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batchtools

JOSS Publicatoin CRAN Status Badge

As a successor of the packages BatchJobs and BatchExperiments, 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 the vignette).

Main features:

Installation

Install the stable version from CRAN:

install.packages("batchtools")

For the development version, use devtools:

devtools::install_github("mllg/batchtools")

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

Why batchtools?

The development of BatchJobs and BatchExperiments is discontinued for the following reasons:

BatchJobs and BatchExperiments will remain on CRAN, but new features are unlikely to be ported back. The vignette contains 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}
}

Related Software

Contributing to batchtools

This R package is licensed under the LGPL-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/templates and send a pull request.