194 lines
4.4 KiB
Markdown
194 lines
4.4 KiB
Markdown
---
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title: 在 macOS 上编译安装 GROMACS 2025.2
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date: 2026-05-17
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tags: [GROMACS, macOS, 分子动力学]
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collections: [分子模拟]
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summary: 记录在 macOS 上使用 GCC 12、OpenMPI、FFTW 和 OpenCL 编译安装 GROMACS 2025.2 的过程。
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draft: false
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featured: false
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---
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# 在 macOS 上编译安装 GROMACS 2025.2
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本文记录一次在 macOS 上编译 GROMACS 2025.2 的流程：使用 Homebrew 提供 GCC 12，自行编译 CMake、OpenMPI 和 FFTW，然后以 OpenCL + MPI 方式构建 GROMACS。
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## 目录约定
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源码压缩包统一放在 `$SOFT_ROOT/compressed` 下，安装结果放回各软件源码目录中的版本子目录。
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```bash
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export SOFT_ROOT=/path/to/biosoft
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export CMAKE_VERSION=4.0.2
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export OPENMPI_VERSION=5.0.8
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export FFTW_VERSION=3.3.10
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export GROMACS_VERSION=2025.2
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export CMAKE_HOME="$SOFT_ROOT/cmake-$CMAKE_VERSION/v$CMAKE_VERSION"
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export OPENMPI_HOME="$SOFT_ROOT/openmpi-$OPENMPI_VERSION/v$OPENMPI_VERSION"
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export FFTW_HOME="$SOFT_ROOT/fftw-$FFTW_VERSION/v$FFTW_VERSION-float"
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export GROMACS_HOME="$SOFT_ROOT/gromacs-$GROMACS_VERSION/v$GROMACS_VERSION"
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```
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## 安装 GCC 12
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开始时尝试从源码编译 GCC 12.1.0：
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```bash
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cd "$SOFT_ROOT"
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tar -zxf compressed/gcc-12.1.0.tar.gz
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cd gcc-12.1.0
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./contrib/download_prerequisites
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mkdir -p v12.1.0 build
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cd build
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../configure \
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--prefix="$SOFT_ROOT/gcc-12.1.0/v12.1.0" \
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--enable-languages=c,c++ \
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--disable-multilib
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```
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本次 `make -j5` 编译未通过，实际改用 Homebrew 安装 GCC 12：
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```bash
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brew install gcc@12
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```
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后续命令使用 Homebrew 的 GCC 路径：
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```bash
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export CC=/opt/homebrew/bin/gcc-12
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export CXX=/opt/homebrew/bin/g++-12
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```
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## 安装 CMake
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```bash
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cd "$SOFT_ROOT"
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tar -zxf "./compressed/cmake-$CMAKE_VERSION.tar.gz"
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cd "cmake-$CMAKE_VERSION"
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mkdir -p "v$CMAKE_VERSION"
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./bootstrap --prefix="$CMAKE_HOME"
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make -j5
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make install
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```
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## 安装 OpenMPI
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```bash
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cd "$SOFT_ROOT"
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tar zxf "./compressed/openmpi-$OPENMPI_VERSION.tar.gz"
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cd "openmpi-$OPENMPI_VERSION"
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mkdir -p "v$OPENMPI_VERSION" build
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cd build
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export CC=/opt/homebrew/bin/gcc-12
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export CXX=/opt/homebrew/bin/g++-12
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../configure --prefix="$OPENMPI_HOME"
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make -j5
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make check
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make install
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```
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## 安装 FFTW
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GROMACS 使用单精度 FFTW，因此这里打开 `--enable-float`，并使用 OpenMPI 提供的 `mpicc` 作为 C 编译器。
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```bash
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cd "$SOFT_ROOT"
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tar -zxf "./compressed/fftw-$FFTW_VERSION.tar.gz"
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cd "fftw-$FFTW_VERSION"
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mkdir -p "v$FFTW_VERSION" build
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cd build
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export CC=/opt/homebrew/bin/gcc-12
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export MPICC="$OPENMPI_HOME/bin/mpicc"
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../configure \
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--prefix="$FFTW_HOME" \
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--enable-float \
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--enable-threads \
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--enable-openmp \
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--enable-mpi \
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CC="$MPICC" \
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CPPFLAGS="-I$OPENMPI_HOME/include" \
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LDFLAGS="-L$OPENMPI_HOME/lib" \
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LT_SYS_LIBRARY_PATH="$OPENMPI_HOME/lib"
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make -j5
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make check
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make install
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```
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## 安装 GROMACS
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macOS 上使用 OpenCL 构建 GPU 版本，并打开 MPI 支持。
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```bash
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cd "$SOFT_ROOT"
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tar zxf "./compressed/gromacs-$GROMACS_VERSION.tar.gz"
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cd "gromacs-$GROMACS_VERSION"
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mkdir -p "v$GROMACS_VERSION" build
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cd build
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export PATH="$OPENMPI_HOME/bin:$PATH"
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export CPPFLAGS="-I$FFTW_HOME/include"
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export LDFLAGS="-L$FFTW_HOME/lib"
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"$CMAKE_HOME/bin/cmake" .. \
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-DGMX_GPU=OpenCL \
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-DCMAKE_INSTALL_PREFIX="$GROMACS_HOME" \
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-DGMX_MPI=ON \
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-DCMAKE_C_COMPILER=/opt/homebrew/bin/gcc-12 \
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-DCMAKE_CXX_COMPILER=/opt/homebrew/bin/g++-12 \
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-DGMX_FFT_LIBRARY=fftw3 \
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-DGMX_BUILD_OWN_FFTW=OFF \
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-DMPI_C_COMPILER="$OPENMPI_HOME/bin/mpicc"
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make -j5
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make check
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make install
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```
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安装完成后可先确认 `gmx_mpi` 是否可执行：
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```bash
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"$GROMACS_HOME/bin/gmx_mpi"
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```
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## CUDA 构建参考
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如果是在 Linux + CUDA 环境下构建，可以参考下面的参数形态，按实际 CUDA、GCC 和安装目录调整路径：
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```bash
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export LD_LIBRARY_PATH="/path/to/gcc/lib64:$LD_LIBRARY_PATH"
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cmake .. \
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-DREGRESSIONTEST_DOWNLOAD=ON \
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-DGMX_GPU=CUDA \
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-DCMAKE_INSTALL_PREFIX=/path/to/gromacs/install \
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-DGMX_MPI=ON \
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-DCMAKE_CUDA_ARCHITECTURES=89 \
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-DCMAKE_CUDA_COMPILER=/usr/local/cuda/bin/nvcc \
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-DCMAKE_C_COMPILER=/path/to/gcc/bin/gcc \
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-DCMAKE_CXX_COMPILER=/path/to/gcc/bin/g++
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```
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## 简单测试
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准备好 `ions.mdp`、`mix_two_mol_solv.gro` 和 `topol.top` 后，可以用 `grompp` 生成测试输入文件。
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```bash
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cd /path/to/gromacs-test
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"$GROMACS_HOME/bin/gmx_mpi" grompp \
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-f ions.mdp \
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-c mix_two_mol_solv.gro \
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-p topol.top \
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-o ion.tpr
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```
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