ecomod/effortsinvest

rstudio-docker

heavily inspired by https://github.com/PawseySC/rstudio-nginx

Setup

GWDG Cloud server

Create a server with the most recent Ubuntu and make sure that the ports 80, 443 and 22 are open. SSH into your server, change the password and update all packages:

sudo apt update && sudo apt -y dist-upgrade # might be blocked due to auto update... just be patient

Install docker:

sudo apt -y install curl gnupg2 apt-transport-https ca-certificates  software-properties-common

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"

sudo apt update
sudo apt -y install docker-ce

Install docker-compose

Have a look at https://github.com/docker/compose/releases and see which is the most recent release. At the time of this writing, it is version 1.29.1

sudo curl -L "https://github.com/docker/compose/releases/download/1.29.1/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose

sudo chmod a+x /usr/local/bin/docker-compose

docker-compose --version  # just checkin'

Clone this repository

git clone https://github.com/ecomod-code/rstudio-docker.git
cd rstudio-docker

Create a custom Docker image (optional)

Either use my image (default, just skip this paragraph) or create your own local version of it. Adjust the Dockerfile to your needs and run the following command to build the image from that Dockerfile (this will take a while).

sudo docker build -t sebastianhanss/rstudio:latest .

If you use a different tag than sebastianhanss/rstudio:latest remember to adjust your docker-compose.yml accordingly.

Quick Start

• Edit the environment file, e.g. nano .env
  • Server_URL is the domain name of your server (e.g. c10x-xxx.cloud.gwdg.de)
  • RStudio_Username and RStudio_Password will be the user name and password for your RStudio Server. Choose a strong password as your server is available from the Internet
  • your e_mail_address will be associated with the generated certificates for the encrypted connection to your server. It does not generate Spam you will just be notified when your certificate is about to expire
  • ROOT=false means that your RStudio user will have no admin rights in the container. This improves security, but you can change it to yes if you need admin rights
• Save your changes Ctrl+O and exit the editor Strl+X
• Run sudo docker-compose up -d to start the containers

You should now have a working RStudio server that you can access via a web browser at c10x-xxx.cloud.gwdg.de.

More explanations at https://github.com/PawseySC/rstudio-nginx

Installing Efforts and Netlogo

Via the Terminal in R: Clone EFForTS-ABM with

git clone https://github.com/EFForTS-B10/EFForTS-ABM.git

Netlogo will be automatically downloaded when executing some of our EFForTS-simulation-skripts but in case you want to download Netlogo manually:

wget http://ccl.northwestern.edu/netlogo/6.1.1/NetLogo-6.1.1-64.tgz

and unzip it (slightly more complicated command makes sure the created directory is called 'netlogofolder' for later reference in nlrx)

mkdir netlogofolder && tar xf NetLogo-6.1.1-64.tgz -C netlogofolder --strip-components 1