M.Sc. Lukas Hübner
- Raum: 222
- Tel.: +49 721 608-46603
- Fax: +49 721 608-43088
- huebner ∂does-not-exist.kit edu
Forschungsschwerpunkte
- Effiziente Algorithmen in der Populationsgenetik
- Fehlertoleranz in Hochperformanzrechnern
- Reproduzierbarkeit von Berechnungen
- Softwareentwicklung für Systeme mit verteiltem Speicher (MPI)
- Anwendungen des o.g. auf die evolutionäre Bioinformatik
Software
- KaMPIng (Karlsruhe MPI Next Generation): (Fast) mehrkostenfreie Abstraktion über das Message Passing Interface in modernen C++
- gfkit (Genealogical Forest Kit): Berechnungseffiziente Statistiken in der Populationsgenetik
- ReStore (in-memory REplicated STORagE for rapid recovery in fault-tolerant algorithms): Replizierter Speicher optimiert auf die schnelle Wiederherstellung von Daten zur Verwendung in fehlertoleranten Anwendungen
- Fault-Tolerant RAxML-NG (FT-RAxML-NG) Fehlertolerante Version des bekannten RAxML-NG Tool für Phylogenetische Inferenz
- Coraxlib (COre RAXml LIBrary) kapselt Funktionalität für Likelihood-basierte Phylogenetische Software
Publikationen
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests
Hübner, L.; Stamatakis, A.
2024. 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Ed.: S.P. Pissis, 5:1–5:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (LZI). doi:10.4230/LIPIcs.WABI.2024.5
Hübner, L.; Stamatakis, A.
2024. 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Ed.: S.P. Pissis, 5:1–5:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (LZI). doi:10.4230/LIPIcs.WABI.2024.5
KaMPIng
Hespe, D.; Hübner, L.; Kurpicz, F.; Schimek, M.; Seemaier, D.; Uhl, T. N.
2024, Juni 27. doi:10.5281/zenodo.13120159
Hespe, D.; Hübner, L.; Kurpicz, F.; Schimek, M.; Seemaier, D.; Uhl, T. N.
2024, Juni 27. doi:10.5281/zenodo.13120159
Brief Announcement: (Near) Zero-Overhead C++ Bindings for MPI
Hespe, D.; Hübner, L.; Kurpicz, F.; Sanders, P.; Schimek, M.; Seemaier, D.; Uhl, T. N.
2024. SPAA ’24: Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Nantes, 17th-21st June 2024, 289–291, Association for Computing Machinery (ACM). doi:10.1145/3626183.3660260
Hespe, D.; Hübner, L.; Kurpicz, F.; Sanders, P.; Schimek, M.; Seemaier, D.; Uhl, T. N.
2024. SPAA ’24: Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Nantes, 17th-21st June 2024, 289–291, Association for Computing Machinery (ACM). doi:10.1145/3626183.3660260
KaMPIng: Flexible and (Near) Zero-Overhead C++ Bindings for MPI
Uhl, T. N.; Schimek, M.; Hübner, L.; Hespe, D.; Kurpicz, F.; Seemaier, D.; Stelz, C.; Sanders, P.
2024. International Conference for High Performance Computing, Networking, Storage and Analysis (SC24), 689–709, IEEE Computer Society. doi:10.1109/SC41406.2024.00050
Uhl, T. N.; Schimek, M.; Hübner, L.; Hespe, D.; Kurpicz, F.; Seemaier, D.; Stelz, C.; Sanders, P.
2024. International Conference for High Performance Computing, Networking, Storage and Analysis (SC24), 689–709, IEEE Computer Society. doi:10.1109/SC41406.2024.00050
KaMPIng: Flexible and (Near) Zero-overhead C++ Bindings for MPI
Hespe, D.; Hübner, L.; Kurpicz, F.; Sanders, P.; Schimek, M.; Seemaier, D.; Stelz, C.; Uhl, T. N.
2024. arxiv. doi:10.48550/arXiv.2404.05610
Hespe, D.; Hübner, L.; Kurpicz, F.; Sanders, P.; Schimek, M.; Seemaier, D.; Stelz, C.; Uhl, T. N.
2024. arxiv. doi:10.48550/arXiv.2404.05610
The Free Lunch is not over yet—systematic exploration of numerical thresholds in maximum likelihood phylogenetic inference
Haag, J.; Hübner, L.; Kozlov, A. M.; Stamatakis, A.
2023. Bioinformatics Advances, 3 (1), Art.-Nr.: vbad124. doi:10.1093/bioadv/vbad124
Haag, J.; Hübner, L.; Kozlov, A. M.; Stamatakis, A.
2023. Bioinformatics Advances, 3 (1), Art.-Nr.: vbad124. doi:10.1093/bioadv/vbad124
Scalable discrete algorithms for big data applications
Hespe, D.; Hübner, L.; Hübschle-Schneider, L.; Sanders, P.; Schreiber, D.
2023. High Performance Computing in Science and Engineering ’21 – Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2021. Ed.: W. Nagel, 439–449, Springer International Publishing. doi:10.1007/978-3-031-17937-2_27
Hespe, D.; Hübner, L.; Hübschle-Schneider, L.; Sanders, P.; Schreiber, D.
2023. High Performance Computing in Science and Engineering ’21 – Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2021. Ed.: W. Nagel, 439–449, Springer International Publishing. doi:10.1007/978-3-031-17937-2_27
ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms
Hübner, L.; Hespe, D.; Sanders, P.; Stamatakis, A.
2022. 2022 IEEE/ACM 12th Workshop on Fault Tolerance for HPC at eXtreme Scale (FTXS), Dallas, TX, USA, 13-18 November 2022, 24–35, Institute of Electrical and Electronics Engineers (IEEE). doi:10.1109/FTXS56515.2022.00008
Hübner, L.; Hespe, D.; Sanders, P.; Stamatakis, A.
2022. 2022 IEEE/ACM 12th Workshop on Fault Tolerance for HPC at eXtreme Scale (FTXS), Dallas, TX, USA, 13-18 November 2022, 24–35, Institute of Electrical and Electronics Engineers (IEEE). doi:10.1109/FTXS56515.2022.00008
Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG
Hübner, L.; Kozlov, A. M.; Hespe, D.; Sanders, P.; Stamatakis, A.
2021. Bioinformatics, 37 (22), 4056–4063. doi:10.1093/bioinformatics/btab399
Hübner, L.; Kozlov, A. M.; Hespe, D.; Sanders, P.; Stamatakis, A.
2021. Bioinformatics, 37 (22), 4056–4063. doi:10.1093/bioinformatics/btab399
Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult
Morel, B.; Barbera, P.; Czech, L.; Bettisworth, B.; Hübner, L.; Lutteropp, S.; Serdari, D.; Kostaki, E.-G.; Mamais, I.; Kozlov, A. M.; Pavlidis, P.; Paraskevis, D.; Stamatakis, A.
2021. Molecular biology and evolution, 38 (5), 1777–1791. doi:10.1093/molbev/msaa314
Morel, B.; Barbera, P.; Czech, L.; Bettisworth, B.; Hübner, L.; Lutteropp, S.; Serdari, D.; Kostaki, E.-G.; Mamais, I.; Kozlov, A. M.; Pavlidis, P.; Paraskevis, D.; Stamatakis, A.
2021. Molecular biology and evolution, 38 (5), 1777–1791. doi:10.1093/molbev/msaa314
Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning
Baar, I.; Hübner, L.; Oettig, P.; Zapletal, A.; Schlag, S.; Stamatakis, A.; Morel, B.
2019. IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Rio de Janeiro, Brazil, Brazil, 20-24 May 2019, 175–184, Institute of Electrical and Electronics Engineers (IEEE). doi:10.1109/IPDPSW.2019.00038
Baar, I.; Hübner, L.; Oettig, P.; Zapletal, A.; Schlag, S.; Stamatakis, A.; Morel, B.
2019. IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Rio de Janeiro, Brazil, Brazil, 20-24 May 2019, 175–184, Institute of Electrical and Electronics Engineers (IEEE). doi:10.1109/IPDPSW.2019.00038
| Title | Author(s) | Source | Date |
|---|---|---|---|
| Scalable Fault-Tolerant MapReduce | Demian Hespe, Lukas Hübner, Charel Mercatoris, and Peter Sanders |
November 2024 | |
| 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 |
Mai 2024 | |
| ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms | Lukas Hübner, Demian Hespe, Peter Sanders, Alexandros Stamatakis |
Januar 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 |
Juli 2022 | |
| Exploring Parallel MPI Fault Tolerance Mechanisms for Phylogenetic Inference with RAxML-NG | Lukas Hübner, Alexey M. Kozlov, Demian Hespe, Peter Sanders, Alexandros Stamatakis |
Januar 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 |
März 2019 |
| Titel | Tagung | Autoren | Referent |
|---|---|---|---|
| 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 |
| Titel | Typ | Semester | Ort |
|---|---|---|---|
| Parallele Algorithmen | Vorlesung (V) | WS 24/25 | Geb. 50.34, Hörsaal -101 |
| Where can I go in n hours? Isochrone routing | Praxis der Softwareentwicklung | SS 23 | |
| Can we accelerate Maximum-Likelihood Computations on GPUs? | Praxis der Forschung | WS 23/24 + SS 24 | |
| Parallele Algorithmen | Vorlesung (V) | WS 23/24 | Geb. 50.34, Hörsaal -101 |
| Hands-on Bioinformatics Practical | Praktikum (P) | SS 2021 | |
| Parallele Algorithmen | Vorlesung (V) | WS 21/22 | Geb. 50.34, Hörsaal -101 |
| Parallele Algorithmen | Vorlesung (V) | WS 22/23 | Geb. 50.34, Hörsaal -101 |
| Titel | Forschungsthema | Typ |
|---|---|---|
| Scalable Fault-Tolerant MapReduce | Fault-Tolerance, Map Reduce, HPC | Masterarbeit |
| Data-Redistribution for Malleable Algorithms | Malleability, HPC | Masterarbeit |
| Titel | Forschungsthema | Betreuung | Bearbeitung |
|---|---|---|---|
| Lightweight Checkpointing and Recovery for Iterative Converging Algorithms | Fehlertoleranz | Demian Hespe, Lukas Hübner, Peter Sanders |
Guido Zeitzmann |
| Faster Sorting of Aligned DNA-Read Files | Effiziente Evolutionäre Bioinformatik | Lukas Hübner, Alexandros Stamatakis |
Dominik Siebelt |
| Re-Engineering Genomic Tree Sequence Inference Algorithms | Effiziente Evolutionäre Bioinformatik | Lukas Hübner, Alexandros Stamatakis |
Johannes Hengstler |
| Core-Count Independent Reproducible Reduce | Fehlertoleranz, Reproduzierbare Berechnungen | Lukas Hübner, Alexandros Stamatakis, Peter Sanders |
Christoph Stelz |
| Empirical Numerical Properties of Maximum Likelihood Phylogenetic Inference | Phylogenetische Inferenz, Effiziente Bioinformatikalgorithmen | Lukas Hübner, Alexandros Stamatakis |
Julia Haag |
| Scalable Decentralized Fault-Tolerant MapReduce for Iterative Algorithms | Fehlertoleranz | Demian Hespe, Lukas Hübner, Peter Sanders |
Charel Mercatoris |