Run fresh_install.sh script on a new linux install.

fresh_install.sh

#!/bin/bash
### Fresh install for a new Ubuntu derivative

# Assign user name
read -p "Enter your user name: " UserName
read -p "Enter your full name: " MyName
read -p "Enter your email address: " MyEmail

# update all
apt-get update
apt-get -y upgrade

# usr functions
apt-get -y install vim
apt-get -y install vim-nox-py2 # Python 2.x support for vim
apt-get -y install synapse
apt-get -y install guake

# python
apt-get -y install ipython
apt-get -y install python-dev
apt-get -y install python-numpy
apt-get -y install python-scipy
apt-get -y install python-matplotlib
apt-get -y install dvipng # Required for matplotlib to use latex
apt-get -y install python-ase
apt-get -y install python-gpgme # for dropbox
apt-get -y install python-pip
pip install --upgrade pyflakes
# Pypar
apt-get -y install build-essential openmpi-bin openmpi-doc libopenmpi-dev 
sudo -u $UserName wget -P ~/Downloads https://pypar.googlecode.com/files/pypar-2.1.5_108.tgz
cd ~/Downloads
sudo -u $UserName tar xzf pypar-2.1.5_108.tgz
cd pypar_2.1.5_108/source
python setup.py install
cd ~


# tools
apt-get -y install ssh
apt-get -y install filezilla
apt-get -y install openshot
apt-get -y install skype
apt-get -y install kile
apt-get -y install texlive
apt-get -y install texlive-xetex
apt-get -y install texlive-publishers
apt-get -y install texlive-latex-extra
apt-get -y install texlive-math-extra
apt-get -y install latex-beamer
apt-get -y install sam2p
apt-get -y install git
# git commands
sudo -u $UserName git config --global user.name $MyName
sudo -u $UserName git config --global user.email $MyEmail
sudo -u $UserName git config --global core.editor vim
sudo -u $UserName git config --global core.excludesfile ~/.gitignore_global
sudo -u $UserName git config --global color.ui true

# for looks
apt-get -y install conky
apt-get -y install lsb-release scrot
sudo -u $UserName wget -P ~/Downloads http://github.com/downloads/djmelik/archey/archey-0.2.8.deb
dpkg -i ~/Downloads/archey-0.2.8.deb
rm ~/Downloads/archey-0.2.8.deb

# compilers
apt-get -y install gfortran


## ## ## Lammps parallel install ## ## ##

apt-get -y install build-essential openmpi-bin openmpi-doc libopenmpi-dev fftw2 fftw-dev

# Check/remove lammps.tar.gz
if [ -f ~/Downloads/lammps.tar.gz ]
	then
		rm ~/Downloads/lammps.tar.gz
fi

# Downloads lammps.tar.gz
sudo -u $UserName wget -P ~/Downloads http://lammps.sandia.gov/tars/lammps.tar.gz

cd ~/Downloads
sudo -u $UserName tar xzf ~/Downloads/lammps.tar.gz
cd lammps-*
cd src
cd MAKE
sudo -u $UserName cp Makefile.openmpi Makefile.mint
sudo -u $UserName sed -i -e 's/# openmpi/ # mint = Linux Mint, mpic++, OpenMPI-1.1, FFTW2/g' Makefile.mint
sudo -u $UserName sed -i -e 's/-DFFT_FFTW3/-DFFT_FFTW2/g' Makefile.mint
cd ..
make yes-kspace
make yes-user-phonon
make mint

# Make static and shared libraries
# Static library
sudo -u $UserName make makelib
sudo -u $UserName make -f Makefile.lib mint
# Sharded library
sudo -u $UserName make makeshlib
sudo -u $UserName make -f Makefile.shlib mint

# Make python library
make install-python

cd ~
 
## ## ## ATLAS install ## ## ##
# Number of CPUs
CPUNum=$(nproc)

# Install required packages
apt-get -y install build-essential gfortran cpufrequtils

# Turn off CPU throttling
for (( i=0; i<$CPUNum; i++ ))
do
	echo "cpufreq-set -c $i -g performance"
	cpufreq-set -c $i -g performance
done

cd ~/Downloads

# Check/remove atlas3.10.1.tar.bz2
if [ -f ~/Downloads/atlas3.10.1.tar.bz2 ]
	then
		rm ~/Downloads/atlas3.10.1.tar.bz2
fi

# Check/remove lapack-3.4.2.tgz
if [ -f ~/Downloads/lapack-3.4.2.tgz ]
	then
		rm ~/Downloads/lapack-3.4.2.tgz 
fi

# Download atlas3.10.1.tar.bz2
sudo -u $UserName wget http://softlayer-dal.dl.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10.1.tar.bz2

# Download lapack-3.4.2.tgz 
sudo -u $UserName wget http://www.netlib.org/lapack/lapack-3.4.2.tgz

# Extract atlas3.10.1.tar.bz2
sudo -u $UserName tar xjf ~/Downloads/atlas3.10.1.tar.bz2

# Compile and Install
cd ATLAS
sudo -u $UserName mkdir obj64
cd obj64
sudo -u $UserName mkdir ~/Downloads/atlasComp
sudo -u $UserName ../configure -b 64 -D c -DPentiumCPS=3000 --shared --prefix=~/Downloads/atlasComp --with-netlib-lapack-tarfile=~/Downloads/lapack-3.4.2.tgz
sudo -u $UserName make
sudo -u $UserName make check
sudo -u $UserName make ptcheck
sudo -u $UserName make time
sudo -u $UserName make install
cd ~

# Move files
mkdir /usr/local/include/atlas
cp -r ~/Downloads/atlasComp/include/atlas/* /usr/local/include/atlas/
cp -r ~/Downloads/atlasComp/include/cblas.h /usr/local/include/atlas/
cp -r ~/Downloads/atlasComp/include/clapack.h /usr/local/include/atlas/
cp -r ~/Downloads/atlasComp/lib/* /usr/local/lib/

# Cleanup
rm ~/Downloads/atlas3.10.1.tar.bz2
rm ~/Downloads/lapack-3.4.2.tgz
rm -r ~/Downloads/ATLAS
rm -r ~/Downloads/atlasComp

echo "ATLAS Install Complete"


## ## ## spglib install ## ## ##
# Install required packages

cd ~/Downloads

# Check/remove spglib-1.4.1.tar.gz
if [ -f ~/Downloads/spglib-1.4.1.tar.gz ]
	then
		rm ~/Downloads/spglib-1.4.1.tar.gz 
fi

# Download spglib-1.4.1.tar.gz 
sudo -u $UserName wget http://hivelocity.dl.sourceforge.net/project/spglib/spglib/spglib-1.4/spglib-1.4.1.tar.gz

# Extract spglib-1.4.1.tar.gz 
sudo -u $UserName tar xzf ~/Downloads/spglib-1.4.1.tar.gz 

# Compile and Install
cd spglib-1.4.1
sudo -u $UserName ./configure
sudo -u $UserName make
cd ~

# Move files
mkdir /usr/local/include/spglib
cp ~/Downloads/spglib-1.4.1/src/.libs/libsymspg.a /usr/local/lib
cp ~/Downloads/spglib-1.4.1/src/*.h /usr/local/include/spglib

# Cleanup
rm -r ~/Downloads/spglib-1.4.1 ~/Downloads/spglib-1.4.1.tar.gz

echo "spglib Install Complete"


## ## ## LAPACK install ## ## ##

# Install required packages
apt-get -y install gfortran

cd ~/Downloads

# Check/remove lapack-3.4.2.tgz
if [ -f ~/Downloads/lapack-3.4.2.tgz ]
	then
		rm ~/Downloads/lapack-3.4.2.tgz 
fi

# Download lapack-3.4.2.tgz 
sudo -u $UserName wget http://www.netlib.org/lapack/lapack-3.4.2.tgz

# Extract lapack-3.4.2.tgz
sudo -u $UserName tar xzf ~/Downloads/lapack-3.4.2.tgz

# Compile and Install
cd ~/Downloads/lapack-3.4.2
sudo -u $UserName cp make.inc.example make.inc
sudo -u $UserName sed -i -e 's/..\/..\/librefblas.a/-lf77blas -lcblas -latlas -lgfortran/g' make.inc
sudo -u $UserName make
cd lapacke
sudo -u $UserName make
cd ~ 

# Change Change lapacke.h file
sudo -u $UserName sed -i -e 's/\/* Complex types are structures equivalent to the/*\/\n\n#define lapack_complex_float std::complex<float>\n#define lapack_complex_double std::complex<double>\n\n\/* Complex types are structures equivalent to the/g' ~/Downloads/lapack-3.4.2/lapacke/include/lapacke.h

# Move files
mkdir /usr/local/include/lapack/
cp ~/Downloads/lapack-3.4.2/lapacke/include/* /usr/local/include/lapack/
cp ~/Downloads/lapack-3.4.2/liblapack.a ~/Downloads/lapack-3.4.2/liblapacke.a ~/Downloads/lapack-3.4.2/libtmglib.a /usr/local/lib/

# Cleanup
rm ~/Downloads/lapack-3.4.2.tgz
rm -r ~/Downloads/lapack-3.4.2

echo "LAPACK Install Complete"