wvictor14 / aws_ec2

For setting up EC2 instance

1. Create EC2

These settings are for all-purpose bioinformatic analyses. Prioritize RAM.

OS: Ubuntu 22.04 key pair name: victor-sonoma-thinkpad Instance type m5.xlarge (32 CPUs, 128 gb RAM) volumes: root 64 Gb, workspace 1 Tb

Configure networking to open ports for for rshiny and rstudio server

For accessing rstudio-server, set security group to allow incoming traffic with following settings: Port range:8787, TCP, 0.0.0.0/0

2. Login via terminal (linux)

chmod 400 [instructor-key].pem ssh -i [instructor-key].pem ubuntu@[public.ip.address] #ssh -i "victor-sonoma-thinkpad.pem" [email protected]

3. Setup data mounts and install software sudo bash setup.sh

4. Rstudio setup

Ensure incoming traffic is enabled (create new rule, add TCP, port 8787, and 0.0.0.0/0) Install Rstudio server Add user / pw

EC2 management tips

Taking stock of compute resources within an Ubuntu Linux instance

How are storage volumes mounted?

lsblk

How much storage space in being used for various mount points?

df -h

Detailed description of hardware

lshw

See active resource usage right now with top. Use 1 to see all CPUs individually. Use q to exit

top

Transferring data

Easiest is drag and drop from vscode ssh remote <-> local

Other options like PuTTY + winscp:

Create PuTTY Private Key file (.ppk)

Then, in WinSCP, add new site with public DNS of EC2 instance. Under Advanced Site Settings, SSH, add .ppk file.

rstudio server

update version

https://support.posit.co/hc/en-us/articles/216079967-Upgrading-RStudio-Workbench-or-RStudio-Server

sudo rstudio-server stop
sudo apt remove rstudio-server
sudo gdebi <rstudio-server-package.deb>

# configure password
sudo passwd ubuntu

style

# vscode style theme
remotes::install_github("anthonynorth/rscodeio")
rscodeio::install_theme()

# others
devtools::install_github("max-alletsee/rstudio-themes")
library(rstudiothemes)
install_rstudio_themes(theme = "all_dark")

rstudio settings

copy rstudio-prefs.json to ~/.config/rstudio

touch ~/.config/rstudio/rstudio-prefs.json
code  ~/.config/rstudio/rstudio-prefs.json #interactively copy

Resources

Griffith lab "Intro to AWS" workshop

Running R on AWS EC2 and Logging into RStudio from Anywhere