feat: parallel execution chapter #173

cmeesters · 2024-11-22T09:24:48Z

addresses issues #168 and #163

Summary by CodeRabbit

Configuration Updates
- Updated course date in configuration file from September 2024 to January 2025
New Scripts
- Added copy_script_mogonNHR.sh for cluster setup
- Added install_conda.sh for Conda installation
New Workflow Examples
- Added MPI example with Snakefile and C implementation for π calculation
Documentation
- Expanded slides on parallel computing and Snakemake execution strategies

coderabbitai · 2024-11-22T09:24:56Z

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Review failed

The pull request is closed.

📝 Walkthrough

Walkthrough

This pull request encompasses multiple changes across different files and scripts. The primary modifications include updating the course date in a configuration file, enhancing the rendering function for table of contents, adding new setup scripts for cluster and conda installation, introducing a new MPI example for calculating pi, and expanding LaTeX slides with content on parallel computing. The changes appear to be part of a broader effort to update tutorial materials and computational workflow scripts.

Changes

File	Change Summary
`config/config_Mainz_NHR.yaml`	Updated course date from "23.-27. September 2024" to "29.-30. January 2025"
`render`	Modified `find_and_replace_sections` function: - Changed `min` to `max` for upper boundary calculation - Updated error handling with more specific logging
`setup_creators/copy_script_mogonNHR.sh`	New script for setting up tutorial workflow on Mogon II cluster
`setup_creators/install_conda.sh`	New script to download and install Miniforge from conda-forge
`setup_creators/solutions/mpi_example/Snakefile`	Added Snakefile with rules for compiling and calculating pi using MPI
`setup_creators/solutions/mpi_example/pi_MPI.c`	New MPI implementation for calculating pi using Monte Carlo method
`slides/Snakemake_HPC_User_Creator_Combi.tex`	Added commented-out background package configuration
`slides/creators/Parallel_Execution.tex`	Added new section on parallel computing and Snakemake

Sequence Diagram

sequenceDiagram
    participant User
    participant Cluster
    participant MPI Program
    
    User->>Cluster: Upload tutorial files
    User->>Cluster: Run installation script
    Cluster->>Cluster: Install Miniforge/Conda
    User->>Cluster: Compile MPI Program
    Cluster->>MPI Program: Compile pi_MPI.c
    User->>Cluster: Execute MPI Program
    Cluster->>MPI Program: Calculate Pi
    MPI Program-->>Cluster: Return Pi Calculation

Possibly related PRs

feat: central software path #138: Modifies the date field in the same configuration file
feat: mogon ondemand #142: Updates the date field in the configuration file
feat: optional question time encouragement #171: Adds a question field to the configuration file

Suggested reviewers

brand-fabian

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 073eb60 and a02bc62.

⛔ Files ignored due to path filters (1)

images/humor/DALLE_runners.jpg is excluded by !**/*.jpg

📒 Files selected for processing (8)

config/config_Mainz_NHR.yaml (1 hunks)
render (1 hunks)
setup_creators/copy_script_mogonNHR.sh (1 hunks)
setup_creators/install_conda.sh (1 hunks)
setup_creators/solutions/mpi_example/Snakefile (1 hunks)
setup_creators/solutions/mpi_example/pi_MPI.c (1 hunks)
slides/Snakemake_HPC_User_Creator_Combi.tex (1 hunks)
slides/creators/Parallel_Execution.tex (1 hunks)

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…ble it automatically when rendering a handout version

github-actions · 2025-01-28T16:15:15Z

Artifacts

Slides

…iniconda due to libmamba in conda

…clusters

feat: first two dummy slides to start the chapter

76cf9de

cmeesters added 5 commits January 28, 2025 13:37

fix: merge conflict

4b36870

fix: updated date

3d5a5b6

feat: added option to create Handout background. Would be nice to ena…

836902c

…ble it automatically when rendering a handout version

fix: boundary fix for the n-th time - peril of mergers

964750c

feat: introducing threading

028d09b

cmeesters added 11 commits January 28, 2025 17:48

feat: update to copy script

56fdd44

feat: immediate install of conda, without reliance on micromamba or m…

ef5c2d7

…iniconda due to libmamba in conda

feat: added mpi example code

de7c827

feat: added 2nd version of copy script

bee7ba5

fix: merge conflict

53678c0

feat: added example Snakefile for MPI runs

569197e

fix: removed mpi example copy

52993f5

fix: mpi example under solutions

2c548b1

feat: finished MPI example setup - need generalization for different …

2bd909c

…clusters

feat: added MPI intro

2432c31

fix: syntax

a02bc62

cmeesters marked this pull request as ready for review January 28, 2025 21:51

cmeesters merged commit 7d4fccc into main Jan 28, 2025
5 of 6 checks passed

cmeesters deleted the feat/parallel_execution branch January 28, 2025 21:51

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feat: parallel execution chapter #173

feat: parallel execution chapter #173

cmeesters commented Nov 22, 2024 •

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feat: parallel execution chapter #173

feat: parallel execution chapter #173

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