M.Sc. Lukas Hübner
- Room: 222
- Phone: +49 721 608-46603
- Fax: +49 721 608-43088
- huebner ∂does-not-exist.kit edu
Research Interest: Scalable Evolutionary Bioinformatics
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- Compute-efficient algorithms in population genetics
- Fault-Tolerance in HPC-algorithms
- Computational reproducibility
- Distributed-memory development (MPI)
- Applications of the above to evolutionary bioinformatics
Software
- KaMPIng (Karlsruhe MPI Next Generation): (Near) zero-overhead modern C++ abstraction over the Message Passing Interface
- gfkit (Genealogical Forest Kit): Compute-efficient statistics in population genetics
- ReStore An in-memory REplicated STORagE for rapid recovery of data in fault-tolerant HPC-algorithms
- Fault-Tolerant RAxML-NG (FT-RAxML-NG) Fault-tolerant version of the popular RAxML-NG phylogenetic inference tool
- Coraxlib (COre RAXml LIBrary) encapsulates common routines used by likelihood-based phylogenetic software
| Title | Author(s) | Source | Date |
|---|---|---|---|
| KaMPIng: Flexible and (Near) Zero-overhead C++ Bindings for MPI | Demian Hespe, Lukas Hübner, Florian Kurpicz, Peter Sanders, Matthias Schimek, Daniel Seemaier, Christoph Stelz, Tim Niklas Uhl |
April 2024 | |
| Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests | Lukas Hübner, Alexandros Stamatakis |
27th of Mai 2024 | |
| ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms | Lukas Hübner, Demian Hespe, Peter Sanders, Alexandros Stamatakis |
January 2023 | |
| The Free Lunch is not over yet - Systematic Exploration of Numerical Thresholds in Phylogenetic Inference | Julia Haag, Lukas Hübner, Alexey M. Kozlov, Alexandros Stamatakis |
July 2022 | |
| Exploring Parallel MPI Fault Tolerance Mechanisms for Phylogenetic Inference with RAxML-NG | Lukas Hübner, Alexey M. Kozlov, Demian Hespe, Peter Sanders, Alexandros Stamatakis |
January 2021 | |
| Phylogenetic analysis of SARS-CoV-2 data is difficult | Benoit Morel, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukas Hübner, Sarah Lutteropp, Dora Serdari, Evangelia-Georgia Kostaki, Ioannis Mamais, Alexey M. Kozlov, Pavlos Pavlidis, Dimitrios Paraskevis, Alexandros Stamatakis |
August 2020 | |
| Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning | Ivo Baar, Lukas Hübner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel |
March 2019 |
| Title | Conference | Author(s) | Speaker |
|---|---|---|---|
| Future-Proofing Bioinformatic Applications: Handling CPU-failures, abstracting MPI & reproducible experiments | High-Performance Computing |
Lukas Hübner |
Lukas Hübner |
| Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests | WABI 2024 |
Lukas Hübner & Alexandros Stamatakis |
Lukas Hübner |
| The Computational Stumbling Blocks: Fault-Tolerance and Reproducibility | Biodiversity Bioinformatics Workshop 2023 |
Lukas Hübner |
Lukas Hübner |
| ReStore: In-Memory REplicated STORagE for Rapid Recovery | Fault-Tolerance at eXtreme Scale (FTXS) 2022 |
Lukas Hübner, Demian Hespe, Peter Sanders, Alexandros Stamatakis |
Lukas Hübner |
| Title | Type | Semester | Location |
|---|---|---|---|
| Parallele Algorithmen | Vorlesung (V) | WS 24/25 | |
| Where can I go in |
Praxis der Softwareentwicklung (PSE) | SS 2023 | |
| Can we accelerate Maximum-Likelihood Computations on GPUs? | Praxis der Forschung | WS 23/24 + SS 24 | |
| Parallel Algorithms | lecture | WS 23/24 | Building 50.34, Lecture Hall -101 |
| Hands-on Bioinformatics Practical | lab course | SS 21 | |
| Parallel Algorithms | lecture | WS 21/22 | Building 50.34, Lecture Hall -101 |
| Parallel Algorithms | lecture | WS 22/23 | Building 50.34, Lecture Hall -101 |
| Titel | Forschungsthema | Typ |
|---|---|---|
| Scalable Fault-Tolerant MapReduce | Fault-Tolerance, Map Reduce, HPC | Masterarbeit |
| Data-Redistribution for Malleable Algorithms | Malleability, HPC | Masterarbeit |
| Title | Subject | Supervisor | Student |
|---|---|---|---|
| Empirical Numerical Properties of Maximum Likelihood Phylogenetic Inference | Phylogenetic Inference, Efficient Evolutionary Bioinformatics | Lukas Hübner, Alexandros Stamatakis |
Julia Haag |
| Re-Engineering Genomic Tree Sequence Inference Algorithms | Efficient Evolutionary Bioinformatics | Lukas Hübner, Alexandros Stamatakis |
Johannes Hengstler |
| Lightweight Checkpointing and Recovery for Iterative Converging Algorithms | Fault-Tolerance | Demian Hespe, Lukas Hübner, Peter Sanders |
Guido Zeitzmann |
| Faster Sorting of Aligned DNA-Read Files | Efficient Evolutionary Bioinformatics | Lukas Hübner, Alexandros Stamatakis |
Dominik Siebelt |
| Core-Count Independent Reproducible Reduce | Fault-Tolerance, Computational Reproducibility | Lukas Hübner, Alexandros Stamatakis, Peter Sanders |
Christoph Stelz |
| Scalable Decentralized Fault-Tolerant MapReduce for Iterative Algorithms | Fault-Tolerance | Demian Hespe, Lukas Hübner, Peter Sanders |
Charel Mercatoris |