Make command failing with NVCC 13.0 on GROMACS 2025.2

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,
1

GROMACS version: 2025.2
GROMACS modification: No
CUDA Version: 13.0

CMake Version: 3.28.3

CMake Command: “cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON --DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda13.0”

Hello, I am having an issues when I try running the “make” command after the “cmake ..” command when trying to install CUDA acceleration with GROMACS

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/usr/bin/ld: CMakeFiles/libgromacs.dir/nbnxm/cuda/nbnxm_cuda.cu.o: in function `gmx::gpu_launch_kernel_pruneonly(gmx::NbnxmGpu*, gmx::InteractionLocality, int)':
tmpxft_0000b0ce_00000000-6_nbnxm_cuda.compute_120.cudafe1.cpp:(.text+0x621): undefined reference to `void gmx::nbnxn_kernel_prune_cuda<false>(gmx::NBAtomDataGpu, gmx::NBParamGpu, gmx::GpuPairlist, int)'
/usr/bin/ld: CMakeFiles/libgromacs.dir/nbnxm/cuda/nbnxm_cuda.cu.o: relocation R_X86_64_PC32 against undefined hidden symbol `_ZN3gmx23nbnxn_kernel_prune_cudaILb0EEEvNS_13NBAtomDataGpuENS_10NBParamGpuENS_11GpuPairlistEi' can not be used when making a shared object
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/build.make:14518: lib/libgromacs.so.10.0.0] Error 1
make[1]: *** [CMakeFiles/Makefile2:4454: src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

Is there any solution to this or do I have to wait until there is a new release of GROMACS that could patch this? Thank You :)

2

Hi!

This issue will be fixed in GROMACS 2025.3 (planned for September).

For now, you fix the problem by adding -DCMAKE_CUDA_FLAGS=-static-global-template-stub=false to your CMake command. Or downgrade CUDA to 12.9, that one works without any extra steps.

3

Thank you so much!