Compilation and Installation

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the main program installation directory.

   cd /path/to/GROMACS

3. Decompress the installation package.

   tar -xvf gromacs-2019.3.tar.gz

4. Go to the directory generated after the decompression and create a build directory.

   cd gromacs-2019.3
   mkdir build

5. Edit the configuration file.
   1. Open the configuration file.

      vi cmake/gmxManageNvccConfig.cmake

   2. Press i to enter the insert mode and comment out lines 116, 117, 120, and 121.

      

      

      After performing 5.a, press Esc, type :set nu, and press Enter to display the line number.

   3. Press Esc, type :wq!, and press Enter to save the settings and exit.
6. Perform the configuration.

   sed -i '212s/return fftw_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp
   sed -i '214s/return fftwf_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp
   sed -i '457s/int fftwflags = FFTW_DESTROY_INPUT;/int fftwflags = 0;/g' src/gromacs/fft/fft5d.cpp
   sed -i '587s/FFTWPREFIX(cleanup)();/fftwf_cleanup_threads();/g' src/gromacs/fft/fft_fftw3.cpp
   cd build
   FLAGS="-march=armv8.2-a -mcpu=tsv110"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS LDFLAGS="-fuse-ld=lld" CC=mpicc CXX=mpicxx \
   cmake -DCMAKE_INSTALL_PREFIX=/path/to/GROMACS  \
   -DBUILD_SHARED_LIBS=on \
   -DBUILD_TESTING=on \
   -DREGRESSIONTEST_DOWNLOAD=off \
   -DGMX_BUILD_OWN_FFTW=off \
   -DGMX_SIMD=ARM_NEON_ASIMD \
   -DGMX_DOUBLE=off \
   -DGMX_EXTERNAL_BLAS=on \
   -DGMX_EXTERNAL_LAPACK=on \
   -DGMX_FFT_LIBRARY=fftw3 \
   -DGMX_BLAS_USER=/path/to/OPENBLAS/lib/libopenblas.a \
   -DGMX_LAPACK_USER=/path/to/OPENBLAS/lib/libopenblas.a \
   -DFFTWF_LIBRARY=/path/to/FFTW/lib/libfftw3f.so \
   -DFFTWF_INCLUDE_DIR=/path/to/FFTW/include \
   -DGMX_GPU=on \
   -DGMX_OPENMP=on \
   -DGMX_X11=off  \
   -DGMX_MPI=on \
   -DHWLOC_LIBRARIES=/usr/lib64 \
   -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
   ../

7. Perform the compilation.

   make -j40 V=1
   make -j40 install

8. Check whether an executable file is generated.

   ll /path/to/GROMACS/bin/gmx_mpi

   If the command output contains the gmx_mpi file information, an executable file is successfully generated.

9. Configure the environment variables.

   export PATH=/path/to/GROMACS/bin:$PATH