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L:  Lecture

CA: Class Activity/Active Learning

DateLecture #TopicLearning OutcomesHomeworkSlides / ActivityAdditional Notes
8/27/20191(L) Intro to Course

Course introduction an dorientation

Importance of Cyberinfrastructure and Data Science

Homework 1- Intro and Data ScientistsLecture 1 Google Slides 
8/29/20192(CA) Working as a Team

Strengths and weaknesses of teams

Problems and solutions to common team problems

Homework 2 - Good enough practices

Team presentations

Discussion on teams

Teams give presentations on data scientists. Discussion on teams.
9/2/2019
Software Carpentry
Bootcamp for anyone in command line and intro programmingLinux Command Line and Shell workshop  Optional for those wanting training/practice at the command line
9/3/20193(L) Good enough practices for data scienceData Science is a Team Activity
How to take care of code, project planning, etc.
Homework 3 - Best practicesLecture 3 Google Slides 
9/5/20194(CA) Take a big project and breaking it down

Overall project plan (and what it takes to plan a project)

Organization: Project Planning, Documentation, GitHub

Homework 3 - Best practicesLecture 4 Google Slides 
9/10/20195(L) Client Project: Wilson Leung (guest lecture)Mid-term project overviewHomework 4 - Client project setup

Slides (Wilson)

Lecture 5 Google Slides

 

Project Page for Midterm
9/12/20196(CA)

Overview of breakdown projects: what do you need to deliver? How do you ensure everyone is on the same page for requirements.

 How will you utilize the resources to which you have access

Homework 5 - Client project concept maps and preliminary planLecture 6 Google Slides 
9/17/20197(L) What is the cloud and virtualizationCloud howto, introduction to Atmosphere, Chameleon , Jetstream Lecture 7 Google Slides 
9/19/20198(L) What is the cloud and virtualization (part 2)Hands on cloud and mapping things needed for Wilsons projectHomework 6 - Cloud costsLecture 7 Google SlidesNote – had additional discussion from previous lecture.
9/24/20199(CA) Hands on with the cloud and virtual machinesGetting comfortable with CLI and managing VM/installing s/w . Introduction to ContainersHomework 7 - Launching and Logging into a VM and command line tools Lecture 8 Google SlidesDue in class
9/26/201910(L) What are containers and how they different than virtual machines

What is virtualization, and the difference between VMs and Containers.

Homework 8 - Install SequenceServer on a VMLecture 9 - Virtualization and containers 
10/1/201911(L/CA) Hands on with containers

Differences between VMs and Containers (part II).

  • Hand's on (if there is time):
    • How to run a container
    • Modify a container
    • Create a docker file
    • Redistribute containers
Work on midtermLecture 10 - Virtualization and Containers Part II 
10/3/201912

(CA) Hands on with containers

Backup: HPC Lecture

  • How to run a container

  • Modify a container

  • Create a docker file

  • Redistribute containers

Work on midtermLecture 11 - HPC TheoryAtmosphere may be down and interfere with in class Docker activities.
10/8/201913(CA) High performance computing

Intro to HPC and UA HPC

  • Logging into the system
  • How can I use the HPC?
  • Basics about the system and why it's good to know it
  • Useful commands on the HPC
  • How can I get help?
Work on midterm

Hands-on with containers

 

 
10/10/201914(CA) Hands on with HPC

How to log in and run applications on UA HPC

  • Docker -> Singularity
  • Using Singularity to access GPUs
Work on midtermUA HPC lecture: Blake Joyce 
10/15/201915(CA) Hands on with HPC/Singularity

Singularity is another container technology, but has additional security over Docker and user-level permissions (required for shared HPC resources)

Work on midtermHands-on 
10/17/201916(CA) Hands on with HPC and Benchmarking

Benchmarking is critical to scaling out analyses:

  • How long does an analysis take
  • What resources are required (CPUs, Memory, GPUs, etc.)
  • Where are there bottlenecks during scaling (e.g., multiple jobs reading/writing to a shared filesystem)
HPC homeworkSingularity and UA HPC Tutorial 
10/22/201917(L) Intro to workflow managers

What are workflow managers

Why are workflow managers needed

When to use a workflow manager

 

Homework - 9

Work on midterm

http://ccl.cse.nd.edu/software/tutorials/acic19/

Recorded lecture

 
10/24/201918(CA) Hands on with workflowshands on exercises, run workflows on HPC, cloud, etc

Workflow homework

Note: Bonus homework (use your new-found distributed computing skills)

http://ccl.cse.nd.edu/software/tutorials/acic19/

Recorded lecture

 
10/29/201919(L) Midterm updates and discussions

Midterm update

Theory to data management and data grids

Midterm progress reports

Work on midterm

Intro to data management theory

No slides 
10/31/201920(CA) Midterm presentationsHands-on with iRODS

Midterm progress reports

Hands-on with iRODS

CyVerse Data Store Quick Start Guide 
11/5/201921(CA)Midterm presentations    
11/7/201922(CA)Midterm presentations
    
11/12/201923(L)Final project/Special topics    
11/14/201924(CA)Final project/Special topics    
11/19/201925(L)Final project/Special topics    
11/21/201926(CA)Final project/Special topics    
11/26/201927(L)Final project/Special topics    
11/28/2019No Class     
12/3/201928(L)Final project/Special topics    
12/5/201929(CA)Final project/Special topics    
12/10/2019Last Class     
12/12/2019Reading Day     
12/17/2019
Scheduled Final
8-10 AM in ECE 107https://www.registrar.arizona.edu/courses/final-examination-schedule-fall-2019Final presentations, all term papers due  
12/19/2019All Work Due     

Syllabus-UA-format.docx

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