Skip to main content

Set up R/Stan on Amazon EC2

A few months ago I posted the script that I use to set up my R/JAGS working environment on an Amazon EC2 instance.

Since then I've largely transitioned to using R/Stan to estimate my models. So, I've updated my setup script (see below).

There are a few other changes:

  • I don't install/use RStudio on Amazon EC2. Instead, I just use R from the terminal. Don't get me wrong, I love RStudio. But since what I'm doing on EC2 is just running simulations (I handle the results on my local machine), RStudio is overkill.

  • I don't install git anymore. Instead I use source_url (from devtools) and source_data (from repmis) to source scripts from GitHub. Again all of the manipulation I'm doing to these scripts is on my local machine.

########################################################
# Set up RStudio and JAGS on an Amazon EC2 instance
# Using Ubuntu 64-bit
# Christopher Gandrud
# 16 December 2014
# Partially from http://blog.yhathq.com/posts/r-in-the-cloud-part-1.html
# See yhat for EC2 instance set up
########################################################
# In your terminal navigate to key pair
# ssh -i YOUR_KEYPAIR.pem ubuntu@PUBLIC_DNS
# Get all programs up to date
sudo apt-get update
# Install latest g++ and clang
sudo apt-get install gcc
sudo apt-get install clang
# Install prerequisites for RCurl
sudo apt-get install libcurl4-openssl-dev
# Check that you have the latest R installed
## see also: http://askubuntu.com/a/352438
sudo apt-get update
apt-cache showpkg r-base
# If R is not the latest version add latest PACKAGE_VERSION returned
# from the pervious line to:
sudo apt-get install -f r-base=PACKAGE_VERSION
# Install rJava
apt-get install r-cran-rjava
# Install Stan and rstan
# First find the number of cores
lscpu
# Load r, set cores, and install
R
Sys.setenv(MAKEFLAGS = "-j4")
source('http://mc-stan.org/rstan/install.R', echo = TRUE,
max.deparse.length = 2000)
install_rstan()
# Install other packages I often use
## Dependencies include reshape2, dplyr
pkgs <- c('repmis', 'DataCombine', 'devtools')
install.packages(pkgs)
q()
######## Running Scripts and Downloading Results onto Local ####
# Run a script so that it runs even if the terminal hands up
# sudo nohup Rscript R_SCRIPT_PATH
# Download a file from Amazon EC2 to your local machine
# (current working directory)
# scp -i YOUR_KEYPAIR.pem ubuntu@PUBLIC_DNS:EC2_FILE_PATH .
view raw r_stan_setup.sh hosted with ❤ by GitHub

Labels

Labels:

Comments

likitha said…
Thank you for your guide to with upgrade information about AWS keep update at
AWS Online Course
12:11
Online Training said…
Very informative blog and useful article thank you for sharing with us , keep posting learn more about aws with cloud computing

AWS Training

AWS Online Training
06:44
chinni said…
Data scientists are in demand because the old employees are not as skilled in using new tools to handle big data.
data science course in gurgaon

06:43
Post a Comment

Popular posts from this blog

Dropbox & R Data

I'm always looking for ways to download data from the internet into R. Though I prefer to host and access plain-text data sets (CSV is my personal favourite) from GitHub (see my short paper on the topic) sometimes it's convenient to get data stored on Dropbox . There has been a change in the way Dropbox URLs work and I just added some functionality to the repmis R package. So I though that I'ld write a quick post on how to directly download data from Dropbox into R. The download method is different depending on whether or not your plain-text data is in a Dropbox Public folder or not. Dropbox Public Folder Dropbox is trying to do away with its public folders. New users need to actively create a Public folder. Regardless, sometimes you may want to download data from one. It used to be that files in Public folders were accessible through non-secure (http) URLs. It's easy to download these into R, just use the read.table command, where the URL is the file name...
54 comments
Read more

Slide: one function for lag/lead variables in data frames, including time-series cross-sectional data

I often want to quickly create a lag or lead variable in an R data frame. Sometimes I also want to create the lag or lead variable for different groups in a data frame, for example, if I want to lag GDP for each country in a data frame. I've found the various R methods for doing this hard to remember and usually need to look at old blog posts . Any time we find ourselves using the same series of codes over and over, it's probably time to put them into a function. So, I added a new command– slide –to the DataCombine R package (v0.1.5). Building on the shift function TszKin Julian posted on his blog , slide allows you to slide a variable up by any time unit to create a lead or down to create a lag. It returns the lag/lead variable to a new column in your data frame. It works with both data that has one observed unit and with time-series cross-sectional data. Note: your data needs to be in ascending time order with equally spaced time increments. For example 199...
46 comments
Read more

A Link Between topicmodels LDA and LDAvis

Carson Sievert and Kenny Shirley have put together the really nice LDAvis R package. It provides a Shiny-based interactive interface for exploring the output from Latent Dirichlet Allocation topic models. If you've never used it, I highly recommend checking out their XKCD example (this paper also has some nice background). LDAvis doesn't fit topic models, it just visualises the output. As such it is agnostic about what package you use to fit your LDA topic model. They have a useful example of how to use output from the lda package. I wanted to use LDAvis with output from the topicmodels package. It works really nicely with texts preprocessed using the tm package. The trick is extracting the information LDAvis requires from the model and placing it into a specifically structured JSON formatted object. To make the conversion from topicmodels output to LDAvis JSON input easier, I created a linking function called topicmodels_json_ldavis . The full function is below. To...
23 comments
Read more