Building cmake pybind11 project fails with libatomic link error #257
Description
I tried to build a project which uses CMake and Pybind11 for pyodide-0.29 on Python 3.13 but get a linker error:
wasm-opt: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory
em++: error: error running binaryen executable (wasm-opt). Please check your binaryen installation
I also tested this with the Pybind11/cmake example project where I updated the pybind11 submodule to v3.0.0 and changed the CMakeList.txt file to:
cmake_minimum_required(VERSION 3.4...3.18)
project(cmake_example)
cmake_policy(SET CMP0148 OLD) # New policy gives error finding Python
if (EMSCRIPTEN)
set(PYBIND11_USE_CROSSCOMPILING TRUE)
endif()
add_subdirectory(pybind11)
pybind11_add_module(cmake_example src/main.cpp)
# EXAMPLE_VERSION_INFO is defined by setup.py and passed into the C++ code as a
# define (VERSION_INFO) here.
target_compile_definitions(cmake_example
PRIVATE VERSION_INFO=${EXAMPLE_VERSION_INFO})
and get the same error.
I think a change in CPython-3.13.1 ( python/cpython#127708 ) might be the issue.
If I use pyodide-0.28 and Python-3.12 then pyodide build works fine.
Output of pyodide config list:
emscripten_version="4.0.9"
python_version="3.13.2"
rustflags="-C link-arg=-sSIDE_MODULE=2 -Z link-native-libraries=yes -Z emscripten-wasm-eh"
cmake_toolchain_file="~/.conda/envs/ems313/lib/python3.13/site-packages/pyodide_build/tools/cmake/Modules/Platform/Emscripten.cmake"
rust_toolchain="nightly-2025-02-01"
rust_emscripten_target_url="https://github.com/pyodide/rust-emscripten-wasm-eh-sysroot/releases/download/emcc-4.0.9_nightly-2025-02-01/emcc-4.0.9_nightly-2025-02-01.tar.bz2"
cflags="-O2 -g0 -fPIC -fwasm-exceptions -sSUPPORT_LONGJMP -I~/.cache/.pyodide-xbuildenv-0.30.9/0.29.0/xbuildenv/pyodide-root/cpython/installs/python-3.13.2/include/python3.13"
cxxflags=""
ldflags="-O2 -g0 -L~/.cache/.pyodide-xbuildenv-0.30.9/0.29.0/xbuildenv/pyodide-root/cpython/installs/python-3.13.2/lib/ -s WASM_BIGINT -fwasm-exceptions -sSUPPORT_LONGJMP -s SIDE_MODULE=1"
meson_cross_file="~/.conda/envs/ems313/lib/python3.13/site-packages/pyodide_build/tools/emscripten.meson.cross"
xbuildenv_path=""
pyodide_abi_version="2025_0"
pyodide_root="~/.cache/.pyodide-xbuildenv-0.30.9/0.29.0/xbuildenv/pyodide-root"
dist_dir="~/.cache/.pyodide-xbuildenv-0.30.9/0.29.0/xbuildenv/pyodide-root/dist"
python_include_dir="~/.cache/.pyodide-xbuildenv-0.30.9/0.29.0/xbuildenv/pyodide-root/cpython/installs/python-3.13.2/include/python3.13"
ignored_build_requirements="patchelf oldest-supported-numpy"
interpreter="~/.cache/.pyodide-xbuildenv-0.30.9/0.29.0/xbuildenv/pyodide-root/dist/python"
package_index="~/.cache/.pyodide-xbuildenv-0.30.9/0.29.0/xbuildenv/pyodide-root/package_index"
I'm using a conda environment created with mamba create -n ems313 python=3.13 pyodide-build
I noticed that one of the recipes project uses a restriction to pybind < 3 but even if I use pybind-2.9.2 I still get the libatomic error (also the macro PYBIND11_USE_CROSSCOMPILING was only introduced in pybind-3 so you have to replace that line with unset(CMAKE_SIZEOF_VOID_P) otherwise you get a Python config failure: Python is 64-bit, chosen compiler is 32-bit error.