Setup R with Visual Studio Code

This setup guides you through setting up R in VSCode so you can use it on dancmpn01fl and dancmpn02fl computing nodes.

Info

The original RStudio server is using 4.0.5 version. If you want to stick this version, make sure to specify it when loading modules.

Why do you need this?

Because RStudio server sucks when you don't have a license and our place, so alternative it is. Also, VSCode has a bunch of plugins.

Setting up Remote Tunnels

Warning

In this example we use version R/4.2.1. If you want to use a different one change the R version!

Requirements

• VSCode
• Terminal

Setting up first time

1. Login to head node: ssh $USER@danhead01fl.unicph.domain
2. Start a new tmux session: tmux new -s rstudio
3. Start a new job: srun -c 2 --mem=30gb --time=0-4:00:00 --pty bash
4. Load modules: module load vscode_cli gcc/11.2.0 R/4.2.1 quarto
5. Run command: code tunnel
   1. Choose Microsoft account when asked how you would like to log in to VScode
   2. Open the link from terminal and paste the CODE
   3. Login with your KU credentials
   4. Go back to terminal and wait
   5. Hit ENTER on questions about tunnel name
   6. If everything went well you should see some random messages about port forwarding
6. Go to your VSCode and on the left panel search for Remote Explorer
7. Click Sign in to the tunnels registered with Microsoft
   1. You should see dancmpn01flunicphdom or dancmpn02flunicphdom
8. Move cursor on it and click the ->
9. Install extension Remote Tunnels

To use R, install additional packages by clicking Extensions in the left panel. Search for packages:

• R

• Quarto

• Next, top panel lick View -> Terminal -> Write R and hit ENTER

• install.packages("languageserver")
  1. If it asks to install to stuff to other directory type YES then hit ENTER
  2. When asking about mirror type 30 (Denmark servers to download packages)
• install.packages("httpgd")
• q() to get out
• Top left panel: Code -> Settings -> Settings
  1. Type in search r.plot.useHttpgd
  2. Tick the box if it is not checked

If everything went well, you should be able to do this. If not, you know what to do.

I already did the setup, I want my R again

1. Login to head node: ssh $USER@danhead01fl.unicph.domain
2. Start a new tmux session: tmux new -s rstudio
3. Start a new job: srun -c 2 --mem=30gb --time=0-4:00:00 --pty bash
4. Load modules: module load vscode_cli gcc/11.2.0 R/4.2.1 quarto
5. Run command: code tunnel
6. Go to your VSCode and on the left panel search for Remote Explorer
7. Click dancmpn01flunicphdom or dancmpn02flunicphdom

Admins: How to install

Creating module

curl -Lk 'https://code.visualstudio.com/sha/download?build=stable&os=cli-alpine-x64' --output vscode_cli.tar.gz
tar -xf vscode_cli.tar.gz

Known issues

VSCode can be installed as a server code-server, however it is not possible to listen on the port when on computing node. This works only in the case of dangpu01fl.

Error when trying to do reverse ssh:

error listen EADDRINUSE: address already in use 127.0.0.1:8080

VSCode code-server is an alternative to code tunnel that consists of running code-server on a compute node and accessing it via a web browser using reverse ssh tunnel.

curl -fL https://github.com/coder/code-server/releases/download/v4.90.2/code-server-4.90.2-linux-amd64.tar.gz | tar -C /maps/projects/dan1/data/Brickman/shared/modules/software/code-server/4.90.2 -xz

ssh user@danhead01fl.unicph.domain
tmux new
srun -c 2 --mem=30gb --time=0-4:00:00 -p gpuqueue --pty bash
module load code-server
code-server
# On local machine
ssh -fNL localhost:8080:localhost:8080 $USER@dangpu01fl.unicph.domain