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Local Setup - Windows host.md

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Multi-node Multi-core R / Shiny

Instructions for a Local Setup: Windows host / Ubuntu guest

Test Hardware & Software

The following setup was used for testing purposes. Compare it with your setup and make adjustments as necessary.

Setup

Some of the instructions might be too detailed / obvious - feel free to create a setup that works best for you.

  1. On Virtual Box, create an Ubuntu 64 bit VM with:
  • 4GB memory
  • 2 vCPU
  • 10GB HDD (check SSD if needed)
  • CD linked to the downloaded ubuntu-14.04.2-server-amd64.iso image
  • Bridged networking with the correct network adapter (or Host-only networking, but not NAT).
    Note that you might have to re-select the network adapter if you switch between wired / wireless.
    Also, Bridge networking will expose your Ubuntu VM to the local network - depending on your environment, use it with care.
  • Disable audio (optional).
  1. Install Ubuntu Server with default settings
  • hostname: [your choice] something unique since many others will have the same setup
  • username: ubuntu (this is what Amazon EC2 uses)
  • password: [your choice]
  • do not encrypt your home directory (this is just a test machine)
  • partition: Guided - use entire disk (this is just a test machine)
  • select "install security updates automatically"
  • select [*] OpenSSH server
  • Install GRUB [Yes]

Let it reboot. Also, I did not install Virtual Box Guest Additions.

  1. We need to connect to Ubuntu using ssh. For this, we need to generate a key pair on Windows.
  • open puttygen.exe
  • press Generate
  • move the mouse
  • enter a Key comment
  • do not enter a Key passphrase
  • save the private key as a .ppk file
  • leave the puttygen.exe window open
  1. Find Ubuntu's local IP address
  • login in the Virtual Box console and type
$ ifconfig
  • note the IP address for eht0 (maybe something like 192.168.x.x)

Use this step later on if you need to find the IP after you restart Virtual Box.
Host names should work too, but IP addresses work with certainty.

  1. Connect with PuTTY and create the authorized_keys file
  • open PuTTY
  • create a connection to Ubuntu IP address
  • create authorized_keys file and open it using
$ mkdir ~/.ssh
$ chmod 700 ~/.ssh
$ vi ~/.ssh/authorized_keys
  • on Windows, from the puttygen.exe window (top box), copy (Ctrl-V) the Public Key
  • go back to the PuTTY window where vi is open
  • switch to insert mode (command i)
  • paste (Shift-Insert) the key into vi
  • save and close vi using the command sequence ESC, :w and :q
  • change the permissions on authorized_keys to read + write by owner only
$ chmod 600 ~/.ssh/authorized_keys
$ exit
  • close puttygen.exe
  • Restart PuTTY
    • enter Ubuntu IP address
    • go to Connection > SSH > Auth > Private key file ...
    • browse and select the saved .ppk file
    • save session settings (optional)
  • test the connection

From now on, we will not be using the password to make a connection to the Ubuntu VM.

  1. Install Ubuntu updates and R
  • run basic updates:
$ sudo apt-get update
$ sudo apt-get upgrade
$ sudo apt-get dist-upgrade
  • add CRAN repository to get the latest R version
$ sudo vi /etc/apt/sources.list
  • add the following line at the end (use command i)
deb http://cran.rstudio.com/bin/linux/ubuntu trusty/

  • save and close vi using the command sequence ESC, :w and :q

  • install R and reboot

$ sudo apt-get update
$ sudo apt-get install r-base
$ sudo reboot

After apt-get update, you should see a message saying that public key is not available. It's safe to ignore it.
Answer yes (Y/y) when installing r-base.

  • re-login with PuTTY and test R
$ R
> library(parallel)
> detectCores()
[1] 2
> q()

If successful, you have completed the steps needed for the local setup on a Windows host.