Installation guide for exotic configurations#

Special instructions for building GROMACS on less-common systems#

These instructions pertain to building GROMACS 2024.2. This document is complementary to the up-to-date installation instructions instructions.

The configurations listed here are expected to work, but are not recommended for typical users.

SYCL GPU acceleration for AMD and NVIDIA GPUs using Intel oneAPI DPC++#

AMD and NVIDIA GPUs can also be used with Intel oneAPI BaseKit and Codeplay oneAPI plugins.

For most users, we recommend using CUDA for NVIDIA GPUs and AdaptiveCpp for AMD GPUs instead.

With some versions of oneAPI, you might receive “The compiler you are using does not support OpenMP parallelism” error from CMake. In this case, please add the following options to your CMake command:

  • For oneAPI 2024.x: -DCMAKE_C_FLAGS="-isystem /opt/intel/oneapi/compiler/latest/opt/compiler/include"  -DCMAKE_CXX_FLAGS="-isystem /opt/intel/oneapi/compiler/latest/opt/compiler/include"

  • For oneAPI 2023.x: -DCMAKE_C_FLAGS="-isystem /opt/intel/oneapi/compiler/latest/linux/compiler/include"  -DCMAKE_CXX_FLAGS="-isystem /opt/intel/oneapi/compiler/latest/linux/compiler/include"

AMD GPUs#

After installing Intel oneAPI toolkit 2023.0 or newer, a compatible ROCm version, and the Codeplay plugin, set up the environment by running source /opt/intel/oneapi/setvars.sh --include-intel-llvm or loading an appropriate module load on an HPC system.

Then, configure GROMACS using the following command (replace gfxXYZ with the target architecture):

cmake .. -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \
         -DGMX_GPU=SYCL -DGMX_SYCL=DPCPP \
         -DGMX_GPU_NB_CLUSTER_SIZE=8 -DGMX_GPU_FFT_LIBRARY=vkfft \
         -DSYCL_CXX_FLAGS_EXTRA='-fsycl-targets=amdgcn-amd-amdhsa;-Xsycl-target-backend;--offload-arch=gfxXYZ'

NVIDIA GPUs#

After installing Intel oneAPI toolkit 2023.0 or newer, a compatible CUDA version, and the Codeplay plugin, set up the environment by running source /opt/intel/oneapi/setvars.sh --include-intel-llvm or loading an appropriate module load on an HPC system.

Then, configure GROMACS using the following command:

cmake .. -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \
         -DGMX_GPU=SYCL -DGMX_SYCL=DPCPP \
         -DGMX_GPU_NB_CLUSTER_SIZE=8 -DGMX_GPU_FFT_LIBRARY=vkfft \
         -DSYCL_CXX_FLAGS_EXTRA=-fsycl-targets=nvptx64-nvidia-cuda

SYCL GPU acceleration for NVIDIA GPUs using AdaptiveCpp (hipSYCL)#

For most users, we recommend using CUDA for NVIDIA GPUs.

Build and install AdaptiveCpp with CUDA backend (we recommend using the mainline Clang, not the ROCm-bundled one).

Then, use the following command to build GROMACS (make sure to use the same compiler and set target GPU architecture instead of sm_XY):

cmake .. -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \
         -DGMX_GPU=SYCL -DGMX_SYCL=ACPP -DHIPSYCL_TARGETS='cuda:sm_XY'

Static linking#

Dynamic linking of the GROMACS executables will lead to a smaller disk footprint when installed, and so is the default on platforms where we believe it has been tested repeatedly and found to work. In general, this includes Linux, Windows, Mac OS X and BSD systems. Static binaries take more space, but on some hardware and/or under some conditions they are recommended or even necessary, most commonly when you are running large parallel simulation using MPI libraries (e.g. Cray).

  • To link GROMACS binaries statically against the internal GROMACS libraries, set -DBUILD_SHARED_LIBS=OFF.

  • To link statically against external (non-system) libraries as well, set -DGMX_PREFER_STATIC_LIBS=ON. Note, that in general cmake picks up whatever is available, so this option only instructs cmake to prefer static libraries when both static and shared are available. If no static version of an external library is available, even when the aforementioned option is ON, the shared library will be used. Also note that the resulting binaries will still be dynamically linked against system libraries on platforms where that is the default. To use static system libraries, additional compiler/linker flags are necessary, e.g. -static-libgcc -static-libstdc++.

  • To attempt to link a fully static binary set -DGMX_BUILD_SHARED_EXE=OFF. This will prevent CMake from explicitly setting any dynamic linking flags. This option also sets -DBUILD_SHARED_LIBS=OFF and -DGMX_PREFER_STATIC_LIBS=ON by default, but the above caveats apply. For compilers which don’t default to static linking, the required flags have to be specified. On Linux, this is usually CFLAGS=-static CXXFLAGS=-static.

Building on Solaris#

The built-in GROMACS processor detection does not work on Solaris, so it is strongly recommended that you build GROMACS with -DGMX_HWLOC=on and ensure that the CMAKE_PREFIX_PATH includes the path where the hwloc headers and libraries can be found. At least version 1.11.8 of hwloc is recommended.