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# Content
# 1. install basic packages
# 2. mount a second hard drive if needed
# 3. installing cuda toolkit and driver 
# 4. installing amber 12
#
# OS = ubuntu 12.04 desktop
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# install basic packages
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sudo apt-get aptitude vim openssh-client opessh-server gparted gfortran g++

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# mount a second hard drive if needed
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# http://askubuntu.com/questions/125257/how-do-i-add-an-additional-hard-drive
# relative tool = gparted

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# installing cuda toolkit and driver 
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# check amber version requirement for cuda version
# amber 12 support cuda 5.0 but not 5.5

#download cuda-driver from https://developer.nvidia.com/cuda-downloads

# if installation said nouveau driver being using
sudo vi /etc/modprobe.d/blacklist.conf 
# add the 5 blacklist lines below to the end of the file
blacklist vga16fb
blacklist nouveau
blacklist rivafb
blacklist nvidiafb
blacklist rivatv
# then remove nouveau and reboot
sudo apt-get remove --purge nouveau*
reboot

# install graphic card driver
sudo stop lightdm
# run cuda driver installation, require sudo account
sudo start lightdm

# set evn variables for cuda
export CUDA_HOME=/opt/cuda-5.0
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/opt/cuda-5.0/lib64":"opt/cuda-5.0/lib"

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# installing amber 12
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# install required packages
sudo apt-get install vim tcsh gfortran g++ flex mpich2 libmpich2-dev zlib-bin zlib1g-dev byacc libbz2-dev libcufft4 openmpi-bin libopenmpi-dev
# this will ask to remove some packages
sudo apt-get install xorg-dev

# add ENV variables to .bashrc for amber 12
export AMBERHOME=/opt/amber12
export PATH=$PATH:$AMBERHOME/bin

# extract amber/ambertools to the directory you want it installed
tar xf amber12.tar.gz
# AmberTools13.tar.bz2 can be downloaded from http://ambermd.org/AmberTools-get.html
tar xf AmberTools13.tar.bz2

# apply patches
$AMBERHOME/update_amber --update
# sometimes need redo the update because the update_amber script itself is updated

# install amber 12 and ambertools 13
cd $AMBERHOME
./configure gnu
make install

# install amber 12 and ambertools 13 MPI
./configure -mpi gnu
make install

# install amber 12 and ambertools 13 cuda
./configure -cuda gnu
make instal

# install amber 12 and ambertools 13 cuda MPI
./configure -cuda -mpi gnu
make install