Instructor Notes
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Introduction
Instructor Note
The primary goal of this session is to present potential use cases for JUBE and enable participants to apply these insights to their own workflows on HPC systems.
Instructor Note
It is important for the learners to understand that JUBE itself does know what makes your workflow reproducible on its own. To create a reproducible workflow learners will have to identify which information and actions make the specific workflow reproducible, and use JUBE to automatically collect and execute those, respectively.
An example application
Instructor Note
We use GROMACS for this example, as it is a known code in the HPC community, it is readily available, and from installation to execution needs several steps in a workflow.
Working with JUBE
An initial workflow specification
Spanning parameter spaces
Using templates
Instructor Note
This episode introduces the simple text-based substitution system of JUBE to create text-based input files or batch scripts for submission to an HPC workload manager.
Instructor Note
We end this without an exercise, as the next episode will include the generation of batch scripts using the above steps.