Compilation and Installation

Procedure

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

   cd /path/to/GROMACS

3. Decompress the GROMACS 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
   cd build

5. Perform the configuration.

   FLAGS="-mcpu=tsv110"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS LDFLAGS="-lflang" CC=mpicc CXX=mpicxx \
   /path/to/CMAKE/bin/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=off \
   -DGMX_MPI=on \
   -DGMX_OPENMP=on \
   -DGMX_X11=off \
   ../

6. Perform the compilation and installation.

   make -j40 V=1
   make -j40 install

7. Check whether an executable file is generated.

   ll /path/to/GROMACS/bin/gmx_mpi

8. Set the environment variables.

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