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DAPT: A package enabling distributed automated parameter testing
Modern agent-based models (ABM) and other simulation models require evaluation and testing of many different parameters. Managing that testing for large scale parameter sweeps (grid searches), as well as storing simulation data, requires multiple, potentially customizable steps that may vary across...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
GigaScience Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9631979/ https://www.ncbi.nlm.nih.gov/pubmed/36824329 http://dx.doi.org/10.46471/gigabyte.22 |
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author | Duggan, Ben Metzcar, John Macklin, Paul |
author_facet | Duggan, Ben Metzcar, John Macklin, Paul |
author_sort | Duggan, Ben |
collection | PubMed |
description | Modern agent-based models (ABM) and other simulation models require evaluation and testing of many different parameters. Managing that testing for large scale parameter sweeps (grid searches), as well as storing simulation data, requires multiple, potentially customizable steps that may vary across simulations. Furthermore, parameter testing, processing, and analysis are slowed if simulation and processing jobs cannot be shared across teammates or computational resources. While high-performance computing (HPC) has become increasingly available, models can often be tested faster with the use of multiple computers and HPC resources. To address these issues, we created the Distributed Automated Parameter Testing (DAPT) Python package. By hosting parameters in an online (and often free) “database”, multiple individuals can run parameter sets simultaneously in a distributed fashion, enabling ad hoc crowdsourcing of computational power. Combining this with a flexible, scriptable tool set, teams can evaluate models and assess their underlying hypotheses quickly. Here, we describe DAPT and provide an example demonstrating its use. |
format | Online Article Text |
id | pubmed-9631979 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | GigaScience Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-96319792023-02-22 DAPT: A package enabling distributed automated parameter testing Duggan, Ben Metzcar, John Macklin, Paul GigaByte Technical Release Modern agent-based models (ABM) and other simulation models require evaluation and testing of many different parameters. Managing that testing for large scale parameter sweeps (grid searches), as well as storing simulation data, requires multiple, potentially customizable steps that may vary across simulations. Furthermore, parameter testing, processing, and analysis are slowed if simulation and processing jobs cannot be shared across teammates or computational resources. While high-performance computing (HPC) has become increasingly available, models can often be tested faster with the use of multiple computers and HPC resources. To address these issues, we created the Distributed Automated Parameter Testing (DAPT) Python package. By hosting parameters in an online (and often free) “database”, multiple individuals can run parameter sets simultaneously in a distributed fashion, enabling ad hoc crowdsourcing of computational power. Combining this with a flexible, scriptable tool set, teams can evaluate models and assess their underlying hypotheses quickly. Here, we describe DAPT and provide an example demonstrating its use. GigaScience Press 2021-06-04 /pmc/articles/PMC9631979/ /pubmed/36824329 http://dx.doi.org/10.46471/gigabyte.22 Text en © The Author(s) 2021. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Technical Release Duggan, Ben Metzcar, John Macklin, Paul DAPT: A package enabling distributed automated parameter testing |
title | DAPT: A package enabling distributed automated parameter testing |
title_full | DAPT: A package enabling distributed automated parameter testing |
title_fullStr | DAPT: A package enabling distributed automated parameter testing |
title_full_unstemmed | DAPT: A package enabling distributed automated parameter testing |
title_short | DAPT: A package enabling distributed automated parameter testing |
title_sort | dapt: a package enabling distributed automated parameter testing |
topic | Technical Release |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9631979/ https://www.ncbi.nlm.nih.gov/pubmed/36824329 http://dx.doi.org/10.46471/gigabyte.22 |
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