1. 1 Applied CyberInfrastructure Concepts ISTA 420/520 Fall 2013 1 Nirav Merchant (nirav@email.arizona.edu) Bio Computing & iPlant Collaborative Eric Lyons (ericlyons@email.arizona.edu) Plant Sciences & iPlant Collaborative University of Arizona http://goo.gl/p4j3mhttp://goo.gl/p4j3m or https://sites.google.com/site/appliedciconcepts/ Will Computers Crash Genomics? Science Vol 331 Feb 2011

2. Tasks for today  Lets get the ssh shenanigans under control  Homework for next week  Docker concept (slides from lecture 4)  Discuss components for Docker  Tour of Docker resources/documentation  Prepare for hands on Docker session (Thu)  Get ready for UA HPC and Futuregrid account applications/access

3. SSSH keys  Public and Private  Where do you keep the authorized_keys  What is the permission on the folder and keys ?  What about the “pass phrase” and when to use it  How to transfer your keys to a new machine – Simple sftp method

4. Homework Due Sept 22  http://blog.comsysto.com/2013/04/25/data- analysis-with-the-unix-shell/ http://blog.comsysto.com/2013/04/25/data- analysis-with-the-unix-shell/  How are you going to get the data from git ?  What is missing in this data set ? (how to fix ?)  Do you have access to gnuplot ?  Make a plot described in this exercise – Save the plot as pdf output (attach it for homework) – How are you going to view the pdf – Run this without interactive prompts i.e straight from command line

5. Homework (continued) csvkit Install the csvkit (follow instructions) – http://csvkit.readthedocs.org/ http://csvkit.readthedocs.org/ – Download the sample data set from city country – Install pip and then install csvkit – Explore the multiple commands – Post screen shot output from 3 csvkit commands with this data set – How would you add suitable csv header to the 2 csv file (think echo, cat)

6. Intro to Docker See Docker slides

7. Virtual Machine V/s Docker https://www.docker.com/whatisdocker/

8. What do we get with Docker ?  An easy and lightweight way to create dedicated containers  Consistent environment (regardless of host OS)  Quick development cycle (add things to bare OS via simple file)  Encourages service oriented architecture (SOA) and allows you to create “microservices” that can be stitched together http://martinfowler.com/articles/microservices. html

9. So what do I get with Docker ?  Docker server/daemon  Docker Images (and Docker File)  Registries  Containers  Command line tools for management  REST API for management (and automation)  Git philosophy and Docker images

10. Understanding how the pieces work Your Virtual Box/Ubuntu Docker Registry (public or private) Run docker.io daemon Gets and pushes images Maintains local Cache Container CentOS Container CentOS Containers CentOS+GN Uplot Containers CentOS+GN Uplot Containers CoreOS You run copies of images from the local cache which become “containers” when they “run”

11. Lets visit Docker Website  Installation  Documentation  Repository  Some interesting science projects http://nucleotid.es/ http://ferry.opencore.io/en/latest/ http://nucleotid.es/ http://ferry.opencore.io/en/latest/

12. Connecting the dots  Dockerizing your applications.  Run your own containers.  Build Docker images.  Share your Docker images with others.

13. Accounts to be had  iPlant  Github (link it with docker registry)  UA HPC https://account.arizona.edu/welcome https://account.arizona.edu/welcome  Chameleon https://chameleoncloud.org/user/register/ https://chameleoncloud.org/user/register/