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Software website : http://ambermd.org/Installation.php

Amber20 for CPU Installation

This is for running Amber20 on compute and memory node(s).

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

2. Upload and extract amber source codes at your project home director

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

3. Set the AMBERHOME home directory environment variable

   Code Block
   cd amber20_src export AMBERHOME=$PWD

4. Load modules and prepare for AMBER20 installation

   Code Block
   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

5. Go to the amber directory and execute the compilation script

   Code Block
   cd $AMBERHOME ./configure -noX11 gnu

6. Install and test

   Code Block
   source ./amber.sh make install make test

7. After the installation is successful, you can compile parallel (MPI) versions of Amber20 by load OpenMPI module

   Code Block
   module load OpenMPI/3.1.4-GCC-8.3.0

8. Then, recompilation with MPI

   Code Block
   ./configure -mpi -noX11 gnu make install

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Amber20 for GPU Installation

This is for running Amber20 on GPU node. After finishing the Amber20 for CPU installation, please follow the following steps to install Amber20 on GPU.

1. Go to the AMBERHOME home directory environment variable

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

2. Load modules and prepare for AMBER20 installation

   Code Block
   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

3. Go to the amber directory and execute the compilation script for the installation with cuda

   Code Block
   cd $AMBERHOME ./configure -noX11 -cuda gnu make install

4. Testing

   Code Block
   make test.cuda_serial

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

   Code Block
   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/

6. Then, recompilation with MPI for GPU

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

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