Compilation and Installation

Procedure

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

Install the dependencies using Yum.

yum install cmake* flex* bison* bison* -y

Go to the /path/to/AMBER directory.
```
cd /path/to/AMBER
```
Decompress the installation package.
```
tar -xvf AmberTools21.tar.bz2
```
Go to the directory generated after the decompression.
```
cd amber20_src
```
Modify the compiler option.
1. Open the compiler.
```
vim amber20_src/cmake/AmberCompilerConfig.cmake
```
2. Press i to enter the edit mode and change gfortran in line 136 to flang.
  
  After performing 6.a, press Esc, type :set nu, and press Enter to display the line number.
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Go to the build directory of AMBER.
```
cd amber20_src/build
```

Modify the configuration items in the run_cmake file.

Open the run_cmake file.
```
vi run_cmake
```

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

#  Assume this is Linux:
  CFLAGS="-O3 -mllvm -force-customized-pipeline -march=armv8.2-a -mcpu=tsv110 -Wl,-z,muldefs -fuse-ld=lld" \
CXXFLAGS="-O3 -mllvm -force-customized-pipeline -march=armv8.2-a -mcpu=tsv110 -Wno-c++11-narrowing -Wl,-z,muldefs -fuse-ld=lld" \
FCFLAGS="-O3 -mllvm -force-customized-pipeline -march=armv8.2-a -mcpu=tsv110 -I/path/to/Hmpi111Bisheng210/hmpi/include -L/path/to/Hmpi111Bisheng210/hmpi/lib -fuse-ld=lld" \
cmake $AMBER_PREFIX/amber20_src \
 -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
 -DCOMPILER=CLANG  \
 -DMPI=TRUE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
 -DDOWNLOAD_MINICONDA=FALSE -DMINICONDA_USE_PY3=FLASE \
 -DCMAKE_VERBOSE_MAKEFILE=ON \
 -DCMAKE_C_FLAGS="-O3 -mllvm -force-customized-pipeline -march=armv8.2-a -mcpu=tsv110 -Wl,-z,muldefs -fuse-ld=lld" \
  -DCMAKE_CXX_FLAGS="-O3 -mllvm -force-customized-pipeline -march=armv8.2-a -mcpu=tsv110 -Wno-c++11-narrowing -Wl,-z,muldefs -fuse-ld=lld" \
  -DCMAKE_Fortran_FLAGS="-O3 -mllvm -force-customized-pipeline -march=armv8.2-a -mcpu=tsv110 -I/path/to/Hmpi111Bisheng210/hmpi/include -L/path/to/Hmpi111Bisheng210/hmpi/lib -fuse-ld=lld" \
   2>&1 | tee  cmake.log

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

Modify the se_etimer.F configuration file.
1. Open the se_etimer.F configuration file.
```
vi ../../amber20_src/AmberTools/src/sebomd/se_etimer.F
```
2. Press i to enter the edit mode, deregister tnow = 0.01*mclock() in line 28, and add the following content:
```
call cpu_time(tnow)
```
  After performing 9.a, press Esc, type :set nu, and press Enter to display the line number.
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Compile AmberTools.
```
./run_make
```
Perform the installation.
```
make install
```
Set the environment variables.
```
source /path/to/AMBER/amber20/amber.sh
```

Parent topic: AmberTools 21 Porting Guide (openEuler 21.03)