Compiling and Installing GROMACS

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to decompress the GROMACS installation package:

   tar -xvf gromacs-2019.3.tar.gz

3. Run the following command to switch to the directory generated after the package is decompressed:

   cd Gromacs-2019.3

4. Run the following commands to create a build directory and switch to the directory:

   mkdir build
   cd build

5. Run the following command to perform configuration:

   FLAGS="-mcpu=tsv110"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS LDFLAGS="-lgfortran" CC=mpicc CXX=mpicxx \
   /path/to/CMAKE/bin/cmake \
   -DCMAKE_INSTALL_PREFIX=/path/to/GROMACS/gromacs-2019.3 \
   -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/OpenBLAS-0.3.6/lib/libopenblas.a \
   -DGMX_LAPACK_USER=/path/to/OPENBLAS/OpenBLAS-0.3.6/lib/libopenblas.a \
   -DFFTWF_LIBRARY=/path/to/FFTW/libfftw3f.so \
   -DFFTWF_INCLUDE_DIR=/path/to/FFTW/include \
   -DGMX_GPU=off \
   -DGMX_MPI=on \
   -DGMX_OPENMP=on \
   -DGMX_X11=off \
   ../

6. Run the following commands to perform compilation and installation:

   make -j40 V=1
   make -j40 install

7. Run the following command to check whether an executable file is generated:

   ll /path/to/GROMACS/bin/gmx_mpi

   -rwxr-xr-x 1 root root 83656 Jul 31 02:51 gmx_mpi

8. Run the following commands to set environment variables:

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