AMBER Installation

Here are the steps to install Amber20 at TARA HPC.

Obtain Amber20 at http://ambermd.org and download source codes

Upload and extract amber source codes at your project home director

cd /tarafs/data/project/projxxxx  #change projxxxx to your project ID  
tar xvfj AmberTools20.tar.bz2  
tar xvfj Amber20.tar.bz2

Set the AMBERHOME home directory environment variable
```
cd amber20_src
export AMBERHOME=$PWD
```

Load modules and prepare for AMBER20 installation

module purge
module load bzip2/1.0.8-GCCcore-8.3.0
module load GCC/8.3.0
module load XZ/5.2.4-GCCcore-8.3.0

Go to the amber directory and execute the compilation script
```
cd $AMBERHOME
./configure -noX11 gnu
```

Install and test

source ./amber.sh
make install
make test

After the installation is successful, you can compile parallel (MPI) versions of Amber20 by load OpenMPI module
```
module load OpenMPI/3.1.4-GCC-8.3.0
```

Then, recompilation with MPI

./configure -mpi -noX11 gnu
make install

To compile Amber20 for GPU

Go to the AMBERHOME home directory environment variable

cd /tarafs/data/project/projxxxx  #change projxxxx to your project ID  
cd amber20_src
export AMBERHOME=$PWD

Load modules and prepare for AMBER20 installation

module purge
module load bzip2/1.0.8-GCCcore-8.3.0
module load XZ/5.2.4-GCCcore-8.3.0
module load gcccuda/2019b
module load CUDA/10.1.243

Go to the amber directory and execute the compilation script for the installation with cuda
```
cd $AMBERHOME
./configure -noX11 -cuda gnu
make install
```
Testing
```
make test.cuda_serial
```

After the installation is successful, you can compile parallel (MPI) versions with cuda

module load OpenMPI/3.1.4-gcccuda-2019b
module load NCCL/2.4.8-gcccuda-2019b
export NCCL_HOME=/tarafs/utils/modules/software/NCCL/2.4.8-gcccuda-2019b/

Then, recompilation with MPI for GPU

./configure -noX11 -cuda -mpi -nccl gnu
make install