Introduction & Computing Resources

# Introduction & Computing Resources
## 2020 DSS Bootcamp
### Colin Rundel
### 08-02-21

---

## Welcome

Welcome to the Department of Statistical Science (DSS). The following slides,
slide decks, and exampls will serve to

- give you an understanding of the computing resources available to you within 
  the DSS and Duke University;
  
- inform you on the best way to get help with your computing needs within the 
  DSS and Duke University;
  
- introduce you to R, Python, and version control with Git/GitHub;

- highlight the importance of reproducible research and how the aforementioned
  software can help.

---

# Duke Computing Resources

---

## Duke NetID

Your Duke NetID is the electronic key to making many Duke resources work.  
Make sure your Duke Account has been setup.

All of the following can be accomplished at 
https://idms-web.oit.duke.edu/portal/:

- Changing your password
  
  - Changing your challenge questions
  
  - Setup multi-factor authentication (Duo recommended)

---

## Duke email

With your NetID and password, you can access your email on the web at
http://mail.duke.edu

**Your Duke email is not permanent; your account expires once you leave Duke.**

---

## Duke WiFi

Duke network connections:

- Dukeblue:

- 24-hour access to secure (encrypted) wireless throughout Duke's 
      residence halls, academic and administrative buildings

- DukeOpen:

- unencrypted wireless access for devices such as gaming systems, or 
      other devices

- Eduroam (education roaming):

- secure (encrypted) wireless access using your Duke NetID and password
    
    - To use eduroam at a participating institution, configure 
      your machine ahead of time while at Duke - 
      https://dukeblue.duke.edu/eduroam/.
      
---

## Duke VPN

- Duke's virtual private network (VPN) allows you to create a secure connection 
  from your computer to Duke over a public network while working remotely. This
  will be necessary for you to use, if you want to access certain Duke and DSS
  resources off campus.

<br/>

- Instructions to get started with the VPN are available on the next slide.
  For more information on Duke's VPN visit
  https://oit.duke.edu/what-we-do/services/vpn.

---

## Duke VPN set-up

1. Download and install the free Cisco AnyConnect VPN 
   [software](https://software.duke.edu)

2. Launch Cisco AnyConnect on your machine and enter `vpn.duke.edu` in the box.
   Click `Connect`.<br/>
   <center>
   <img src="images/cisco_launch.png" height=150, width=300>
   </center>
   
3. Another dialog box will appear. Choose `INTL-DUKE` from the dropdown menu
   for `GROUP`, and enter your Duke NetID and password. Click `OK` and you 
   should connect.
   <br/>
   <center>
   <img src="images/cisco_group.png" height=150, width=300>
   </center>
   
---

## Software Site Licenses

- Duke offers software for download to students, faculty, and staff through 
  https://software.duke.edu/

- Duke negotiates with vendors to make software available to the Duke community 
  for discounted rates or, in many cases, for free. If you have any questions, 
  comments or suggestions, please e-mail the site-license office at 
  [site@duke.edu](mailto:site@duke.edu).

- Some free software relevant to you as students:

- Cisco VPN Client
  - Microsoft Office
  - MATLAB & Simulink
  - SAS Education Analytical Suite
  - Mathematica
  - Tableau
  - Adobe Creative Cloud
  
---

## Virtual computing

Duke OIT offers virtual software containers and semester-long virtual machines.

- [Virtual Software Containers](https://vm-manage.oit.duke.edu/containers) – 
  Students and instructors can reserve personal computer environments running 
  applications such as RStudio, the Eclipse IDE, Jupyter Notebooks, Matlab, 
  Octave, Mathematica, and others for a semester. These are run through your
  web browser; no software download is required. Two containers you will find
  most useful are:
    
    - `RStudio - statistics application with Rmarkdown and knitr support`
    - `Jupyter - interactive data science and scientific computing notebooks`

- [Virtual Machine (VM)](https://vcm.duke.edu/) – Your Duke VM is like having a 
  second computer that lives at Duke. You can log into and use your VM 
  from your own machine. It allows you to access specialized software without 
  installing it on your own computer, host your own server for development 
  projects and coursework, or customize your own environment to use for the 
  semester.
  
    - Run Windows or Linux VMs
    - Computing resources are light: 2 processors and 2GB of memory
    
---

## Duke Compute Cluster

The Duke Compute Cluster (DCC) consists of machines that the University has 
provided for community use and that researchers have purchased to conduct their 
research. You will need to be granted access before use.

- Runs on Linux - Red Hat Enterprise Linux 7

- Offers over 200 compute nodes and over 20,000 cores

- Most nodes are purchased by labs and departments. The DSS has three nodes.

- Uses the SLURM job management system

- Requires sponsorship by a faculty member to use

The [DCC User Guide](https://rc.duke.edu/dcc/dcc-user-guide/) will help you
get up and running. They also host workshops to help new users.

---

## Getting help with Duke resources

Duke Office of Information Technology (OIT) manages Duke’s technology 
infrastructure and application support.
    
- https://oit.duke.edu/help

- Live chat, 24 hours a day, Monday - Thursday; chat is available on a limited
  basis Fridays and Sundays

- Walk up hours are available at the [Link](https://link.duke.edu/about-link) in 
  [Perkins Library](http://www.google.com/maps?q=William+R.+Perkins+Library,+Durham,+NC&hl=en&sll=36.001827,-78.884911&sspn=0.486055,0.681839&oq=perkins+&hq=William+R.+Perkins+Library,+Durham,+NC&t=m&z=15).
  
- Live service status dashboard available at https://status.oit.duke.edu/

---

# DSS Computing Resources

---

## RStudio Workbench

The DSS has an RStudio Workbench (formerly Pro) license that will allow you to connect to an instance of RStudio (and Jupyter) in your browser while harnessing the computing power of a remote multiprocessor server.

To access RStudio Pro:

1. If off campus, use the VPN to create a secure connection from your computer 
   to Duke. If you are on campus, be sure you are connected to the Dukeblue
   network.

2. Navigate to:

- http://rstudio.stat.duke.edu:8787

3. Log-in with your NetID and password.

---

## Other resources

- Local file system on DSS servers

- Connect via SSH to 
      - rstudio.stat.duke.edu
      - pawn.stat.duke.edu
      - rook.stat.duke.edu
      - knight.stat.duke.edu
    
- RStudio Connect

- a publishing platform for the work you do in R and Python 
  
  - share Shiny applications, R Markdown reports, Plumber APIs, dashboards, 
    Jupyter Notebooks, interactive Python content, and more
    
  - if you need access, ask and we can help get you set-up

- Email aliases: https://stat.duke.edu/resources/email/aliases
  
- Departmental IT resources page is coming soon

---

## Getting help with DSS resources

The best way to get help with DSS computing resources is to email 
[stat-help@duke.edu](mailto:stat-help@duke.edu). One of our great IT staff
members will get back with you ASAP.
  
[Zoyia Melton](https://stat.duke.edu/people/zoyia-melton) - Senior IT Analyst

- Phone: 919-684-5419
  - Location: 027 Old Chemistry

[Frisco Rose](https://stat.duke.edu/people/francis-rose-0) - Assistant Research 
Professor in the Department of Mechanical Engineering and Materials Science

- Phone: 919-660-5496
  - Location: 026 Old Chem