Known issues affecting users of GROMACS#
Here is a non-exhaustive list of issues that are we are aware of that are affecting regular users of GROMACS.
Unable to compile with CUDA 11.3#
Due to a bug in the nvcc compiler, it is currently not possible to compile NVIDIA GPU-enabled GROMACS with version 11.3 of the CUDA compiler. We recommend using CUDA 11.4 or newer.
Verlet buffer underestimated for inhomogeneous systems#
The current Verlet buffer estimation code assumes that the density in the system is uniform. This leads to an underestimate of the buffer for strongly inhomogeneous systems. The temporary solution to this is to lower the verlet-buffer-tolerance parameter value by the factor between the uniform density and the local density. In the 2023 release this correction will be performed automatically.
Verlet buffer underestimated when using only r^-12 potentials#
When only the repulsive part of the Lennard-Jones potential is used, as can be the case in coarse-grained systems, the Verlet buffer can be underestimated due to the extremely non-linear nature of the r^-12 potential. A temporary solution is to decrease the verlet-buffer-tolerance until you get a non-zero Verlet buffer. This issue will be fixed in the 2023 release.
The deform option is not suitable for flow#
The deform option currently scales the coordinates, but for flow the deformation should only be driven by changing periodic vectors. In addition the velocities of particles need to be corrected when they are displaced by periodic vectors. Therefore the deform option is currently only suitable for slowly deforming systems.
Build is fragile with gcc 7 and CUDA#
Different forms of gcc 7 have different behaviour when compiling test programs with nvcc. This prevents GROMACS from reliably testing compilation flags for use with nvcc. So in this case we use flags unilaterally and this could lead to compilation errors. The best way to avoid these potential problems is to use a more recent version of gcc.
SYCL build unstable when using oneAPI with LevelZero backend#
There are multiple issues with different versions of Intel oneAPI when using the LevelZero backend.
In many cases, it works fine, and if it fails, it does so explicitly (either crash or hang), so it should be fine to experiment with.
For most cases, we recommend using OpenCL backend (the default) when running SYCL build of GROMACS on Intel GPUs.
Unable to build with CUDA 11.5-11.6 and GCC 11 on Ubuntu 22.04#
A bug in the nvcc toolchain, versions 11.5.0-11.6.1, makes it impossible to build recent GROMACS with GCC 11.2 shipped with Ubuntu 22.04. We recommend the users to either use an different version of GCC (at the time of writing 9.x or 10.x have been reported to work), or manually update the nvcc toolchain to version 11.6.2 or newer.
Some non-Ubuntu installations of GCC 11.2 library have been observed to work fine.
When an incompatible combination is used, an error will be raised from CMake or later during build.
“Cannot find a working standard library” error with ROCm Clang#
Some Clang installations don’t contain a compatible C++ standard library.
In such cases, you might have to install g++ and help CMake find it
by setting -DGMX_GPLUSGPLUS_PATH=/path/to/bin/g++.