GROMACS version:2023 release
git clone GROMACS / GROMACS · GitLab
cd gromacs
git checkout v2023
GROMACS modification: No
Environment: The environment is Environment:
NVIDIA-SMI 535.154.05 Driver Version: 535.154.05 CUDA Version: 12.2
nvhpc nompi/22.11 openmpi4.0.5 cudaaware (gdrcoy+cuda11.8+ucx1.14) gnu 9.3. I have also tried the same openmpi4.1.5 combination with the previous one
Attempted mpicc mpicxx and mpicc mpic++, both reported errors as follows
IB network hardware supports GPU DORECT P2P GPU DICT RDMA
Reference https://developer.nvidia.com/zh-cn/blog/massively-improved-multi-node-nvidia-gpu-scalability-with-gromacs/
Currently, an error is reported during CMake-- Found CUDA: /home/paraai_test/project/xiefh/soft/source/soft/nvhpc/Linux_x86_64/22.11/cuda/11.8 (found suitable version “11.8”, minimum required is “11.0”)
– Check for working NVCC/C++ compiler combination with nvcc ‘/home/paraai_test/project/xiefh/soft/source/soft/nvhpc/Linux_x86_64/22.11/cuda/11.8/bin/nvcc’
– lstest,/home/paraai_test/project/xiefh/soft/source/soft/nvhpc/Linux_x86_64/22.11/cuda/11.8/bin/nvcc --compiler-bindir=/home/paraai_test/project/xiefh/soft/source/soft/openmpi4.0.5-install/bin/mpicc -c /home/paraai_test/project/xiefh/soft/source/soft/gromacs/cmake/TestCUDA.cu
– Check for working NVCC/C compiler combination - broken
– /home/paraai_test/project/xiefh/soft/source/soft/nvhpc/Linux_x86_64/22.11/cuda/11.8/bin/nvcc standard output: ‘’
– /home/paraai_test/project/xiefh/soft/source/soft/nvhpc/Linux_x86_64/22.11/cuda/11.8/bin/nvcc standard error: 'nvcc fatal : Unsupported NVHPC compiler found. nvc++ is the only NVHPC compiler that is supported.
’
CMake Error at cmake/gmxManageNvccConfig.cmake:106 (message):
NVCC/C++ compiler combination does not seem to be supported. CUDA
frequently does not support the latest versions of the host compiler, so
you might want to try an earlier C++ compiler version and make sure your
CUDA compiler and driver are as recent as possible. Set the GMX_NVCC_WORKS
CMake cache variable to bypass this check if you know what you are doing.
Call Stack (most recent call first):
cmake/gmxManageCuda.cmake:105 (include)
CMakeLists.txt:649 (include)
– Configuring incomplete, errors occurred!
See also “/home/paraai_test/project/xiefh/soft/source/soft/gromacs/build1/CMakeFiles/CMakeOutput.log”.
See also “/home/paraai_test/project/xiefh/soft/source/soft/gromacs/build1/CMakeFiles/CMakeError.log”.
The compile command is: cmake- DGMX_NVCC_WORKS=ON -DCMAKE_C_COMPILER=/home/paraai_test/project/xiefh/soft/source/soft/openmpi4.0.5-install/bin/mpicc -DCMAKE_CXX_COMPILER=/home/paraai_test/project/xiefh/soft/source/soft/openmpi4.0.5-install/bin/mpicxx -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=CUDA -DCMAKE_BUILD_TYPE=Release -DGMX_DOUBLE=off -DGMX_USE_CUFFTMP=ON -DcuFFTMp_ROOT=/home/paraai_test/project/xiefh/soft/source/soft/nvhpc/Linux_x86_64/22.11/math_libs -DCMAKE_INSTALL_PREFIX=/home/paraai_test/project/xiefh/soft/source/soft/gromacs/install-bak -DCMAKE_CXX_FLAGS=“–gcc-toolchain=/opt/rh/devtoolset-9/root/usr” -DCMKAE_C_FLAGS=" --gcc-toolchain=/opt/rh/devtoolset-9/root/usr"^Chome/paraai_test/project/xiefh/soft/source/soft/gromacs/install-bak -DCMAKE_CXX_FLAGS=[ paraai_test@g0127 build1]$ cmake … - DGMX_NVCC_WORKS=ON -DCMAKE_C_COMPILER=/home/paraai_test/project/xiefh/soft/source/soft/openmpi4.0.5-install/bin/mpicc -DCMAKE_CXX_COMPILER=/home/paraai_test/project/xiefh/soft/source/soft/openmpi4.0.5-install/bin/mpicxx -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=CUDA -DCMAKE_BUILD_TYPE=Release -DGMX_DOUBLE=off -DGMX_USE_CUFFTMP=ON -DcuFFTMp_ROOT=/home/paraai_test/project/xiefh/soft/source/soft/nvhpc/Linux_x86_64/22.11/math_libs -DCMAKE_INSTALL_PREFIX=/home/paraai_test/project/xiefh/soft/source/soft/gromacs/install-bak -DCMAKE_CXX_FLAGS=“–gcc-toolchain=/opt/rh/devtoolset-9/root/usr” -DCMKAE_C_FLAGS=“–gcc-toolchain=/opt/rh/devtoolset-9/root/usr”
The error message CMakeError. log is Determining if the nfileno exists failed with the following output:
Change Dir: /home/paraai_test/project/xiefh/soft/source/soft/gromacs-soft/gromacs/build/CMakeFiles/CMakeTmp
Run Build Command(s):/opt/rh/devtoolset-9/root/usr/bin/gmake -f Makefile cmTC_1478d/fast && /opt/rh/devtoolset-9/root/usr/bin/gmake -f CMakeFiles/cmTC_1478d.dir/build.make CMakeFiles/cmTC_1478d.dir/build
gmake[1]: Entering directory ‘/project/paraai_test/xiefh/soft/source/soft/gromacs-soft/gromacs/build/CMakeFiles/CMakeTmp’
Building CXX object CMakeFiles/cmTC_1478d.dir/CheckSymbolExists.cxx.o
/home/paraai_test/project/xiefh/soft/source/soft/openmpi-4.1.5-install/bin/mpic++ --gcc-toolchain=/opt/rh/devtoolset-9/root/usr --c++17 -MD -MT CMakeFiles/cmTC_1478d.dir/CheckSymbolExists.cxx.o -MF CMakeFiles/cmTC_1478d.dir/CheckSymbolExists.cxx.o.d -o CMakeFiles/cmTC_1478d.dir/CheckSymbolExists.cxx.o -c /home/paraai_test/project/xiefh/soft/source/soft/gromacs-soft/gromacs/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
“/home/paraai_test/project/xiefh/soft/source/soft/gromacs-soft/gromacs/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx”, line 8: error: identifier “_fileno” is undefined
return ((int*)(&_fileno))[argc];
^
1 error detected in the compilation of “/home/paraai_test/project/xiefh/soft/source/soft/gromacs-soft/gromacs/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx”.
gmake[1]: *** [CMakeFiles/cmTC_1478d.dir/build.make:79: CMakeFiles/cmTC_1478d.dir/CheckSymbolExists.cxx.o] Error 2
gmake[1]: Leaving directory ‘/project/paraai_test/xiefh/soft/source/soft/gromacs-soft/gromacs/build/CMakeFiles/CMakeTmp’
gmake: *** [Makefile:127: cmTC_1478d/fast] Error 2
Could a kind-hearted person please tell me how to solve it specifically