GitHub - mlr-org/batchtools: Tools for computation on batch systems (original) (raw)

batchtools

Package website: release |dev

JOSS Publication r-cmd-check CRAN Status Mattermost

As a successor of the packagesBatchJobs andBatchExperiments, batchtools provides a parallel implementation of Map for high performance computing systems managed by schedulers like Slurm, Sun Grid Engine, OpenLava, TORQUE/OpenPBS, Load Sharing Facility (LSF) or Docker Swarm (see the setup section in thevignette).

Main features:

Installation

Install the stable version from CRAN:

install.packages("batchtools")

For the development version, usedevtools:

devtools::install_github("mlr-org/batchtools")

Next, you need to setup batchtools for your HPC (it will run sequentially otherwise). See thevignettefor instructions.

Why batchtools?

The development of BatchJobs andBatchExperiments is discontinued for the following reasons:

BatchJobs andBatchExperiments will remain on CRAN, but new features are unlikely to be ported back. Thevignettecontains a section comparing the packages.

Resources

Citation

Please cite the JOSS paper using the following BibTeX entry:

@article{,
  doi = {10.21105/joss.00135},
  url = {https://doi.org/10.21105/joss.00135},
  year  = {2017},
  month = {feb},
  publisher = {The Open Journal},
  volume = {2},
  number = {10},
  author = {Michel Lang and Bernd Bischl and Dirk Surmann},
  title = {batchtools: Tools for R to work on batch systems},
  journal = {The Journal of Open Source Software}
}

Contributing to batchtools

This R package is licensed under theLGPL-3. If you encounter problems using this software (lack of documentation, misleading or wrong documentation, unexpected behaviour, bugs, …) or just want to suggest features, please open an issue in the issue tracker. Pull requests are welcome and will be included at the discretion of the author. If you have customized a template file for your (larger) computing site, please share it: fork the repository, place your template in inst/templatesand send a pull request.