I recently had the joy of setting up my environment on AWS EC2 and I wanted to put this out there for anyone who just wants to get started as fast as possible.
I’ll assume that you set your EC2 instance up already. Let me note that you should add some type of persistent storage of your data. EC2 instances can be deleted at will by Amazon 😱 (author note: it happened to me). Back up your stuff, this ain’t your grandma’s cloud.
You can add an S3 volume, push to Git, or make images of your instance. You can follow adding S3 through AWS support. Furthermore, I recommend that you UNCHECK delete on termination. As of January 28, 2021 the default is to delete on termination. I am talking to Amazon about this issue and it may get changed.
I’m running Ubuntu on EC2 and these are the steps I take.
Installing RStudio Server
sudo apt update && sudo apt upgrade -y
Download Rstudio by (from Rstudio help)
sudo apt-get install gdebi-core wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.4.1103-amd64.deb sudo gdebi rstudio-server-1.4.1103-amd64.deb
sudo adduser YOURNAME
Set up ports
Need to make sure can access port 8787 for web access
port 22 for ssh
go to the security group for the instance “edit inbound rules” option
Configure Security Group — Create group to open the following ports
1. SSH — Port Range: Port 22 — Source:
2. Custom TCP Rule — Port Range: Port 8787 — Source: 0.0.0.0/0
Installing stuff on AWS linux
rstan for Rstudio to open
.stan files. Before installing
rstan do these two things. Doesn’t matter which one is first.
Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1) install.packages("rstan")
Now, you really do need to open the terminal and add
sudo apt-get install libnode-dev sudo apt-get install libcurl4-openssl-dev sudo apt-get install libxml2-dev
install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) # if you want dev of cmdstanr # remotes::install_github("stan-dev/cmdstanr") cmdstanr::install_cmdstan(version = "2.26.0", cores = 4)
Optional: set unlimited memory
You may not be able to use the full amount of memory on EC2. I followed the steps of increasing the ulimit: How to increase ulimit on Amazon EC2 instance? – Stack Overflow.
Recover files from Rstudio crash
Sometimes Rstudio will crash and you’ll have to SSH into your instance to recover it. The best way I found is by going in to the share folder and copying the
rstudio folder to a new folder aptly named
rstudio-old. Then you can go into
rstudio-old under sources and find the files with s in front. These are all the files you had opened in Rstudio! So you can recover any unsaved work.
cd /.local/share # next line is only needed if rstudio-old already exists # sudo rm -rf rstudio-old sudo mv rstudio rstudio-old # Recover files from Home/.local/share/rstudio-old/sources/s-****
If you are not running Ubuntu the way to install V8 above may not work. You can try installing via the terminal:
sudo apt-get install libv8-dev
2 thoughts on “Setting Up Rstudio and Cmdstanr on AWS EC2”
You did all the work to do this yourself, but there’s actually an even easier way to do it. There’s a guy who maintains Rstudio AWS images and you can avoid all the manual setup: https://www.louisaslett.com/RStudio_AMI/
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That’s cool! This is at work so I have to use our own images and I wanted to share if anyone else needs to do it.
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