nlmixr2, tidyverse and RStudio on AWS

Create an AWS account and set up the Ubuntu server instance

The first step is to create an AWS account. This can be easily done following these instructions.

Instruction for setting up a Linux AWS EC2 instance can be found here.

Note: EC2 instances are associated to the server’s regions, that you can find on the top right of the EC2 dashboard page. You can select the region you prefer.

Briefly,

1. Once you have created your AWS account, go to the AWS EC2 dashboard page.

2. Press Launch an instance.

3. In Name and Tags tab write the instance name.

4. In Application and OS Images (Amazon Machine Image, AMI), Quick Start tab, select the default Ubuntu AMI (we selected Ubuntu Server 22.04 LTS (HVM), SSD Volume Type). Leave the other options as default.

5. In the Instance type tab, we selected the t2.large instance. We found that the free tier eligible t2.micro instance was “too slow” for our purposes. Check here the costs associated to the various instances.

6. In the Key pair tab, you can select a key that you have already created. If you don’t have a key pair, you can create a new one by pressing Create new key pair. A new tab will then open. We selected RSA as Key pair type and .ppk as private key file format (this because, as we will see later, for connecting to the instance through SSH we used PuTTY). Press Create key pair and then the key will be downloaded. Store it safely! We will need it later.

7. In network settings, tick Allow SSH traffic from Anywhere 0.0.0.0/0, Allow HTTPS traffic from the internet and Allow HTTP traffic from the internet. Note: By default, RStudio server listens on port 8787. Later on in this guideline, we will allow RStudio server to listen also on port 80, which is the HTTP default port (which is already accessible by ticking Allow HTTP traffic from the internet in point 7). Optional: if we want to access the RStudio server on port 8787 as well, we should define an additional security rule. In network settings, click edit and then add security group rule. Select Custom TCP, in Port range write 8787 and in source select 0.0.0.0/0.

8. In Configure storage we selected 30 GiB of gp2 General purpose SSD root volume.

9. Press Launch instance and then View all instances.

Now, in the list of all your instances you should find the newly created one in the Running state.

Install R and RStudio

Guidelines for installing R and RStudio server on a Ubuntu server 22 can be found here. For installing R and RStudio we need to access the instance through SSH. For this, we will use PuTTY. You can freely download PuTTY from here. To access the instance through SSH:

1. Launch PuTTY.
2. In the Session tab, under Host Name (or IP address) write ubuntu@X, where X is the public IPv4 DNS address that you can find ticking the instance you want to connect to on the Instances page of the EC2 dashboard. Leave port to 22.
3. Open SSH/Auth tab and click Browse button next to the Private key file for authentication field. Search for the key you associated to the previously generated EC2 instance and open it.
4. Click open and then Accept.

Now, you are in your AWS ubuntu server instance! Until further notice, all the next steps should be done through SSH. First of all, let’s run…

sudo apt-get update
sudo apt-get upgrade

Now let’s install some compilers.

sudo apt-get install build-essential

# install two helper packages we need
sudo apt-get install --no-install-recommends software-properties-common dirmngr

# add the signing key (by Michael Rutter) for these repos
# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

sudo apt-get install --no-install-recommends r-base

R

R.Version()
quit()

sudo apt-get install gdebi-core

wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2022.12.0-353-amd64.deb

sudo gdebi rstudio-server-2022.12.0-353-amd64.deb

sudo chmod a+rw /etc/rstudio/rserver.conf

echo 'www-port=80' >> /etc/rstudio/rserver.conf

sudo rstudio-server restart

sudo adduser new_username

Install tidyverse and nlmixr2

Before installing tidyverse and nlmixr2 we need to install a few libraries. First of all, let’s install make and cmake.

sudo apt-get install make
sudo snap install cmake --classic

Then, let’s install the following libraries.

sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libxml2-dev
sudo apt-get install libmpfr-dev
sudo apt-get install libgmp-dev
sudo apt-get install libboost-all-dev
sudo apt-get install liblapack-dev
sudo apt-get install libopenblas-dev
sudo apt-get install libjpeg-turbo8-dev
sudo apt-get install libpng-dev

Note: Apparently, Ubuntu server 22 on AWS does not come with many libraries. We found that the libraries written above are needed for tidyverse and nlmixr2 installation.

Now, let’s install tidyverse. We can do it both by opening R through SSH or by accessing the RStudio server.

install.packages("tidyverse")

Finally we shall install nlmixr2. If you have installed R versions older than the 4.2, please refer to this page for nlmixr2 installation.

install.packages("rxode2", dependencies=T)
install.packages("nlmixr2", dependencies=T)
install.packages("babelmixr2", dependencies=T)

Now your RStudio server with both tidyverse and rxode2/nlmixr2/babelmixr2 should be up and running on AWS. Feel free to provide feedback/suggestions.

Enjoy!