AWS RStudio

Workflow for running R and RStudio Server on an AWS EC2 instance

Prerequisites:

      a. Create an AWS account
      b. Set IAM permissions to allow Amazon EC2 access
      c. Install and configure AWS Command Line Interface (CLI)
      d. Create and configure an Amazon Virtual Private Cloud (Amazon VPC)
      e. Create an Amazon EC2 key pair

1. Configure a security group that has ports for SSH, HTTP, RStudio

A security group acts as a virtual firewall for an EC2 instance to control incoming and outgoing traffic. Security groups can be created using the Amazon VPC console or using the AWS CLI.

Example security group:

      Security group name: RStudio-security-group
      Description: Allow SSH, HTTP, RStudio
      VPC: <vpc ID>

      Inbound rule 1 - SSH, Anywhere-IPv4, port 22
      Inbound rule 2 - HTTP, Anywhere-IPv4, port 80
      Inbound rule 3 - Custom TCP, Anywhere-IPv4, port 8787 (RStudio)

Outbound rule 1 - All traffic

*Record security group ID

2. Create EC2 instance with an Amazon Linux AMI

Amazon EC2 provides a wide selection of instance types optimized for different uses. General purpose instances provide a balance of compute, memory and networking resources.

An Amazon Machine Image (AMI) is a basic configuration that serves as a template for an EC2 instance.

Free tier availability instance:
t2.micro - 1 vCPU, 1.0 RAM (GiB)

Free tier eligible AMI:
Ubuntu Amazon Machine Image (AMI) Ubuntu Server 18.04 LTS (HVM), SSD Volume Type - ami-023fc89db93991d87 (64-bit (x86))

Launch instance via CLI

$ aws ec2 run-instances --image-id ami-023fc89db93991d87 --count 1 --instance-type t2.micro --key-name <key pair name> --security-group-ids <security group ID> --subnet-id <subnet ID> --tag-specifications 'ResourceType=instance,Tags=[{Key=Name,Value=RStudio}]' #name the instance 'RStudio'

Parameters:

      --image-id: 'AMI catalog' in the EC2 portal
      --key-name: 'Key Pairs' in the EC2 portal
      --security-group-ids: 'Security Groups' in the EC2 portal
      --subnet-id: 'Subnets' in VPC portal
      --tag-specifications: provide an instance name, e.g., 'RStudio'

Check the instance is running

$ aws ec2 describe-instances --filters "Name=tag:Name,Values=RStudio"

*Record instance ID
*Record PublicDnsName

Connect to EC2 instance using Secure Shell Protocol (SSH)

$ ssh -i </path/to/my-key-pair.pem> ubuntu@<my-instance-public-dns-name>

Default usernames for different AMIs are listed here: https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/connection-prereqs.html

3. Install yum

Tool for getting, installing, deleting, querying, and managing Linux software packages.

$ sudo apt install yum  
$ sudo yum installed

4. Add the The Comprehensive R Archive Network (CRAN) package repository

Ubuntu repositories contain an outdated version of R. The most recent version of RStudio Server can be found here: https://www.rstudio.com/products/rstudio/download-server/ and the command below updated accordingly.

$ 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/'

Update Ubuntu package repository

$ sudo apt update

5. Install R and system dependencies

r-base is the basic software which contains the R programming language. r-base-dev is an ubuntu package for compiling R packages and other software depending on R.

$ sudo apt -y install r-base r-base-dev

Install R packages

devtools, tidyverse, sparklyr, RMariaDB

Dependencies:

$ sudo apt -y install libcurl4-openssl-dev 
$ sudo apt -y install libssl-dev libxml2-dev libmariadbclient-dev build-essential libcurl4-gnutls-dev

R packages:

$ sudo R -e "install.packages('RCurl', repos='http://cran.rstudio.com')"
$ sudo R -e "install.packages('devtools', repos='http://cran.rstudio.com')"
$ sudo R -e "install.packages('tidyverse')"
$ sudo R -e "install.packages('RMariaDB')"

6. Install and configure R Studio Server

Install debian package manager, gdebi

GDebi is a package installer for Debian packages on Linux.

$ sudo apt install gdebi-core

Install RStudio Server

$ wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.02.3-492-amd64.deb
$ sudo gdebi -n rstudio-server-2022.02.3-492-amd64.deb
$ sudo rm rstudio-server-2022.02.3-492-amd64.deb

Set RStudio login credentials

Add user information to login to RStudio

$ sudo adduser rstudio (username = rstudio)

Password: rstudio

Username and password set as 'rstudio' for ease of use.

Add RStudio to sudo group

$ sudo usermod -aG sudo rstudio

Install Java for RStudio

Reconfigure the library paths for RStudio use:

$ sudo apt -y install default-jdk
$ sudo R CMD javareconf

Change the access permissions for R library

$ sudo chmod 777 -R /usr/local/lib/R/site-library

Restart RStudio Server

$ sudo rstudio-server restart

7. Access RStudio Server

Open a web browser and enter Public DNS(IPv4) followed by the RStudio port (8787) as the URL:

<Public DNS(IPv4)>:8787

*Use the credentials (rstudio) created earlier in the workflow.

8. Create an AMI from the EC2 Instance

To save the installed programs and settings, an AMI can be created using the EC2 portal or the AWS CLI

Example AMI:

Name: RStudio-Ubuntu-Server-18.04-LTS-(HVM)-SSD-Volume
Description: RStudio Ubuntu Server 18.04 LTS (HVM), SSD Volume

Delete on termination: Disable (EBS volume will not be deleted on termination of the EC2 instance)

*Record AMI ID for future use

dgittins/AWS-RStudio