Fix nvcc/glibc feature macro compatibility in CMake builds

[lahiri-phdworks]

Build related issues.

Faced issues when building the cuda toolkit version 13.1 on Ubuntu operating system. Details from uname are below.

uname -a

Linux ----- 6.17.0-14-generic #14-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan  9 17:01:16 UTC 2026 x86_64 GNU/Linux

CMake Errors.

The following cmake error was encountered.

CMake Error at /usr/share/cmake-3.31/Modules/CMakeDetermineCompilerId.cmake:865 (message): Compiling the CUDA compiler identification source file "CMakeCUDACompilerId.cu" failed. Compiler: /usr/local/cuda-13/bin/nvcc Build flags: Id flags: --keep;--keep-dir;tmp -v The output was: 2 #$ _NVVM_BRANCH_=nvvm #$ _SPACE_= #$ _CUDART_=cudart #$ _HERE_=/usr/local/cuda-13/bin #$ _THERE_=/usr/local/cuda-13/bin #$ _TARGET_SIZE_= #$ _TARGET_DIR_= #$ _TARGET_DIR_=targets/x86_64-linux #$ TOP=/usr/local/cuda-13/bin/.. #$ CICC_PATH=/usr/local/cuda-13/bin/../nvvm/bin #$ NVVMIR_LIBRARY_DIR=/usr/local/cuda-13/bin/../nvvm/libdevice #$ LD_LIBRARY_PATH=/usr/local/cuda-13/bin/../lib::/usr/local/cuda-13/lib64 #$ PATH=/usr/local/cuda-13/bin/../nvvm/bin:/usr/local/cuda-13/bin:/home/clustere502/.opam/default/bin:/home/clustere502/.opencode/bin:/home/clustere502/.nvm/versions/node/v25.6.0/bin:/home/clustere502/bin:/home/clustere502/.local/bin:/usr/local/bin:/home/clustere502/.cargo/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin:/usr/local/cuda-13/bin:/home/clustere502/.fzf/bin #$ INCLUDES="-I/usr/local/cuda-13/bin/../targets/x86_64-linux/include" #$ SYSTEM_INCLUDES="-isystem" "/usr/local/cuda-13/bin/../targets/x86_64-linux/include/cccl" #$ LIBRARIES= "-L/usr/local/cuda-13/bin/../targets/x86_64-linux/lib/stubs" "-L/usr/local/cuda-13/bin/../targets/x86_64-linux/lib" #$ CUDAFE_FLAGS= #$ PTXAS_FLAGS= #$ rm tmp/a_dlink.reg.c #$ gcc -D__CUDA_ARCH_LIST__=750 -E -x c++ -D__CUDACC__ -D__NVCC__ "-I/usr/local/cuda-13/bin/../targets/x86_64-linux/include" "-isystem" "/usr/local/cuda-13/bin/../targets/x86_64-linux/include/cccl" -D__CUDACC_VER_MAJOR__=13 -D__CUDACC_VER_MINOR__=1 -D__CUDACC_VER_BUILD__=115 -D__CUDA_API_VER_MAJOR__=13 -D__CUDA_API_VER_MINOR__=1 -D__NVCC_DIAG_PRAGMA_SUPPORT__=1 -D__CUDACC_DEVICE_ATOMIC_BUILTINS__=1 -include "cuda_runtime.h" -m64 "CMakeCUDACompilerId.cu" -o "tmp/CMakeCUDACompilerId.cpp4.ii" #$ cudafe++ --c++17 --static-host-stub --device-hidden-visibility --gnu_version=150200 --display_error_number --orig_src_file_name "CMakeCUDACompilerId.cu" --orig_src_path_name "/home/clustere502/cuda-samples/build/CMakeFiles/3.31.6/CompilerIdCUDA/CMakeCUDACompilerId.cu" --allow_managed --m64 --parse_templates --gen_c_file_name "tmp/CMakeCUDACompilerId.cudafe1.cpp" --stub_file_name "CMakeCUDACompilerId.cudafe1.stub.c" --gen_module_id_file --module_id_file_name "tmp/CMakeCUDACompilerId.module_id" "tmp/CMakeCUDACompilerId.cpp4.ii" /usr/include/x86_64-linux-gnu/bits/mathcalls.h(206): error: exception specification is incompatible with that of previous function "rsqrt" (declared at line 629 of /usr/local/cuda-13/bin/../targets/x86_64-linux/include/crt/math_functions.h) extern double rsqrt (double __x) noexcept (true); extern double __rsqrt (double __x) noexcept (true); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h(206): error: exception specification is incompatible with that of previous function "rsqrtf" (declared at line 653 of /usr/local/cuda-13/bin/../targets/x86_64-linux/include/crt/math_functions.h) extern float rsqrtf (float __x) noexcept (true); extern float __rsqrtf (float __x) noexcept (true); ^ 2 errors detected in the compilation of "CMakeCUDACompilerId.cu". # --error 0x2 -- Call Stack (most recent call first): /usr/share/cmake-3.31/Modules/CMakeDetermineCompilerId.cmake:8 (CMAKE_DETERMINE_COMPILER_ID_BUILD) /usr/share/cmake-3.31/Modules/CMakeDetermineCompilerId.cmake:53 (__determine_compiler_id_test) /usr/share/cmake-3.31/Modules/CMakeDetermineCUDACompiler.cmake:131 (CMAKE_DETERMINE_COMPILER_ID) CMakeLists.txt:3 (project) -- Configuring incomplete, errors occurred!

The fix has been documented and implemented by changing the CMakeLists.txt files.

What’s actually failing is this: glibc’s <mathcalls.h> now declares rsqrt/rsqrtf, and CUDA 13.1’s header crt/math_functions.h also declares them, but with a different exception spec. When both are visible in the same compilation unit, we get the “exception specification incompatible” error.

Fix

Added the following.

if(NOT CMAKE_CUDA_FLAGS_INIT MATCHES "(^| )-U_GNU_SOURCE( |$)")
    string(APPEND CMAKE_CUDA_FLAGS_INIT " -U_GNU_SOURCE")
endif()
if(NOT CMAKE_CUDA_FLAGS_INIT MATCHES "(^| )-D_DEFAULT_SOURCE( |$)")
    string(APPEND CMAKE_CUDA_FLAGS_INIT " -D_DEFAULT_SOURCE")
endif()


set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Wno-deprecated-gpu-targets -U_GNU_SOURCE -D_DEFAULT_SOURCE")
set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -include ${CMAKE_SOURCE_DIR}/cmake/pthread_clock_compat.h")