Summary and Schedule
This is a new lesson built with The Carpentries Workbench.
Setup Instructions | Download files required for the lesson | |
Duration: 00h 00m | 1. Running a Parallel Application on the Cluster |
What output does the Amdahl code generate? Why does parallelizing the amdahl code make it faster? |
Duration: 00h 12m | 2. Introduction to Snakemake |
What are Snakemake rules? Why do Snakemake rules not always run? |
Duration: 00h 24m | 3. More Complicated Snakefiles |
What is a task graph? How does the Snakemake file express a task graph? |
Duration: 00h 36m | 4. Snakemake and the Cluster | How can we express a one-task cluster operation in Snakemake? |
Duration: 00h 48m | 5. Snakemake Profiles |
How can we encapsulate our desired snakemake configuration? How do we balance non-reptition and customizability? |
Duration: 01h 00m | 6. Amdahl Parallel Runs | How can we collect data on Amdahl run times? |
Duration: 01h 12m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
FIXME: Setup instructions live in this document. Please specify the tools and the data sets the Learner needs to have installed.
Data Sets
Download the data zip file and unzip it to your Desktop
Software Setup
Details
Setup for different systems can be presented in dropdown menus via a
solution
tag. They will join to this discussion block, so
you can give a general overview of the software used in this lesson here
and fill out the individual operating systems (and potentially add more,
e.g. online setup) in the solutions blocks.
Use PuTTY
Use Terminal.app
Use Terminal