Strip /usr/include from apt pybind11's interface include dirs

[whitesscott]

Summary

• On Debian/Ubuntu hosts, the apt pybind11-dev CMake config sets pybind11::pybind11_headers INTERFACE_INCLUDE_DIRECTORIES to ${_IMPORT_PREFIX}/include, where _IMPORT_PREFIX=/usr. That leaks /usr/include into every target using pybind11_add_module — in this repo, _edgellm_runtime.
• nvcc translates it to -isystem /usr/include on the host g++ command line, which reorders g++'s system include chain and puts /usr/include before /usr/include/c++/<ver>. libstdc++'s <cmath> then fails to satisfy #include_next <math.h> and the build dies during device_link_stub.cu.o:

  /usr/include/c++/13/cmath: fatal error: math.h: No such file or directory
     #include_next <math.h>
  

• Fix: after find_package(pybind11 CONFIG REQUIRED), remove the literal /usr/include entry from pybind11::pybind11_headers's interface include dirs. The real pybind11 headers still resolve; only the bogus root include is dropped.
• No-op for pip-installed pybind11 (its _IMPORT_PREFIX is under the venv's site-packages, not /usr).

Reproduction

• Host: Ubuntu 24.04 aarch64 (Jetson Thor), gcc 13.3.0, CUDA 13.2.
• Apt package: pybind11-dev 2.11.1-2 at /usr/lib/cmake/pybind11/.
• Configure:

  cmake .. \
      -DTRT_PACKAGE_DIR=/usr \
      -DCUDA_CTK_VERSION=13.2 \
      -DCMAKE_TOOLCHAIN_FILE=cmake/aarch64_linux_toolchain.cmake \
      -DEMBEDDED_TARGET=jetson-thor \
      -DENABLE_CUTE_DSL=ALL \
      -DENABLE_NVTX_PROFILING=ON \
      -DBUILD_PYTHON_BINDINGS=ON
  

• Without this patch: build fails compiling experimental/pybind/device_link_stub.cu with the <cmath> / math.h error above.
• With this patch: experimental/pybind/CMakeFiles/_edgellm_runtime.dir/includes_CUDA.rsp no longer contains a bare -isystem /usr/include, and _edgellm_runtime.cpython-312-aarch64-linux-gnu.so links successfully.
• Also verified that pip-installed pybind11 3.0.4 (via -Dpybind11_DIR="$(python -m pybind11 --cmakedir)") continues to work with this patch — the workaround is guarded on the presence of /usr/include in the interface list.

Test plan

• Configure + build with apt pybind11-dev on Ubuntu 24.04 aarch64 (Jetson Thor) — _edgellm_runtime target builds.
• Configure + build with pip-installed pybind11 via -Dpybind11_DIR=$(python -m pybind11 --cmakedir) — still builds, no regression.
• python -c "import _edgellm_runtime" succeeds against the resulting .so.
• Spot-check that no other target consuming pybind11::* targets is affected on x86_64.

Related

• Independent of the <cmath> header cleanup in Use <cmath> instead of <math.h> in context attention FMHA headers #120 (which changes source files, not build system); this PR fixes a distinct build-system issue and does not depend on it.

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