Error Building GROMACS 2023.3 with CUDA - NVCC/GCC Compatibility Issue

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1

System Information:

  • GROMACS version: 2023.3
  • GROMACS modification: No
  • OS: Pop!_OS 22.04 LTS

Issue Description:

I’m attempting to install GROMACS 2023.3 with CUDA acceleration. Initially, I used the following cmake command:

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/cuda -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10

I had to specify -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10 because my NVCC version is 11.2, and GCC is 11.4. NVCC 11.2 is incompatible with GCC versions higher than 10. To resolve this, I installed GCC and G++ 10 and created a symbolic link to install Gromacs.

Installation Process:

  • The cmake command executed successfully.
  • The make command also completed without errors.
  • However, the make check command encountered an error at 79%.

Error Details:

[ 79%] Building CXX object src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o
[ 79%] Building CXX object src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o
[ 79%] Linking CXX executable ../../../../bin/fft-test
[ 79%] Built target fft-test
[ 79%] Building NVCC (Device) object src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpu_utils-test_generated_typecasts_runner.cu.o
/usr/include/linux/types.h:12:27: error: expected initializer before ‘__s128’
   12 | typedef __signed__ __int128 __s128 __attribute__((aligned(16)));
      |                           ^~~~~~
CMake Error at gpu_utils-test_generated_typecasts_runner.cu.o.Release.cmake:280 (message):
  Error generating file
  /home/naiad/Downloads/gromacs-2023.3/build/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir//./gpu_utils-test_generated_typecasts_runner.cu.o


make[3]: *** [src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make:84: src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpu_utils-test_generated_typecasts_runner.cu.o] Erro 1
make[2]: *** [CMakeFiles/Makefile2:4927: src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/all] Erro 2
make[1]: *** [CMakeFiles/Makefile2:3306: CMakeFiles/check.dir/rule] Erro 2
make: *** [Makefile:628: check] Erro 2

Seeking Help:

I have not found any related posts or links addressing this specific error. Does anyone have any insights or suggestions on how to resolve this issue?

2

I get the same issue except with cuda toolkit 11.1 (im also on pop os and gcc-10) - any ideas?

3

There seems to be problems with CUDA 11.x in the 2023.3, as you can see here. I don’t know specifically how to help you, but I am using GROMACS2023.2 in my workstation with CUDA12.30 and gcc/g++ 12.3.0. I have a RTX4080. I would say try to install CUDA12 to see if this solves the issue, as I remember having issues as well when I was trying to compile with CUDA11.X (I don’t remember the version). I never found the root of it but directly went for CUDA12. Hope this helps at least a bit!