Gromacs 2026.4 with CUDA support

Webpage

http://www.gromacs.org/

Version

2026.4

Build Environment

  • GCC 13.3.1 (gcc-toolset-13)
  • Open MPI 4.1.8
  • cmake 3.31.6
  • HDF5 1.14.6
    • (./configure --enable-fortran --enable-cxx --enable-hl)
  • openblas 0.3.31 (lp64)
  • libtorch 2.12.0-cu132 (binary package)
    • cudnn 9.22.0-cuda13
    • cudss 0.7.1.4-cuda13
    • cusparselt 0.9.1
    • nccl 2.30.4-1 (cuda13.2)
    • nvshmem 3.6.5-0 (cuda 13.2)
  • heFFTe 2.4.1 (compiled for 2026.2; via a symbolic link)

Files Required

  • gromacs-2026.4.tar.gz
  • regressiontests-2026.4.tar.gz

Build Procedure

#!/bin/sh

VERSION=2026.4
INSTALL_PREFIX=/apl/gromacs/${VERSION}-CUDA

BASEDIR=/home/users/${USER}/Software/Gromacs/${VERSION}/
GROMACS_TARBALL=${BASEDIR}/gromacs-${VERSION}.tar.gz
REGRESSION_TARBALL=${BASEDIR}/regressiontests-${VERSION}.tar.gz
WORKDIR=/gwork/users/${USER}
REGRESSION_PATH=${WORKDIR}/regressiontests-${VERSION}

FFTW_VER=3.3.10
FFTW_PATH=${BASEDIR}/fftw-${FFTW_VER}.tar.gz

PARALLEL=12
export LANG=C

#---------------------------------------------------------------------
umask 0022

module -s purge
module -s load gcc-toolset/13
module -s load openmpi/4.1.8/gcc13-cuda13.2
module -s load cuda/13.2
module -s load cmake/3.31.6
module -s load hdf5/1.14.6
module -s load openblas/0.3.31-lp64
module -s load cudnn/9.22.0-cuda13
module -s load cudss/0.7.1.4-cuda13
module -s load cusparselt/0.9.1
module -s load nccl/2.30.4-1-cuda13.2
module -s load nvshmem/3.6.5-0-cuda13.2

TORCH_DIR=/apl/libtorch/2.12.0/cu132
OPENBLAS_DIR=/apl/openblas/0.3.31/lp64
export CUDNN_ROOT_DIR=/apl/cudnn/9.22.0/cudnn-linux-x86_64-9.22.0.52_cuda13-archive
export CUDSS_ROOT_DIR=/apl/cudss/0.7.1/libcudss-linux-x86_64-0.7.1.4_cuda13-archive
export CUSPARSELT_ROOT_DIR=/apl/cusparselt/0.9.1/libcusparse_lt-linux-x86_64-0.9.1.1_cuda13-archive
#export NVSHMEM_ROOT=/apl/nvshmem/3.6.5-0/cuda13.2
export HEFFTE_ROOT=/apl/gromacs/2026.4-CUDA/heffte-2.4.1

#export CUDA_VISIBLE_DEVICES=0,1
unset OMP_NUM_THREADS

cd ${WORKDIR}
if [ -d gromacs-${VERSION} ]; then
 mv gromacs-${VERSION} gromacs_erase
 rm -rf gromacs_erase &
fi

tar xzf ${GROMACS_TARBALL}
tar xzf ${REGRESSION_TARBALL}
cd gromacs-${VERSION}

# single precision, no MPI
mkdir rccs-s
cd rccs-s
cmake .. \
  -DCMAKE_PREFIX_PATH="${TORCH_DIR};${OPENBLAS_DIR}" \
  -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
  -DCMAKE_VERBOSE_MAKEFILE=ON \
  -DCMAKE_C_COMPILER=gcc \
  -DCMAKE_CXX_COMPILER=g++ \
  -DGMX_MPI=OFF \
  -DGMX_GPU=CUDA \
  -DGMX_DOUBLE=OFF \
  -DGMX_THREAD_MPI=ON \
  -DGMX_USE_CUFFTMP=OFF \
  -DGMX_NNPOT=TORCH \
  -DCAFFE2_USE_CUDNN=ON \
  -DCAFFE2_USE_CUSPARSELT=ON \
  -DUSE_CUDSS=ON \
  -DGMX_USE_EXT_FMM=OFF \
  -DGMX_USE_HDF5=ON \
  -DGMX_BUILD_OWN_FFTW=ON \
  -DGMX_BUILD_OWN_FFTW_URL=${FFTW_PATH} \
  -DREGRESSIONTEST_DOWNLOAD=OFF \
  -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..
rm -rf rccs-s

# single precision, with MPI
mkdir rccs-mpi-s
cd rccs-mpi-s
#   -DGMX_NVSHMEM=ON \
#   -DNVSHMEM_ROOT=${NVSHMEM_ROOT} \
cmake .. \
  -DCMAKE_PREFIX_PATH="${TORCH_DIR};${OPENBLAS_DIR}" \
  -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
  -DCMAKE_VERBOSE_MAKEFILE=ON \
  -DCMAKE_C_COMPILER=mpicc \
  -DCMAKE_CXX_COMPILER=mpicxx \
  -DGMX_MPI=ON \
  -DGMX_GPU=CUDA \
  -DGMX_DOUBLE=OFF \
  -DGMX_THREAD_MPI=OFF \
  -DGMX_USE_CUFFTMP=OFF \
  -DGMX_NNPOT=TORCH \
  -DCAFFE2_USE_CUDNN=ON \
  -DCAFFE2_USE_CUSPARSELT=ON \
  -DUSE_CUDSS=ON \
  -DGMX_USE_EXT_FMM=OFF \
  -DGMX_USE_HDF5=ON \
  -DGMX_USE_PLUMED=ON \
  -DGMX_USE_HEFFTE=ON \
  -DHeffte_ROOT=${HEFFTE_ROOT} \
  -DGMX_BUILD_OWN_FFTW=ON \
  -DGMX_BUILD_OWN_FFTW_URL=${FFTW_PATH} \
  -DREGRESSIONTEST_DOWNLOAD=OFF \
  -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..
rm -rf rccs-mpi-s

Test

All the tests have passed successfully.

Notes