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Amber16 + AmberTool17 installation

posted Dec 30, 2017, 10:07 AM by Dong Xu   [ updated Feb 15, 2018, 3:46 PM ]
sudo conda create -n amber16 python=2.7
install the following packages:
numpy
matplotlib
scipy
ipython
notebook
cython

sudo yast2
install  libbz2-1 libbz2-devel

export AMBERHOME=/garlic/apps/Downloads/Amber16/amber16/
sudo cp -s /usr/bin/gfortran-4.8 /usr/bin/gfortran
./configure --full-help

For GPU
sudo CUDA_HOME=/garlic/apps/cuda8.0 ./configure -cuda -noX11 --with-python /garlic/apps/anaconda3/envs/amber16/bin/python --python-install local gnu
test -f $
AMBERHOME/amber.sh
source
$AMBERHOME/amber.sh
sudo CUDA_HOME=/garlic/apps/cuda8.0 make install

For CPU
sudo ./configure -noX11 --with-python /garlic/apps/anaconda3/envs/amber16/bin/python --python-install local gnu
test -f $
AMBERHOME/amber.sh
source
$AMBERHOME/amber.sh
sudo make install

For MPI
sudo PATH=/garlic/apps/mpich3.1.4/bin:$PATH ./configure -mpi -noX11 --with-python /garlic/apps/anaconda3/envs/amber16/bin/python --python-install local gnu
PATH=/garlic/apps/mpich-3.2.1_gnu/bin:$PATH ./configure -mpi -noX11 --skip-python gnu 2>&1 | tee config.log

test -f $AMBERHOME/amber.sh
source $AMBERHOME/amber.sh
sudo PATH=/garlic/apps/mpich3.1.4/bin:$PATH make install

========================================
For Amber14+AmberTools15:
export AMBERHOME=/garlic/apps/Downloads/Amber14/amber14/
cp -rv pmemd/* /garlic/apps/Downloads/Amber14/amber14/src/pmemd/

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