2022 DSS Bootcamp
Colin Rundel
08-25-22
Welcome to the Department of Statistical Science (DSS). The following slides, slide decks, and examples 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.
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 idms-web.oit.duke.edu/portal/:
Changing your password
Changing your challenge questions
Setup multi-factor authentication (Duo recommended)
Change email alias(es)
ssh keys + default shell
With your NetID and password, you can access your email on the web at mail.duke.edu
Your Duke email is not permanent; your account expires once you leave Duke.
Mail forwarding is possible but not recommended
Duke network connections:
Dukeblue:
DukeOpen:
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’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.
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.
Download and install the free Cisco AnyConnect VPN software
Launch Cisco AnyConnect on your machine
Enter vpn.duke.edu
in the box and click Connect
.
Another dialog box will appear. Choose -Default-
from the Group dropdown menu
Enter your Duke NetID and password and click OK
.
Follow the steps to complete MFA.
Duke offers software for download to students, faculty, and staff through 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.
Some free software relevant to you as students:
Duke OIT offers virtual software containers and semester-long virtual machines.
Virtual Software Containers – Students and instructors can reserve personal computer environments running applications such as RStudio, Eclipse, Jupyter Notebooks, Matlab, and others for a semester. These are run through your web browser; no software download is required.
Two containers liekly to be most useful are:
RStudio
- statistics application with Rmarkdown and knitr supportJupyter
- interactive data science and scientific computing notebooksVirtual Machine (VM) – 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.
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 given access before use.
Runs Linux (CentOS 8) and uses the SLURM job management system
Offers over 1300 nodes with more than 30,000 cores, 750 GPUs, 200 TBs of RAM and 7 PB file system.
Most nodes are purchased by labs and departments. The DSS has three nodes (more soon).
OnDemand for interactive use
Requires sponsorship by a faculty member to use
The DCC User Guide will help you get up and running. They also host workshops to help new users.
Duke Office of Information Technology (OIT) manages Duke’s technology infrastructure and application support.
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 in Perkins Library.
Live service status dashboard available at status.oit.duke.edu or @DukeOIT
The DSS has an RStudio Workbench (formerly Pro) license that will allow you to connect to an instance of RStudio (or Jupyter Lab or VS Code) in your browser while making use of the computing power of a remote multiprocessor server.
To access RStudio Pro:
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.
Navigate to: http://rstudio.stat.duke.edu:8787
Log-in with your NetID and password.
Local file system on DSS servers
Connect via SSH to
RStudio Connect
Email aliases - stat.duke.edu/resources/email/aliases
Departmental IT resources - stat.duke.edu/it-support
Departmental Wiki - wiki.stat.duke.edu
The best way to get help with DSS computing resources is to email stat-help@duke.edu. One of our great IT staff members will get back with you ASAP.
Zoyia Melton - Senior IT Analyst
Science Drive - Academic Technology Support
If you are having trouble getting support contact the department’s computing committee stat-cc@duke.edu.