Basic Linux SysAdmin

Learning objectives

  • Admin stuff that I won’t dig into:
    • Create users in Linux.
    • Check and set Linux file permissions.
    • Install programs on Debian-based Linux distributions.
    • Check storage usage.
    • Manage processes.
    • Implement SSH port forwarding.
    • Locate files on the $PATH.
  • Set up a data science AWS EC2.
    • Run RStudio on an AWS EC2.
    • Run JupyterHub on an AWS EC2.
    • Run a plumber API in a docker container on an AWS EC2.

Stand up an EC2 (chapter 10 lab review)

  • Sign in at console.aws.amazon.com
  • Go to EC2 (via services or other routes)
  • “Launch instances”
  • Fill in the form:
    • Name (do4ds-lab)
    • AMI: ubuntu
    • Type: t2.micro is free, might need larger later.
    • Key pair: Choose or create. pem version no matter what you’re on.
    • Security group: Choose or create.
    • Storage: For now we aren’t using anything more than the root.
      • We’ll add more when we need it in a later lab.
      • It’s fine if you already added some, though.
    • “Launch instance”
  • “Instance state” menu to stop or terminate between labs.

Create a non-root user

  • (“Instance state” > “Start instance” to resume)
  • Copy “Public IPv4 DNS” (will be $SERVER_ADDRESS below)
    • something like “ec2-3-123-456-789.compute-1.amazonaws.com”
  • ssh -i ~/path/to/do4ds-lab-key.pem ubuntu@$SERVER_ADDRESS
  • sudo adduser test-user
    • Give them a password
    • Defaults ok for everything else
  • sudo usermod -aG sudo test-user (add to Group)

Add an ssh key

  • Create new key from your local machine (if you don’t have one):
    • On Windows: ssh-keygen works but it’s fussy
    • I named it id_rsa_test_user (but then I reverted to my personal id_rsa!)
    • I didn’t use a password
  • scp the key to the server
    • scp -i ~/path/to/do4ds-lab-key.pem ~/path/to/id_rsa.pub ubuntu@@$SERVER_ADDRESS:/home/ubuntu
  • On server:
    • mv & chown to user
    • su test-user & cd ~
    • mkdir -p .ssh, chmod 700 .ssh, cat id_rsa.pub >> .ssh/authorized_keys
    • chmod 600 .ssh/authorized_keys
    • rm id_rsa.pub

Notes on personal ssh key

  • I still need -i ~/path/to/id_rsa_test_user in ssh call
  • Is this because I haven’t “set up an SSH config for this server”?
  • Update: Nope! It was because I had 2 keys in my local.ssh folder

Install R

  • curl -Ls https://github.com/r-lib/rig/releases/download/latest/rig-linux-arm64-latest.tar.gz | sudo tar xz -C /usr/local
  • rig add release
  • R

Install RStudio Server

  • Check current installation instructions
  • 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 systemctl status rstudio-server
  • rm rstudio-server-2022.12.0-353-amd64.deb

Tunnel to see it locally

  • On your local machine:
    • ssh -NL 8787:localhost:8787 test-user@$SERVER_ADDRESS
    • I had to add the N, I’m not sure what it does (got it from Google)
  • It’s alive!

Install Python and JupyterLab

  • I did not do this and hope to never do this.

Plumber in docker

  • sudo apt-get install docker.io
    • sudo docker ps to make sure it worked
sudo docker run --rm -d \
  -p 8555:8000 \
  --name palmer-plumber \
  alexkgold/plumber
  • ssh -NL 8555:localhost:8555 test-user@$SERVER_ADDRESS
  • It’s an api!