Name: KCSE Science Day
Start: 2012-11-21T10:00:00+01:00
End: 2012-11-21T15:00:00+01:00
Location: No location set

KCSE Science Day

Wednesday, 21 November 2012 - 10:00

Monday, 19 November 2012
Tuesday, 20 November 2012
Wednesday, 21 November 2012
09:30 Welcome - Erwin Laure (PDC-HPC) Michael Hanke
Welcome
- Erwin Laure (PDC-HPC)
- Michael Hanke
09:30 - 09:40
09:40 Scaling Dalton, a molecular electronic structure program - Xavi Aguilar
Scaling Dalton, a molecular electronic structure program
- Xavi Aguilar
09:40 - 10:00
Dalton is a molecular electronic structure program used for quantum mechanics (QM) and quantum mechanics/ molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties, having a large world-wide user community (over 2000 licenses issued). In this work, we present an extensive characterization and performance optimization of Dalton that increases its scalability and parallel efficiency.
10:00 A new high order method for the accurate simulation of incompressible wall-bounded flows - Peter Lenaers
A new high order method for the accurate simulation of incompressible wall-bounded flows
- Peter Lenaers
10:00 - 10:20
The aim of the project is to develop an efficient high-order method for Direct Numerical Simulations and Large Eddy Simulations of wall-bounded incompressible flows with accurate fulfillment of the divergence-free condition. One of the main issues when numerically solving the Navier– Stokes equations is the absence of an evolution equation for the pressure. Over the years several methods have been developed to deal with this, among the most popular are writing the equations in vorticity-velocity form, and predictor-corrector methods like the pressure correction or fractional step method. In the former method the pressure is eliminated by taking the curl of the momentum equations, while in the latter method a Poisson equation for the pressure is derived by taking the divergence of the momentum equations. But in wall-bounded domains unclarity still remains about the choice of boundary conditions for the pressure. Most implementations of the pressure correction method use a staggered mesh which removes the need to solve for the pressure at the boundary, but it also can filter high frequencies in unintended ways and complicates implementation. Kleiser and Schumann developed the influence matrix method which calculates the boundary conditions for the pressure which ensure that the discrete diver- gence is numerically zero in the whole field. They used Fourier collocation in the stream- and spanwise direction and a Chebyshev-Tau method in wall-normal direction. We extend their method to include the use of compact finite differences on a collocated grid in wall-normal direction. Compact finite difference schemes have better resolution characteristics than the standard finite difference schemes, while maintaining flexibility in the choice of grid spacing and boundary conditions. The resulting Poisson equation for the pressure contains a full matrix in the left- hand side which is numerically expensive to solve. To lower the computational cost and memory requirements, we introduce a new method to solve the Poisson equation which replaces solving the second order full system by solving two first order banded equations. In summary, our method allows the solution of the incompressible Navier–Stokes equations with exactly zero divergence on collocated meshes, in a fully banded formulation.
10:20 Coffee
Coffee
10:20 - 10:40
10:40 An algorithm for efficient evaluation of two-electron repulsion integrals over contracted Gaussian-type basis functions - Rosal Sandberg
An algorithm for efficient evaluation of two-electron repulsion integrals over contracted Gaussian-type basis functions
- Rosal Sandberg
10:40 - 11:00
A new algorithm for the evaluation of two-electron repulsion integrals optimized for high contraction degrees is derived. Both the segmented and general contraction versions of the algorithm show significant theoretical performance gains over the asymptotically fastest algorithms published in the literature so far. A preliminary implementation of the algorithm shows good agreement with the theoretical results and demonstrates substantial average speed-ups in the evaluation of two-electron repulsion integrals over commonly used basis sets with varying degrees of contraction with respect to a mature, highly optimized quantum chemical code.
11:00 Keynote: History and Development of MPI: the Message-Passing Interface - Jesper Träff (Technical University of Vienna)
Keynote: History and Development of MPI: the Message-Passing Interface
- Jesper Träff (Technical University of Vienna)
11:00 - 12:00
MPI, the Message-Passing Interface, has, for better or worse, for a considerable number of years been the de facto programming interface for large scale scientific computing. In this talk we will examine some of the reasons why this has happened, focusing on some of the salient features of the MPI standard that has contributed to its usefulness and longevity. The talk will do so by also looking into the long and perhaps not so well-known history of the development of MPI, will and conclude with an outlook on the recently announced MPI 3.0 version of the standard.
12:00 Lunch
Lunch
12:00 - 13:30
13:30 High performance adaptive finite element methods - Niclas Jansson
High performance adaptive finite element methods
- Niclas Jansson
13:30 - 13:50
The massive computational cost for resolving all turbulent scales makes a direct numerical simulation of the underlying Navier-Stokes equations impossible in most engineering applications. This work concerns the development of an adaptive finite element method that enables efficient computation of time resolved approximations for complex geometries with error control. We present efficient data structures and data decomposition methods for distributed unstructured tetrahedral meshes. Our work also concerns an efficient parallelization of local mesh refinement methods such as recursive longest edge bisection, and the development of an a priori predictive dynamic load balancing method, based on a weighted dual graph.We also address the challenges of emerging supercomputer architectures with the development of new hybrid parallel programming models, combining traditional message passing with lightweight one-sided communication. Our implementation has proven to be both general and efficient, scaling up to more than 12k cores.
13:50 Keynote: Parallel Computing - From 1757 until 2020 and beyond - Thomas Ludwig (DKRZ)
Keynote: Parallel Computing - From 1757 until 2020 and beyond
- Thomas Ludwig (DKRZ)
13:50 - 14:50
High performance computing is an enabling factor for gaining of knowledge and insight in modern sciences. However, even 250 years ago mathematicians were confronted with the fact that a single computer was not powerful enough to complete complex calculations in acceptable time. The talk will give historical details about the history of parallel computing from the times of the Enlightenment until now. It will explain techniques and application fields and we will discuss the future of parallel computing.
14:50 Coffee
Coffee
14:50 - 15:10
15:10 Efficient spike communication in the MUSIC multi-simulation framework - Ekaterina Brocke
Efficient spike communication in the MUSIC multi-simulation framework
- Ekaterina Brocke
15:10 - 15:30
MUSIC is a standard API and software library allowing large- scale neuronal network simulators, or other applications, to exchange data within a parallel computer during runtime. In this talk we will show how the efficiency of point-to-point and collective communication algorithms depends on the topology of the connectivity between the applications. We will present benchmark results comparing the scaling of the two communication algorithms on high number of tasks, and will discuss challenges regarding scheduling of communication in MUSIC.
15:30 Parallelized calculation of vibrationally-resolved electronic spectra with DynaVib software - Guangjun Tian
Parallelized calculation of vibrationally-resolved electronic spectra with DynaVib software
- Guangjun Tian
15:30 - 15:50
Vibrationally resolved electronic spectra can be simulated by calculating the overlap integrals of the vibrational wave functions of initial and final states. This method works fine with small molecules. However, it could be very time consuming for large molecule and high-performance computing is necessary. We have developed a software called DynaVib to calculate the vibrationally-resolved electronic spectra of polyatomic molecules. The parallelization of the code is achieved using OpenMP and MPI. The software can be used to study the optical absorption and emission spectra, photoelectron spectra, X- ray absorption spectra, etc.
15:50 Conclusions - Erwin Laure (PDC-HPC) Michael Hanke
Conclusions
- Erwin Laure (PDC-HPC)
- Michael Hanke
15:50 - 16:10