Compilation and Installation

Procedure

Use PuTTY to log in to the server as the root user.
Go to the installation directory.
```
cd /path/to/NAMD
```
Create and go to the main program installation directory.
```
mkdir NAMD-2.13
cd NAMD-2.13
```
Create a build directory.
```
mkdir build install
```

Perform the configuration.

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

Set the environment variables of the compiler. If the setting fails, use the absolute path.
```
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
```
Go to the build directory.
```
cd /path/to/NAMD/NAMD-2.13/build
```
Upload the Charm package to the build directory.

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

Go to the build directory.
```
cd /path/to/NAMD/NAMD-2.13/build
```
Decompress the NAMD installation package.
```
tar -zxvf NAMD_2.13_Source.tar.gz
```
Go to the directory generated after the decompression.
```
cd NAMD_2.13_Source
```

Rename Linux-ARM64.fftw3.

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

Go to the NAMD-2.13 directory.
```
cd /path/to/NAMD/NAMD-2.13
```
Use an SFTP tool to upload the tcl package to the current directory.

Decompress the tcl file.

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

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.

Modify the Linux-ARM64-g++.arch file.

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

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)

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

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

Go to the Linux-ARM64-g++ directory.
```
cd Linux-ARM64-g++
```
Compile and install NAMD.
```
make
```
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.

Parent topic: NAMD 2.13 Porting Guide (openEuler 21.03)