Compiling and Installing NAMD

Procedure

Use PuTTY to log in to the server as the root user.

Run the following commands to create the NAMD-related directories:

cd /path/to/NAMD
mkdir NAMD-2.13
cd NAMD-2.13
mkdir build install
export BUILD_DIR=`pwd`/build
export INSTALL_DIR=`pwd`/install

Run the following commands to set the environment variables.

export CC=`which gcc`
export CXX=`which g++`
export FC=`which gfortran`

Run the following commands to compile and install CHARM:

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

Run the following commands to decompress the NAMD installation package:

cd /path/to/NAMD/NAMD-2.13/build
tar -zxvf NAMD_2.13_Source.tar.gz
cd NAMD_2.13_Source

Run the following command to create Linux-ARM64.fftw3:
```
cp arch/Linux-x86_64.fftw3 arch/Linux-ARM64.fftw3
```

Run the following commands to upload and decompress the TCL file:

cd /path/to/NAMD/NAMD-2.13
tar -xvf tcl8.5.9-linux-arm64-threaded.tar.gz

Run the following commands to modify the Make.charm file:
1. Open Make.charm.
```
cd /path/to/NAMD/NAMD-2.13/build/NAMD_2.13_Source
vi Make.charm
```
2. Press i to enter the insert mode and modify the file as follows:
```
CHARMBASE = /path/to/NAMD/NAMD-2.13/install/charm690
```
  Change the value of CHARMBASE to the actual installation path of CHARM.
3. Press Esc, enter :wq!, and press Enter to save the file and exit.

Run the following commands to modify the Linux-ARM64-g++.arch file:

Open Linux-ARM64-g++.arch.

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

Press i to enter the insert 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 -march=armv7-a -mcpu=cortex-a9 -mtune=cortex-a9 
FLOATOPTS = -O3 -ffast-math -funsafe-math-optimizations -fomit-frame-pointer -march=armv8-a 
 
CXX = g++ -std=c++11 
CXXOPTS = $(FLOATOPTS) 
CXXNOALIASOPTS = $(FLOATOPTS) -fno-strict-aliasing 
 
CC = gcc 
COPTS = $(FLOATOPTS)

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

Run the following commands to 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
cd Linux-ARM64-g++

Run the following commands to compile and install NAMD:
```
make -j
```

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

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

-rwxr-xr-x 1 root root 16140248 Aug  7 15:50 namd2

Parent topic: NAMD 2.13 Porting Guide (CentOS 7.6)