12 December 2024
ZOOM
Europe/Ljubljana timezone

Excerpt: We will learn the basics of SnakeMake, how to translate a basic workflow, which is partly trivially parallelizable and in parts not, into SnakeMake, and how to utilize HPC resources in conjunction with SnakeMake. We will take a look at a generic workflow, consisting of a set of tasks, with varying interdependencies; we will learn how to identify these interdependencies between our tasks and how to design a workflow diagram around them. 

Description: We will learn the basics of SnakeMake, which is an open-source tool that allows users to describe complex workflows with a hybrid of Python and shell scripting. By transferring our workflow diagram into a SnakeMake we will learn how to automate our workflow. Initial development of our workflow in SnakeMake will be in a terminal setup, as we do generically in our day-to-day lives, however we will then learn how to scale up and perform these tasks on a local supercomputing cluster.

Difficulty: Basic

Language: English

Prerequisite knowledge: Basic knowledge of Linux, the Terminal and Python

Target audience: The workshop is intended for beginners and more experienced people interested in optimizing and automating their workflows and ultimately transferring them to High-Performance Computing machines.

Skills to be gained:

  • Workflow design, identification of interdependencies
  • Basics of SnakeMake
  • Transfering a generic workflow into SnakeMake
  • Testing our SnakeMake in an interactive environment, and upscaling it for use on a supercomputing cluster

 

Workflow: The training is live, in the afternoon. Part of the training will be in the form of a lecture and part will be a practical session, where we will make use of the NSC Cluster at the Jožef Stefan Institute (as an educational member of SLING).

Virtual location: ZOOM (only registered participants will see ZOOM link)

Organizer:

Univerza v Ljubljani v leto 2024 ...

Lecturer:

Name:Luka Leskovec
Description:Scientist and educationalist involved in theoretical physics and supercomputing
E-mail:luka.leskovec@fmf.uni-lj.si

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Europe/Ljubljana
ZOOM
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