Compilation and Installation

Procedure

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

   cd /path/to/NAMD

3. Create and go to the main program installation directory.

   mkdir NAMD-2.13
   cd NAMD-2.13

4. Create a build directory.

   mkdir build install

5. Perform the configuration.

   export BUILD_DIR=/path/to/NAMD/NAMD-2.13/build
   export INSTALL_DIR=/path/to/NAMD/NAMD-2.13/install

6. Set the environment variables of the compiler. If the setting fails, use the absolute path.

   export CC=mpicc
   export CXX=mpicxx
   export FC=mpif90

7. Go to the build directory.

   cd /path/to/NAMD/NAMD-2.13/build

8. Upload the Charm package to the build directory.
9. Install Charm.

   tar -xvf charm-6.9.0.tar.gz
   cd charm-6.9.0
   mkdir ${INSTALL_DIR}/charm690/
   cp src/arch/mpi-linux-x86_64 src/arch/mpi-linux-arm8 -rf
   grep -rl 'm64' src/arch/mpi-linux-arm8 | xargs sed -i 's/\-m64//g'
   ./build charm++ mpi-linux-arm8 smp --with-production --destination=/path/to/NAMD/NAMD-2.13/install/charm690/mpi-linux-arm8

10. Go to the build directory.

    cd /path/to/NAMD/NAMD-2.13/build

11. Decompress the NAMD installation package.

    tar -zxvf NAMD_2.13_Source.tar.gz

12. Go to the directory generated after the decompression.

    cd NAMD_2.13_Source

13. Rename Linux-ARM64.fftw3.

    cp arch/Linux-x86_64.fftw3 arch/Linux-ARM64.fftw3

14. Go to the NAMD-2.13 directory.

    cd /path/to/NAMD/NAMD-2.13

15. Use an SFTP tool to upload the tcl package to the current directory.
16. Decompress the tcl file.

    tar -xzvf tcl8.5.9-linux-arm64-threaded.tar.gz

17. Modify the Make.charm file.
    1. Open the Make.charm file.

       cd /path/to/NAMD/NAMD-2.13/build/NAMD_2.13_Source
       vi Make.charm

    2. Press i to enter the edit mode and modify the file as follows:

       CHARMBASE = /path/to/NAMD/NAMD-2.13/install/charm690

    3. Press Esc, type :wq!, and press Enter to save the file and exit.
18. Modify the Linux-ARM64-g++.arch file.
    1. Open the Linux-ARM64-g++.arch file.

       cd /path/to/NAMD/NAMD-2.13/build/NAMD_2.13_Source
       vi arch/Linux-ARM64-g++.arch

    2. Press i to enter the edit mode and modify the file as follows:

       NAMD_ARCH = Linux-ARM64
           CHARMARCH = mpi-linux-arm8
           #FLOATOPTS = -O2 -ffast-math -funsafe-math-optimizations -fomit-frame-pointer -mcpu=cortex-a9 -mtune=cortex-a9
           FLOATOPTS = -O2 -ffast-math -funsafe-math-optimizations -fomit-frame-pointer 
           CXX = clang++
           CXXOPTS = $(FLOATOPTS)
           CXXNOALIASOPTS = $(FLOATOPTS) -fno-strict-aliasing
           CC = clang
           COPTS = $(FLOATOPTS)

    3. Press Esc, type :wq!, and press Enter to save the file and exit.
19. Configure NAMD.

    ./config Linux-ARM64-g++ --with-fftw3 --fftw-prefix /path/to/FFTW --with-tcl --tcl-prefix /path/to/NAMD/NAMD-2.13/tcl8.5.9-linux-arm64-threaded --charm-arch mpi-linux-arm8

20. Go to the Linux-ARM64-g++ directory.

    cd Linux-ARM64-g++

21. Compile and install NAMD.

    make

22. Check whether an executable file is generated.

    ls /path/to/NAMD/NAMD-2.13/build/NAMD_2.13_Source/Linux-ARM64-g++/namd2

    If the namd2 file exists, the compilation is successful.