Algorithms and implementations for multicore and parallel architectures
Participants
- Morgan Ericsson (PostDoc)
- Magnus Gustafsson (PhD student, Principal advisor: S. Holmgren, Co-advisor: M. Thuné)
- Martin Tillenius (PhD student, Principal advisor: E. Larsson, Co-advisor: S. Holmgren)
The research in the group is performed within the Linnaeus Center of Excellence UPMARC. The work e.g. includes collaboration with the Computer Architecture group at the department. Also, the group has contacts with several applied computing groups who contribute with problem settings.
Research
Dynamic Task Scheduling for Molecular Dynamics
A task-based approach with dynamic task scheduling is used to build a molecular dynamics simulation software targeted for multicore systems. Data dependencies are detected by the task library and the tasks are then scheduled dynamically at run-time to fulfill all data dependencies, releasing the programmer from this burden.
The software will be used to generate node point distributions for use in radial basis function methods.
Available Master Thesis Projects
Articles and Refereed Conference Contributions
- Efficiently implementing Monte Carlo electrostatics simulations on multicore accelerators. In Applied Parallel and Scientific Computing: Part II, volume 7134 of Lecture Notes in Computer Science, pp 379-388, Springer-Verlag, Berlin, 2012. (DOI).
- Communication-efficient algorithms for numerical quantum dynamics. In Applied Parallel and Scientific Computing: Part II, volume 7134 of Lecture Notes in Computer Science, pp 368-378, Springer-Verlag, Berlin, 2012. (DOI).
- Using hardware transactional memory for high-performance computing. In Proc. 25th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum, pp 1660-1667, IEEE, Piscataway, NJ, 2011. (DOI).
- An implementation framework for solving high-dimensional PDEs on massively parallel computers. In Numerical Mathematics and Advanced Applications: 2009, pp 417-424, Springer-Verlag, Berlin, 2010. (DOI).
- An efficient task-based approach for solving the <em>n</em>-body problem on multicore architectures. PARA 2010: State of the Art in Scientific and Parallel Computing, University of Iceland, Reykjavík, 2010. (fulltext:postprint).
- Reconsidering algorithms for iterative solvers in the multicore era. In International Journal of Computational Science and Engineering, volume 4, pp 270-282, 2009. (DOI).
- Geographical locality and dynamic data migration for OpenMP implementations of adaptive PDE solvers. In OpenMP Shared Memory Parallel Programming, volume 4315 of Lecture Notes in Computer Science, pp 382-393, Springer-Verlag, Berlin, 2008. (DOI).
- Dynamic data migration for structured AMR solvers. In International journal of parallel programming, volume 35, pp 477-491, 2007. (DOI).
More articles/conf.contr. will be added soon! (2009-08-29)
Technical Reports and Preprints
- Efficient optimization algorithms and implementations for genetic analysis of complex traits on a grid system with multicore nodes. M. Jayawardena, H. Löf, S. Holmgren. Accepted for publication in Proc. Workshop on State-of-the-art in Scientific and Parallel Computing (PARA 2008).
Theses
- Multithreaded PDE Solvers on Non-Uniform Memory Architectures. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 224, Acta Universitatis Upsaliensis, Uppsala, 2006. (fulltext).
- Iterative and Adaptive PDE Solvers for Shared Memory ArchitecturesIterativa och adaptiva PDE-lösare för parallelldatorer med gemensam minnesorganisation. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 218, Acta Universitatis Upsaliensis, Uppsala, 2006. (fulltext).
- Methods for Creating and Exploiting Data Locality. Ph.D. thesis, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology nr 176, Acta Universitatis Upsaliensis, Uppsala, 2006. (fulltext).
- Parallelizing the Method of Conjugate Gradients for Shared Memory Architectures. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2004-005, Uppsala University, 2004. (fulltext).
- Parallel PDE Solvers on cc-NUMA Systems. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2004-002, Uppsala University, 2004. (fulltext).
- Exploiting data locality in adaptive architectures. Licentiate thesis, IT licentiate theses / Uppsala University, Department of Information Technology nr 2003-010, Uppsala University, 2003. (fulltext).