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NSC Seminars on High Performance Computing

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List of previous seminars

Autumn 2000

Time Place Speaker Title (click to see abstract)
Tue., Nov. 28, 2000, at 13.15 Room Schrödinger Prof. Göran Wahnström, Chalmers University of Technology and Göteborgs University Atomic-Scale Computational Materials Science
Tue., Dec. 12, 2000, at 16.15 Room Schrödinger Prof. Jan Komorowski, Norwegian University of Science and Technology & Linköping University Mining Microarray Data: Predicting Gene Function from Gene Expressions and Background Knowledge

Spring 2001

Time Place Speaker Title (click to see abstract)
Tue., Jan 23, 2001, at 16.15 Room Schrödinger Prof. Matts Karlsson, Dept. of Biomechanical Engineering (IMT), Linköping University Mechanics of the Heart
Tue., Jan. 30, 2001, at 16.15 Room Schrödinger Dr. Alexandr Malusek and Dr. Michael Sandborg, Dept. of Radiation Physics (IMV), Linköping University Monte Carlo modelling of the imaging chain in x-ray diagnostics 
Tue., Feb 20, 2001, at 16.15 Room Schrödinger Prof Kenneth Runesson, Dept. Solid Mechnanics, Chalmers A Paradigm for Error Estimation and Adaptivity in Computational Mechanics
Tue., Mar 13, 2001, at 16.15 Room Schrödinger Dr. Per Weinerfelt, Saab Aerospace Large Scale Aerodynamic Flow Computations on Parallel Computers
Wed., Apr 18, 2001, at 16.15 Room Schrödinger Dr. H. E. Markus Meier (SMHI) and Torgny Faxén (NSC) Climate Modelling of the Baltic Sea


Detailed Programme


Title:        Atomic-Scale Computational Materials Science

Speaker:    Prof. Göran Wahnström, Chalmers University of Technology and Göteborgs University

Time:        Tuesday, Nov. 28, 2000, at 13.15-14.00

Abstract

With the rapid development of advanced technologies materials science is confronted with many challenging problems. Atomic-scale computational materials science has become one important tool in improving our understanding and in facilitating the design of new materials. Quantum mechanical calculations provide a means to describe materials on a truly microscopic level. In principle the laws governing the behaviour of the microscopic constituents of a material, the electrons and atomic nuclei, are well known: it is sufficient to solve the Schrödinger equation. However, besides in some trivial cases this is a formidable numerical task.

I would like to present common approximations and numerical techniques used in solving the Schrödinger equation in the field of real materials. I will use vacancies in aluminium as an illustrative example. Aluminium has often been used as a test case for developing the computational methodology and, to some extent, it can be viewed as the "hydrogen atom" of computational materials science.


Title:        Mining Microarray Data: Predicting Gene Function from Gene Expressions and Background Knowledge -- State-of-the-art and Opportunities for High Performance Computing

Speaker:    Prof. Jan Komorowski

Time:        Tuesday, Dec. 12, 2000, at 16.15-17.00

Abstract

The majority of states in health or disease is most likely controlled by hundreds of genes.  Until recently, molecular biomedicine could study one or very few genes in parallel.  With the advent of the so-called high throughput micro-array technology it is now possible to observe the levels of activity in literally thousands of genes. At the same time, genome mapping projects such as, for instance, the Human Genome Initiative, which is an international research program for the creation of detailed genetic and physical maps of the human genome, generate enormous quantities of data.  For the human genome, there are approximately 100K genes out of which ca 5K genes are known.  The major goal of Functional Genomics is an assignment of function to genes.  State-of-the-art in Functional Genomics is the use of unsupervised learning methods.  Our multidisciplinary team has developed a supervised learning method for inducing predictive rule models for functional classification of gene expressions from microarray hybridization experiments.

In this talk I show how we have resolved some of the thorny issues in the functional classification of gene expressions.  Then, I identify potential research and application areas for High Performance Computing.

Nota bene. The talk is self-contained with respect to the knowledge of molecular biology.


Title:        Mechanics of the Heart

Speaker:    Prof. Matts Karlsson, IMT, Linköping University

Time:        Tuesday, Jan. 23, 2001, at 16.15-17.00

Place:    Room Schrödinger (E324), F-building (Fysikhuset), Campus Valla

Abstract

Non-invasive imaging is the clinical tool of the future for diagnosis of heart diseases. A unique velocity measurement technique enables us to measure 4D (3D+time) velocity fields. By applying newly developed methods in engineering mechanics and image processing we have pioneered the work on visualisation and taken the newly developed
methods into clinical practice. The trend for the next generation in diagnostic tools will be to go from qualitative to quantitative.

Thus, the work includes the possibility to extract established parameters, such as pressure differences, completely non-invasively (without inserting a pressure catheter) from the velocity data. Using a similar data acquisition technique for the velocities of the heart muscle, a 4D (3D+time) mapping of the strain and even stress can be used to describe the mechanical properties of the heart muscle.

The data sets acquired are large (>512 MB for one heart beat). Gradient estimation and computation of important parameters are difficult both due to the size of the data sets but also due to the available time - if these methods are to be used clinically, computational time is very important. Therefore, both increased computer power and faster algorithms are important for the future. In this presentation I will present the work in the group and show some examples of the current research as well as point out a few new directions for the future.


Title:        Monte Carlo modelling of the imaging chain in x-ray diagnostics

Speaker:    Dr. Alexandr Malusek and Dr. Michael Sandborg, Dept. of Radiation Physics, Linköping University

Time:        Tuesday, Jan. 30, 2001, at 16.15-17.00

Place:    Room Schrödinger (E324), F-building (Fysikhuset), Campus Valla

Abstract

X-rays are of great importance in medical imaging. Their ability to penetrate through matter makes them invaluable in examining internal structures. In the simplest approach, they behave like independent particles that are either absorbed by the patient's body or penetrate it, possibly contributing to the image detector signal. To achieve better predictions in modalities like planar X-ray imaging or computed tomography (CT) imaging, more complicated models including photon scatter, generation of secondary particles, etc. have to be considered. Knowing the details of photon interactions with matter, Monte Carlo-method models of photon-transport inside a given geometry can be created. Fortunately, photon Monte Carlo histories can be considered independent and thus a high level of parallelization of the computational task can be achieved. Thousands of CPUs can be used and cheap PC clusters available today permits a whole range of new tasks can be solved.

In this talk, two examples of an application of the Monte Carlo method in X-ray medical imaging will be presented: a model for calculating the optimal imaging parameters in planar imaging and the development of a model of a medical CT scanner. Both models have been developed at the Radiation Physics Department of the Linköping University in collaboration with scientist in London. A short overview of X-ray physics will be given and examples of its application. No special knowledge is required. Issues related to vectorization and parallelization of the code will also be discussed.


Title:    A Paradigm for Error Estimation and Adaptivity in Computational Mechanics

Speaker:    Prof. Kenneth Runesson, Dept. Solid Mechnanics, Chalmers University of Technology, Göteborg

Time:    Tuesday, Feb. 20, 2001, at 16.15-17.00

Place:    Room Schrödinger (E324), F-building (Fysikhuset), Campus Valla

Abstract

In this talk we give an overview of the basic principles behind a paradigm for a posteriori error computation in finite element analysis. An important feature is the possibility to select "goal-oriented" error measures that are of interest to the engineer (and not only to the analyst)! The chosen error measure is used as a part of the associated adaptive refinement in space or space-time in order to meet a predefined stopping criterion (tolerance). A key feature of the error computation is the identification and solution of an auxiliary problem, that is the dual of the actual (primal) problem whose solution is sought. In mechanics the dual solution is known as "influence function". In fact, the dual problem is linear(ized) even when the primal problem is nonlinear, which seems to be an attractive feature for large scale problems in computational mechanics where material and geometric nonlinearities are commonplace. Nevertheless, to compute the dual problem as efficiently as possible is a challenging task. The talk is concluded by some preliminary results concerning the application to nonlinear elasticity (error in space) and viscoplasticity (error in space-time) for simple model problems in 2D. It is conjectured how to use the suggested strategies to large scale problems.

Title:    Large Scale Aerodynamic Flow Computations on Parallel Computers

Speaker:    Dr. Per Weinerfelt, Saab Aerospace

Time:    Tuesday, March 13, 2001, at 16.15-17.00

Place:    Room Schrödinger (E324), F-building (Fysikhuset), Campus Valla

Abstract

The development of high speed parallel computers has made it possible  today to solve realistic industrial flow problems around complex 3D geometries. The talk will discuss a number of aerodynamic flow problems, their difficulties and show how these can be numerically solved using parallel computers. We will also mention the importance of large scale flow calculations to aerodynamic shape optimization and design.

Title:    Climate Modelling of the Baltic Sea

Speakers:    Dr. H.E. Markus Meier (SMHI) and Torgny Faxén (NSC)

Time:    Wednesday, April 18, 2001, at 16.15-17.00

Place:    Room Schrödinger (E324), F-building (Fysikhuset), Campus Valla

Abstract

Within the Swedish Regional Climate Modelling Programme, SWECLIM, a 3D coupled ice-ocean model for the Baltic Sea - the Rossby Centre Ocean model (RCO) - has been developed to simulate physical processes on timescales of hours to decades. The code has been developed based on the massively parallel OCCAM (Ocean Circulation Climate Advanced Modelling project in Southampton, UK) version of the widely used Bryan-Cox-Semtner model. Significant changes of the code have been done with respect to surface fluxes, open boundary conditions, mixing parameterization and sea ice modeling. An elastic-viscous-plastic ice rheology is employed resulting in a fully explicit numerical scheme that improves computational efficiency. An improved two-equation turbulence model has been embedded to simulate the seasonal cycle of surface mixed layer depths as well as deep water mixing on decadal timescale. The model has open boundaries in the northern Kattegat and is forced with realistic atmospheric fields and river runoff. Optimized computational performance and advanced algorithms to calculate processor maps make the code fast and suitable for multi-year simulations.

Selected results from key processes using two different horizontal resolutions are presented and compared to observations. The agreement between model results and observations is regarded as good. On the short time scale, the existing picture of the major inflow event in January 1993 has been completed. On the long timescale, the important question whether 3D models of the Baltic can perform correctly over decades, has been addressed. Especially, the results of the 13-year hindcast period from 1980 until 1993 are impressive as erosion of the halocline in the Baltic proper could be avoided. Hence, a tool to simulate long-term climate change and natural variability of the Baltic Sea is now available.

Computational single and parallel processor performance issues will be discussed.



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