the host machine: /opt/homebrew/opt/llvm/bin/clang ld64 1230.1
  qhull_r| Compiler for C supports arguments -Wno-unused-but-set-variable: YES (cached)
  qhull_r| Build targets in project: 1
  qhull_r| Subproject qhull_r finished.

  Run-time dependency threads found: YES
  numpy-config found: YES (/private/var/folders/nk/yds4mlh97kg9qdq745g715rw0000gn/T/pip-build-env-02uwx2qw/overlay/bin/numpy-config) 2.3.5
  Run-time dependency numpy found: YES 2.3.5
  Message: f2py free-threading enabled
  Library npymath found: YES
  pybind11-config found: YES (/private/var/folders/nk/yds4mlh97kg9qdq745g715rw0000gn/T/pip-build-env-02uwx2qw/overlay/bin/pybind11-config) 3.0.1
  Run-time dependency pybind11 found: YES 3.0.1
  Checking if "thread_local" compiles: NO
  Checking if "_Thread_local" compiles: YES
  Checking if "__thread" compiles: YES
  Configuring scipy_config.h using configuration
  Program f2py found: YES (/private/var/folders/nk/yds4mlh97kg9qdq745g715rw0000gn/T/pip-build-env-02uwx2qw/overlay/bin/f2py)
  Run-time dependency scipy-openblas found: NO (tried pkgconfig)
  Run-time dependency openblas found: YES 0.3.30
  Dependency openblas found: YES 0.3.30 (cached)
  Run-time dependency python found: YES 3.14
  Compiler for C supports arguments -Wno-maybe-uninitialized: NO
  Compiler for C supports arguments -Wno-discarded-qualifiers: NO
  Compiler for C supports arguments -Wno-empty-body: YES
  Compiler for C supports arguments -Wno-implicit-function-declaration: YES
  Compiler for C supports arguments -Wno-parentheses: YES
  Compiler for C supports arguments -Wno-switch: YES
  Compiler for C supports arguments -Wno-unused-label: YES
  Compiler for C supports arguments -Wno-unused-result: YES
  Compiler for C supports arguments -Wno-unused-variable: YES
  Compiler for C supports arguments -Wno-unused-but-set-variable: YES (cached)
  Compiler for C++ supports arguments -Wno-bitwise-instead-of-logical: YES
  Compiler for C++ supports arguments -Wno-cpp: YES
  Compiler for C++ supports arguments -Wno-class-memaccess: NO
  Compiler for C++ supports arguments -Wno-deprecated-declarations: YES
  Compiler for C++ supports arguments -Wno-deprecated-builtins: YES
  Compiler for C++ supports arguments -Wno-format-truncation: YES
  Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES
  Compiler for C++ supports arguments -Wno-sign-compare: YES
  Compiler for C++ supports arguments -Wno-switch: YES
  Compiler for C++ supports arguments -Wno-terminate: NO
  Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES
  Compiler for C++ supports arguments -Wno-unused-function: YES
  Compiler for C++ supports arguments -Wno-unused-local-typedefs: YES
  Compiler for C++ supports arguments -Wno-unused-variable: YES
  Compiler for C++ supports arguments -Wno-int-in-bool-context: YES
  Compiler for Fortran supports arguments -Wno-argument-mismatch: YES
  Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
  Compiler for Fortran supports arguments -Wno-intrinsic-shadow: YES
  Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES
  Compiler for Fortran supports arguments -Wno-surprising: YES
  Compiler for Fortran supports arguments -Wno-uninitialized: YES
  Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES
  Compiler for Fortran supports arguments -Wno-unused-label: YES
  Compiler for Fortran supports arguments -Wno-unused-variable: YES
  Compiler for Fortran supports arguments -Wno-tabs: YES
  Compiler for Fortran supports arguments -Wno-argument-mismatch: YES (cached)
  Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
  Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES (cached)
  Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES (cached)
  Compiler for Fortran supports arguments -Wno-unused-label: YES (cached)
  Compiler for Fortran supports arguments -Wno-unused-variable: YES (cached)
  Compiler for Fortran supports arguments -Wno-tabs: YES (cached)
  Checking if "Check atomic builtins without -latomic" links: YES
  Configuring __config__.py using configuration
  DEPRECATION: Variable substitution with boolean value 'CROSS_COMPILED' is deprecated.
  DEPRECATION: Variable substitution with boolean value 'BLAS_FOUND' is deprecated.
  DEPRECATION: Variable substitution with boolean value 'LAPACK_FOUND' is deprecated.
  Checking for function "open_memstream" : YES
  Configuring messagestream_config.h using configuration
  Program _generate_pyx.py found: YES (/Users/goldbaum/.pyenv/versions/3.14.2/bin/python /Users/goldbaum/Documents/scipy/scipy/special/_generate_pyx.py)
  Program _generate_pyx.py found: YES (/Users/goldbaum/.pyenv/versions/3.14.2/bin/python /Users/goldbaum/Documents/scipy/scipy/linalg/_generate_pyx.py)
  Program ../_generate_sparsetools.py found: YES (/Users/goldbaum/.pyenv/versions/3.14.2/bin/python /Users/goldbaum/Documents/scipy/scipy/sparse/sparsetools/../_generate_sparsetools.py)
  Checking for size of "void*" : 8
  Checking for size of "void*" : 8

  Executing subproject highs

  highs| Project name: highs
  highs| Project version: 1.8.0
  highs| C compiler for the host machine: /opt/homebrew/opt/llvm/bin/clang (clang 21.1.7 "Homebrew clang version 21.1.7")
  highs| C linker for the host machine: /opt/homebrew/opt/llvm/bin/clang ld64 1230.1
  highs| C++ compiler for the host machine: /opt/homebrew/opt/llvm/bin/clang++ (clang 21.1.7 "Homebrew clang version 21.1.7")
  highs| C++ linker for the host machine: /opt/homebrew/opt/llvm/bin/clang++ ld64 1230.1
  highs| Compiler for C++ supports arguments -Wno-invalid-offsetof: YES
  highs| Compiler for C++ supports arguments -Wno-maybe-uninitialized: NO
  highs| Compiler for C++ supports arguments -Wno-reorder: YES
  highs| Compiler for C++ supports arguments -Wno-reorder-ctor: YES
  highs| Compiler for C++ supports arguments -Wno-sometimes-uninitialized: YES
  highs| Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES (cached)
  highs| Compiler for C++ supports arguments -Wno-unused-variable: YES (cached)
  highs| Compiler for C++ supports arguments -Wno-use-after-free: NO
  highs| Compiler for C++ supports arguments -Wno-comment: YES
  highs| Compiler for C supports arguments -Wno-comment: YES
  highs| Compiler for C supports arguments -Wno-invalid-offsetof: YES
  highs| Compiler for C supports arguments -Wno-maybe-uninitialized: NO (cached)
  highs| Compiler for C supports arguments -Wno-sometimes-uninitialized: YES
  highs| Compiler for C supports arguments -Wno-unused-label: YES (cached)
  highs| Compiler for C supports arguments -Wno-use-after-free: NO
  highs| Compiler for C supports arguments -Wno-unused-but-set-variable: YES (cached)
  highs| Compiler for C supports arguments -Wno-unused-variable: YES (cached)
  highs| Compiler for C supports arguments -Wno-use-after-free: NO (cached)
  highs| Dependency threads found: YES unknown (cached)
  highs| Checking if "Check atomic builtins without -latomic" links: YES (cached)
  highs| Dependency zlib skipped: feature use_zlib disabled
  highs| Checking if "mm_pause check" compiles: NO
  highs| Checking if "builtin_clz check" compiles: YES
  highs| Configuring HConfig.h.meson.interim using configuration
  highs| Found git repository at /Users/goldbaum/Documents/scipy/subprojects/highs
  highs| Build targets in project: 144
  highs| Subproject highs finished.

  Build targets in project: 194
  ../scipy/misc/meson.build:7: WARNING: Trying to use ['thread'] sanitizer on Clang with b_lundef.
  This will probably not work.
  Try setting b_lundef to false instead.

  scipy 1.17.0.dev0+git20250716.6ed0250

    Subprojects
      boost_math  : YES
      highs       : YES
      qhull_r     : YES
      xsf         : YES

    User defined options
      Native files: /Users/goldbaum/Documents/scipy/.mesonpy-vh4wyhe9/meson-python-native-file.ini
      b_ndebug    : if-release
      b_sanitize  : thread
      b_vscrt     : md
      buildtype   : release

  Found ninja-1.13.0.git.kitware.jobserver-pipe-1 at /private/var/folders/nk/yds4mlh97kg9qdq745g715rw0000gn/T/pip-build-env-02uwx2qw/normal/bin/ninja

  ERROR: Linker gfortran does not support sanitizer arguments ['-fsanitize=thread']

  A full log can be found at /Users/goldbaum/Documents/scipy/.mesonpy-vh4wyhe9/meson-logs/meson-log.txt

Expected behavior

Meson has some static knowledge that gfortran doesn't support sanitizers and doesn't even try to pass it to gfortran.

system parameters

• Is this a cross build or just a plain native build (for the same computer)? native build
• what operating system (e.g. MacOS Catalina, Windows 10, CentOS 8.0, Ubuntu 18.04, etc.) MacOS Sequoia
• what Python version are you using e.g. 3.8.0 3.14.2
• what meson --version 1.10.0
• what ninja --version if it's a Ninja build 1.13.0.git.kitware.jobserver-pipe-1

[ngoldbaum]

See here for context on where this came up for SciPy.

[eli-schwartz]

This is slightly funky because in principle we do want to error out if you try to enable something but that thing doesn't work, so for example for a fortran-only project we'd want to error out. We should also error out if you try to enable b_sanitize=oobleck in a pure C++ GCC project, of course.

Maybe we should detect mixed language projects (that is, len(compilers) > 1) and grant it a special exemption if a sanitizer value is accepted by at least one compiler, but not by all of them?

[lucascolley]

Maybe we don't even need to check len(compilers), and rather just error if none of the compilers accept the value?