Explanipedia

Scalable Fault-Tolerant MapReduce Open

Demian Hespe, Lukáš Hübner, Charel Mercatoris, Peter Sanders · 2024

Supercomputers getting ever larger and energy-efficient is at odds with the reliability of the used hardware. Thus, the time intervals between component failures are decreasing. Contrarily, the latencies for individual operations of coarse…

Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests Open

Lukáš Hübner, Alexandros Stamatakis · 2024

The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and – in conjunction with recent advances in ancient DNA sequen…

KaMPIng: Flexible and (Near) Zero-Overhead C++ Bindings for MPI Open

Demian Hespe, Lukáš Hübner, Florian Kurpicz, Peter Sanders, Matthias Schimek , et al. · 2024

The Message-Passing Interface (MPI) and C++ form the backbone of high-performance computing, but MPI only provides C and Fortran bindings. While this offers great language interoperability, high-level programming languages like C++ make so…

The Free Lunch is not over yet—systematic exploration of numerical thresholds in maximum likelihood phylogenetic inference Open

Julia Haag, Lukáš Hübner, Alexey M. Kozlov, Alexandros Stamatakis · 2023

Summary Maximum likelihood (ML) is a widely used phylogenetic inference method. ML implementations heavily rely on numerical optimization routines that use internal numerical thresholds to determine convergence. We systematically analyze t…

ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms Open

Lukáš Hübner, Demian Hespe, Peter Sanders, Alexandros Stamatakis · 2022

Fault-tolerant distributed applications require mechanisms to recover data lost via a process failure. On modern cluster systems it is typically impractical to request replacement resources after such a failure. Therefore, applications hav…

The Free Lunch is not over yet – Systematic Exploration of Numerical Thresholds in Phylogenetic Inference Open

Julia Haag, Lukáš Hübner, Alexey M. Kozlov, Alexandros Stamatakis · 2022

Maximum Likelihood (ML) is a widely used phylogenetic inference model. ML implementations heavily rely on numerical optimization routines that use internal numerical thresholds to determine convergence. We systematically analyze the impact…

ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms Open

Demian Hespe, Lukáš Hübner, Peter Sanders, Alexandros Stamatakis · 2022

Fault-tolerant distributed applications require mechanisms to recover data lost via a process failure. On modern cluster systems it is typically impractical to request replacement resources after such a failure. Therefore, applications hav…

Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG Open

Lukáš Hübner, Alexey M. Kozlov, Demian Hespe, Peter Sanders, Alexandros Stamatakis · 2021

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 th…

Exploring Parallel MPI Fault Tolerance Mechanisms for Phylogenetic Inference with RAxML-NG Open

Lukáš Hübner, Alexey M. Kozlov, Demian Hespe, Peter Sanders, Alexandros Stamatakis · 2021

Phylogenetic trees are now routinely inferred on large scale HPC 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, …

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult Open

Benoît Morel, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukáš Hübner , et al. · 2020

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by examp…

Phylogenetic analysis of SARS-CoV-2 data is difficult Open

Benoît Morel, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukáš Hübner , et al. · 2020

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org . Here, we review the difficulties of inferring reliable phylogenies by exam…

Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning Open

Ivo Baar, Lukáš Hübner, Peter Oettig, Adrian Zapletal, Sebastian Schlag , et al. · 2019

The so-called site repeats (SR) technique can be used to accelerate the widely-used phylogenetic likelihood function (PLF) by identifying identical patterns among multiple sequence alignment (MSA) sites, thereby omitting redundant calculat…

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