https://github.com/jemus42/batchtools_minimal

A minimal example of a batchtools setup for local usage
https://github.com/jemus42/batchtools_minimal

Last synced: 15 days ago
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A minimal example of a batchtools setup for local usage

• Host: GitHub
• URL: https://github.com/jemus42/batchtools_minimal
• Owner: jemus42
• Created: 2022-10-06T12:43:21.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2023-10-18T06:24:14.000Z (about 1 year ago)
• Last Synced: 2024-10-11T18:18:32.875Z (about 1 month ago)
• Language: R
• Size: 26.4 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# batchtools_minimal

A minimal example of a [`batchtools`](https://mllg.github.io/batchtools/articles/batchtools.html) setup for local usage.

This is a demonstration project to help people get started with a simple `batchtools` setup that does not rely on

any HPC infrastructure and just runs jobs on your local machine, but in a more structured way that via e.g. `doParallel` and friends.

Please only use this is a point of entry or for quick experimentation, I don't want to be responsible for your burning hardware.

## Setup Notes

- Only required dependencies here are `batchtools`, `ranger` and `ggplot2`: `install.packages(c("batchtools", "ggplot2", "ranger"))`

- `batchtools.conf.R` sets up parallelization for this project only, overriding other config files you might have.

  **Adjust `ncpus` and `max.load` there according to your hardware capabilities!**

## Workflow

- Write your simulation function in `problems.R`.

- Write/wrap your algorithm to be applied on the data in `algorithms.R`.

- Think.

- Adjust `run-experiments.R` for your problems/algorithms/parameter settings

- Run `run-experiments.R`, wait a while. This will block the R session, so beware!

- Hope.

- Optionally run `monitor-running.R` to check on finished/expired jobs.

- Retrieve and analyze your results in `analyze-results.R`.

- Appreciate.