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Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG
MOTIVATION: Phylogenetic trees are now routinely inferred on large scale high performance computing systems with thousands of cores as the parallel scalability of phylogenetic inference tools has improved over the past years to cope with the molecular data avalanche. Thus, the parallel fault toleran...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9502163/ https://www.ncbi.nlm.nih.gov/pubmed/34037680 http://dx.doi.org/10.1093/bioinformatics/btab399 |
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author | Hübner, Lukas Kozlov, Alexey M Hespe, Demian Sanders, Peter Stamatakis, Alexandros |
author_facet | Hübner, Lukas Kozlov, Alexey M Hespe, Demian Sanders, Peter Stamatakis, Alexandros |
author_sort | Hübner, Lukas |
collection | PubMed |
description | MOTIVATION: Phylogenetic trees are now routinely inferred on large scale high performance computing systems with thousands of cores as the parallel scalability of phylogenetic inference tools has improved over the past years to cope with the molecular data avalanche. Thus, the parallel fault tolerance of phylogenetic inference tools has become a relevant challenge. To this end, we explore parallel fault tolerance mechanisms and algorithms, the software modifications required and the performance penalties induced via enabling parallel fault tolerance by example of RAxML-NG, the successor of the widely used RAxML tool for maximum likelihood-based phylogenetic tree inference. RESULTS: We find that the slowdown induced by the necessary additional recovery mechanisms in RAxML-NG is on average 1.00 ± 0.04. The overall slowdown by using these recovery mechanisms in conjunction with a fault-tolerant Message Passing Interface implementation amounts to on average 1.7 ± 0.6 for large empirical datasets. Via failure simulations, we show that RAxML-NG can successfully recover from multiple simultaneous failures, subsequent failures, failures during recovery and failures during checkpointing. Recoveries are automatic and transparent to the user. AVAILABILITY AND IMPLEMENTATION: The modified fault-tolerant RAxML-NG code is available under GNU GPL at https://github.com/lukashuebner/ft-raxml-ng. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-9502163 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-95021632022-09-26 Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG Hübner, Lukas Kozlov, Alexey M Hespe, Demian Sanders, Peter Stamatakis, Alexandros Bioinformatics Original Papers MOTIVATION: Phylogenetic trees are now routinely inferred on large scale high performance computing systems with thousands of cores as the parallel scalability of phylogenetic inference tools has improved over the past years to cope with the molecular data avalanche. Thus, the parallel fault tolerance of phylogenetic inference tools has become a relevant challenge. To this end, we explore parallel fault tolerance mechanisms and algorithms, the software modifications required and the performance penalties induced via enabling parallel fault tolerance by example of RAxML-NG, the successor of the widely used RAxML tool for maximum likelihood-based phylogenetic tree inference. RESULTS: We find that the slowdown induced by the necessary additional recovery mechanisms in RAxML-NG is on average 1.00 ± 0.04. The overall slowdown by using these recovery mechanisms in conjunction with a fault-tolerant Message Passing Interface implementation amounts to on average 1.7 ± 0.6 for large empirical datasets. Via failure simulations, we show that RAxML-NG can successfully recover from multiple simultaneous failures, subsequent failures, failures during recovery and failures during checkpointing. Recoveries are automatic and transparent to the user. AVAILABILITY AND IMPLEMENTATION: The modified fault-tolerant RAxML-NG code is available under GNU GPL at https://github.com/lukashuebner/ft-raxml-ng. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-05-26 /pmc/articles/PMC9502163/ /pubmed/34037680 http://dx.doi.org/10.1093/bioinformatics/btab399 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Original Papers Hübner, Lukas Kozlov, Alexey M Hespe, Demian Sanders, Peter Stamatakis, Alexandros Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG |
title | Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG |
title_full | Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG |
title_fullStr | Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG |
title_full_unstemmed | Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG |
title_short | Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG |
title_sort | exploring parallel mpi fault tolerance mechanisms for phylogenetic inference with raxml-ng |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9502163/ https://www.ncbi.nlm.nih.gov/pubmed/34037680 http://dx.doi.org/10.1093/bioinformatics/btab399 |
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