Gmx 2025.4 in Ubuntu 26.04

User discussions
1

GROMACS version:2025.4
GROMACS modification: No

I have updated my computer to Ubuntu 26.04, and have 7.0.0-15-generic kernel, cuda-13.2
and compiled gmx 2025.4 using gcc13 and nvcc 13.1.r13.1/compiler.37061995_0.

I can prepare the input (pdb2gmx, editconf, solvate…) with the newly compiled code, but when I issue the gmx mdrun… it just hangs and do nothing.

Here are the commands I used for compiling the code:

cmake .. -DCMAKE_C_COMPILER=gcc-13 -DCMAKE_CXX_COMPILER=g+±13 -DCMAKE_CUDA_HOST_COMPILER=/usr/bin/g+±13 -DCMAKE_CUDA_COMPILER=/usr/local/cuda-13.1/bin/nvcc -DCUDAToolkit_ROOT=/usr/local/cuda-13.1 -DGMX_SIMD=AVX2_256 -DGMX_GPU=CUDA -DCMAKE_CUDA_ARCHITECTURES=120 -DGMX_OPENMP=ON -DGMX_MPI=OFF -DGMX_DOUBLE=OFF -DGMX_BUILD_OWN_FFTW=ON -DBUILD_SHARED_LIBS=ON -DGMX_HWLOC=ON -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_INSTALL_PREFIX=/opt/gromacs-2025 -DCMAKE_BUILD_TYPE=Release

make -j 20 >& make.log &
sudo make install -j 20

I should add that this was working all right with Ubuntu 25.10

I would appreciate any suggestions.

Sandor

2

Hi Sandor,

By “it just hangs and do nothing” do you mean it does not even print the version header? Is the md.log file completely empty?

Which command-line options are you using? Have you tried running without GPU (do export CUDA_VISIBLE_DEVICES= before launching gmx mdrun; to revert do unset CUDA_VISIBLE_DEVICES)?

Sidenote 1: -DCMAKE_CUDA_ARCHITECTURES is only supported in GROMACS 2026. For 2025 you should use -DGMX_CUDA_TARGET_SM=120. Should not matter for your problem, though.; without the correct option it will just take slightly longer to compile.

Sidenote 2: You say “cuda-13.2”, but the command line shows paths to cuda-13.1. Which one is the typo?

3

Not even a log file created. It does not show up in nvidia-smi

ok the nvidia-driver is 13-2, but the available cuda is 13-1