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Current Configuration Ubuntu Server 18.04 (Bionic Beaver)

This script details how to create a Virtual machine (instance) directly in the resource panel (Azure Portal)

For use in Atlantis simulations

Does not use a template

NOTE DS SERIES AND SSD AS STORAGE CANNOT BE USED WITH THESE INSTRUCTIONS, AND IS MORE EXPENSIVE.

Check the version of your OS

 lsb_release -a

1. Set current time zone and users

Time zone

sudo timedatectl set-timezone America/Los_Angeles

To list all possible zones

timedatectl list-timezones
Add new user (optional)

Rstudio often requires the password to be reset Will need input for password

sudo adduser data_user
sudo passwd data_user 
sudo usermod data_user -G sudo # gives root privileges
sudo su - data_user # change user

2. Add and update packages

Install required packages per Atlantis wiki and utilities

Silent installs, copy in blocks

    sudo apt-get update -y
    sudo apt-get dist-upgrade -y

    sudo apt-get install -y subversion build-essential subversion flip autoconf libnetcdf-dev libxml2-dev libproj-dev lsscsi cdo nco libudunits2-dev curl gdebi-core libssl-dev openssl libapparmor1 libv8-dev libgeos-dev libgdal-dev libproj-dev proj-bin proj-data rpm ntp ntpdate gdal-bin libproj12 libproj-dev libgdal-dev libgeo-proj4-perl libgeos++-dev python2.7 python-pip python-dev libpoppler-cpp-dev htop libprotobuf-dev protobuf-compiler librsvg2-dev libx11-dev mesa-common-dev libglu1-mesa-dev texlive-latex-extra libcairo2 libcairo2-dev netcdf-bin
    
    sudo apt-get update -y
    sudo apt-get dist-upgrade -y
    
    sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
    sudo apt install gdal-bin python-gdal python3-gdal
    
    sudo add-apt-repository -y ppa:opencpu/jq
    sudo apt-get update
    sudo apt-get install libjq-dev -y
    
    sudo apt-get -f install -y # missing dependencies
    sudo apt autoremove -y #unused packages

4. Install R and R Studio Server

Update repository so that we get the latest R

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'

sudo sh -c 'echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" >> /etc/apt/sources.list'
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update
sudo apt-get -y install r-base
Download the latest package from the RStudio website and install it with gdebi.
Note all VM instances are 64 bit, so you will need the 64 bit package.
https://www.rstudio.com/products/rstudio/download-server/#
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.1093-amd64.deb
sudo gdebi rstudio-server-1.3.1093-amd64.deb

Verify installation

sudo rstudio-server verify-installation

You can now access your RStudio server at http://your-instance-ip:8787

i.e. 192.241.209.245:8787

Obtain r packages

Install R packages to common library. These These are some common packages for data analysis, spatial analysis, map creation, and Atlantis. Also includes packages to create markdown documents.

sudo su - -c "R --vainilla -e \"install.packages(c('tidyverse','sp','dismo', 'data.table', 'XML','jsonlite','httr','rvest', 'knitr','rgdal','proj4','ggthemes','ggmap','RColorBrewer','RNetCDF','readr', 'classInt','rgeos','maps','maptools','knitcitations','plotrix','gridExtra',
'devtools','scales','magrittr','Hmisc','readxl','cowplot','xtable','gtable',
'raster','reshape2', 'RNetCDF','doSNOW','stringr','stringi','parallel','future'), repos = 'http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('devtools', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('pdftools', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"devtools::install_github('alketh/atlantistools')\""
sudo su - -c "R -e \"devtools::install_github('jporobicg/shinyrAtlantis')\""

5. Build Atlantis

Check out Atlantis code
Put the username and password at the end

svn co https://svnserv.csiro.au/svn/ext/atlantis/Atlantis/trunk --username <username> --password <password> --quiet
Compile Atlantis
Switch folder

cd trunk/atlantis
Build Atlantis code

        aclocal
        autoheader
        autoconf
        automake -a
        ./configure
        sudo make CFLAGS='-Wno-misleading-indentation -Wno-format -Wno-implicit-fallthrough'
        sudo make -d install
        cd atlantismain

If building Atlantis does not work, switch to root user

sudo su -

and try again

check that atlantisNew.exe has been created

 ls -l

6. Install AzCopy

wget -O azcopy.tar.gz https://aka.ms/downloadazcopylinux64
tar -xf azcopy.tar.gz
sudo ./install.sh

OPTIONAL. Install eclipse development environment for Linux

Use if for some reason you need a browser or other GUI based software

Install a minimal Gnome desktop
sudo apt-get install xorg gnome-core gnome-system-tools gnome-app-install
Install a Virtual Desktop using VNC

Using instructions from http://www.havetheknowhow.com/Configure-the-server/Install-VNC.html

sudo apt-get install vnc4server

vncserver

You'll then be prompted to create and verify a new password

Kill vnc session

vncserver -kill :1

Open up the config file

vim .vnc/xstartup

Edit the file as follows

Unmask the unset SESSION_MANAGER line and masked out all the rest. We've then added the last 3 lines.

!/bin/sh

Uncomment the following two lines for normal desktop:

unset SESSION_MANAGER

exec /etc/X11/xinit/xinitrc

[ -x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup

[ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources

xsetroot -solid grey

vncconfig -iconic &

x-terminal-emulator -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" &

x-window-manager &

metacity &

gnome-settings-daemon &

gnome-panel &