Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG
| Autor: | Alexandros Stamatakis, Demian Hespe, Lukas Hübner, Alexey M. Kozlov, Peter Sanders |
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| Rok vydání: | 2021 |
| Předmět: |
Statistics and Probability
Phylogenetic inference Computer science Maximum likelihood Inference 010103 numerical & computational mathematics Parallel computing 01 natural sciences Biochemistry 03 medical and health sciences Software Code (cryptography) 0101 mathematics Molecular Biology 030304 developmental biology Supplementary data 0303 health sciences Phylogenetic tree business.industry DATA processing & computer science Fault tolerance Computer Science Applications Computational Mathematics Computational Theory and Mathematics Scalability ddc:004 business |
| Zdroj: | Bioinformatics, 37 (22), 4056–4063 |
| ISSN: | 1367-4811 1367-4803 1460-2059 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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