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Computational Methods in Systems and Control Theory

Linux Cluster otto


MPG Funded Project

otto

The Linux Cluster at MPI Magdeburg




Project leader: Researcher: Duration: online since 12/2010

Project description:
The compute cluster otto is the new central compute ressource at the MPI Magdeburg. Researchers of all groups can use it for simultations, large and especially distributed computations. The CSC group uses otto especially for the development of scientific software and for computations related to our further research activities.

Hardware

otto is a heterogeneous cluster with two different kinds of compute nodes.
Node type 1 Node type 2
CPU: 2x Intel Xeon Westmere-EP X5650 2x AMD Opteron Magny Cours 6168
Cores per CPU: 6 12
Clockrate: 2.67 GHz 1.9 GHz
RAM: 48 GB DDR3 ECC 96 GB DDR3 ECC
Harddisk: keine 600GB SAS
Network: 40 Gbit/s Infiniband QDR 40 Gbit/s Infiniband QDR
Theoretical peak performance per node: 128 GFlop/s 182 GFlop/s
Number of nodes: 90+1 16
Linpack peak performance of all nodes: 10.36 TFlop/s 2.3 TFlop/s
Other hardware components are:
  • 1 login node using two Intel Xeon E5620 CPUs
  • 1 service node using two Intel Xeon E5620 CPUs
  • 1 appliance with a Intel Xeon L3406 CPU
  • 28 TB Panasas PanFS network storage
  • 4 Voltaire QDR Infiniband switches

Software

The users of otto has various software for mathematical and software engineering purposes installed. Some highlights are:
  • GNU Compiler Collection 4.5.1
  • Intel C/C++/Fortran Compiler 12
  • Matlab 2010b
  • Gromacs 4.5
  • Sun Grid Engine 6.2
  • several mathematical libraries (BLAS, Lapack, Deal.II, Fenics)
The installed software is configured and selected using the Modules-system. This gives an easy means to setup a designated working environment, or switch ,e.g., to a different compiler suite. Additional software is installed upon request to optimally fulfill the needs of all researchers.

In order to use otto researchers have to sign a separate policy. More details can be found in the internal wiki of our institute.


Selected publications:

HPC en simulación y control a gran escala (in Spanish);
Peter Benner, Pablo Ezzatti, Hermann Mena, Enrique S. Quintana-Ortí, and Alfredo Remón;
; November 2011.
Solving Matrix Equations on Multi-core and Many-core Architectures;
Peter Benner, Pablo Ezzatti, Hermann Mena, Enrique S. Quintana-Ortí, and Alfredo Remón;
; MPI Magdeburg Preprint MPIMD/11-07, October 2011.
Efficiency improving implementation techniques for large scale matrix equation solvers;
Köhler, Martin; Saak, Jens;
CSC Preprint 09-10;
; 2009.
Parallel Implementation of LQG Balanced Truncation for Large-Scale Systems;
Badía, José M., Benner, Peter, Mayo Rafael, Quintana-Ortí Enrique S.; Quintana-Ortí, Gregorio; Remón, Alfredo;
; 2007.
Stabilizing Large-Scale Generalized Systems on Parallel Computers Using Multithreading and Message-Passing;
Peter Benner, Maribel Castillo, Rafael Mayo, Enrique S. Quintana-Ortí, and Gregorio Quintana-Ortí;
Concurrency and Computation: Practice and Experience, Vol. 19, No. 4, pp. 531-542, 2007.;
DOI: 10.1002/cpe.1148
Efficient Algorithms for Generalized Algebraic Bernoulli Equations based on the Matrix Sign Function;
Sergio Barrachina, Peter Benner, and Enrique S. Quintana-Ortí;
Numerical Algorithms, Vol. 46, No. 4, pp. 351-368, 2007.;
Parallel Solution of Large-Scale and Sparse Generalized Algebraic Riccati Equations;
Badía, José M., Benner, Peter, Mayo Rafael, Quintana-Ortí Enrique S.;
in W. E. Nagel, W. V. Walter, and W. Lehner: Euro-Par 2006 Parallel Processing: 12th International Euro-Par Conference  :  Lecture Notes in Computer Science, Vol. 4128, pp. 710-719;
Springer-Verlag, Berlin, Heidelberg, New York; 2006. ISBN/ISSN: 978-3-540-37783-2
DOI: 10.1007/11823285_74.
Solution of Discrete-Time Riccati Equations via Structure-Preserving Doubling Algorithms on a Cluster of SMPs;
Barrachina, Sergio; Benner, Peter; Quintana-Ortí, Enrique S.;
submitted for publication; 2006.
Parallel Algorithms for Balanced Truncation Model Reduction of Sparse Systems;
Benner, Peter; Quintana-Ortí, Enrique S.; Mayo, Rafael; Badía, José Manuel;
in J. Dongarra, K. Madsen, J. Wasniewski: Applied Parallel Computing: 7th International Conference, PARA 2004, Lyngby, Denmark, June 20-23, 2004. Revised Selected Papers  :  Lecture Notes in Computer Science, Vol. 3732, pp. 267-275;
Springer-Verlag; 2006. ISBN/ISSN: 3-540-29067-4
Original available from SpringerLink, DOI: 10.1007/11558958_32.
Balanced Truncation Model Reduction of Large and Sparse Generalized Linear Systems;
M. Badía, José; Benner, Peter; Mayo, Rafael; Quintana-Ortí, Enrique S.; Quintana-Ortí, Gregorio; Remón, Alfredo;
Chemnitz Scientific Computing Preprints 06-04, TU Chemnitz; 2006. ISBN/ISSN: 1864-0087
Parallel Order Reduction via Balanced Truncation for Optimal Cooling of Steel Profiles;
Badia, Jose M.; Benner, Peter; Mayo, Rafael; Quintana-Ortí, Enrique; Quintana-Ortí, Gregorio; Saak, Jens;
in J.C. Cunha and P.D. Mdeiros (eds.): Euro-Par 2005 Parallel Processing: 11th International Euro-Par Conference, Lisbon, Portugal, August 30 - September 2  :  Lecture Notes in Computer Science, Vol. 3648, pp. 857-866;
Springer-Verlag; 2005.
see also SfB393 Preprint 05-02.
Parallel Solution of Large-Scale Algebraic Bernoulli Equations with the Matrix Sign Function Method;
Benner, Peter; Barrachina, Sergio; Quintana-Ortí, Enrique S.;
International Journal of Computational Science and Engineering (IJCSE); 2005.
Parallel Algorithms for Balanced Truncation of Large-Scale Unstable Systems;
Benner, Peter; Barrachina, Sergio; Quintana-Ortí, Enrique S.; Quintana-Ortí, Gregorio;
Proceedings of 44th IEEE Conference on Decision and European Control Conference  :  pp. 2248-2253;
ECC; 2005. ISBN/ISSN: 0-7803-9568-9
Solving Stable Sylvester Equations via Rational Iterative Schemes;
Benner, Peter; Quintana-Ortí, Enrique S., Quintana-Ortí, Gregorio;
Journal of Scientific Computing  :  
Original available from SpringerLink.; 2005.
Solving Linear-Quadratic Optimal Control Problems on Parallel Computers;
Benner, Peter; Quintana-Ortí, Enrique S.; Quintana-Ortí, Gregorio;
Preprintreihe des Chemnitzer SFB 393  :  Preprint 19 / 2005;
; 2005.
Parallel Model Reduction of Large-Scale Unstable Systems;
Benner, Peter; Castillo, Maribel; Quintana-Ortí, Enrique S.; Quintana-Ortí, Gregorio;
in G.R. Joubert, W.E. Nagel, F.J. Peters, W.V Walter: Parallel computing: Software Technology, Algorithms, Architectures & Applications, Advances in Parallel Computing, Vol. 13, pp. 251-258;
Elsevier B.V (North-Holland); 2004. ISBN/ISSN: 0-444-51689-1
Parallel Model Reduction of Large-Scale Linear Descriptor Systems via Balanced Truncation;
Benner, Peter; Quintana-Ortí, Enrique S.; Quintana-Ortí, Gregorio;
in M. Daydé, J.J. Dongarra, V. Hernández, J.M.L.M. Palma: High Performance Computing for Computational Science - VECPAR 2004  :  Lecture Notes in Computer Science, No. 3402, pp. 340-353;
Springer-Verlag, Berlin, Heidelberg; 2004. ISBN/ISSN: 3-540-25424-2
State-Space Truncation Methods for Parallel Model Reduction of Large-Scale Systems;
Benner, Peter; Quintana-Ortí, Enrique S.; Quintana-Ortí, Gregorio;
Parallel Computing  :  Vol. 29 (special issue on "Parallel and Distributed Scientific and Engineering Computing"), pp. 1701-1722;
; 2003.
Parallel Algorithms for Model Reduction of Discrete-Time Systems;
Benner, Peter; Quintana-Ortí, Enrique S.; Quintana-Ortí, Gregorio;
International Journal of System Sciences  :  Vol. 34, No. 5, pp. 319-333;
; 2003.
The retrievable version appeared as Berichte aus der Technomathematik, Report 00-18, December 2000..
Numerical Solution of Discrete Stable Linear Matrix Equations on Multicomputers;
Peter Benner, Enrique S. Quintana-Ortí, and Gregorio Quintana-Ortí;
Parallel Algorithms and Applications (since 2005: International Journal of Parallel, Emergent and Distributed Systems) Vol. 17, No. 2, pp. 127-146, 2002.;
DOI: 10.1080/10637190208941436
Free preprint available at Berichte aus der Technomathematik, Report 99-13, November 1999.
Parallel Algorithms for LQ Optimal Control of Discrete-Time Periodic Linear Systems;
Peter Benner, Ralph Byers, Rafael Mayo, Enrique S. Quintana-Ortí, and Vicente Hernández;
Journal of Parallel and Distributed Computing, vol. 62, pp. 306-325, 2002.;
The retrievable version appeared as Berichte aus der Technomathematik, Report 01-02, February 2001.
Efficient Numerical Algorithms for Balanced Stochastic Truncation;
Peter Benner, Enrique S. Quintana-Ortí, and Gregorio Quintana-Ortí;
International Journal of Applied Mathematics and Computer Science, Vol. 11, No. 5, pp. 1123-1150, 2001.;
The retrievable version appeared as Berichte aus der Technomathematik, Report 01-03, March 2001.
Balanced Truncation Model Reduction of Large-Scale Dense Systems on Parallel Computers;
Peter Benner, Enrique S. Quintana-Ortí, and Gregorio Quintana-Ortí;
Mathematical and Computer Modelling of Dynamical Systems, Vol. 6, No.4, pp. 383-405, 2000.;
The retrievable version appeared as Berichte aus der Technomathematik, Report 99-07, September 1999.


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Jens Saak, Martin Köhler, saak, koehlerm@mpi-magdeburg.mpg.de
08 März 2013