Projects 2013

Dušan Fedorčák Czech Republic Visualization of air pollution models using volumetric rendering Tomas Karasek Czech Republic Visualization of large data sets from CFD simulations using OpenFoam and Paraview Mads Kristensen Denmark Accelerate routines within the CCSM4 project using GP-GPU Mads

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Material Science

This is a joint proposal which has three mentors. The project is for two students (either undergraduates or postgraduates). Students will become acquainted with user friendly HPC tools: profiler, grid middleware (ARC), visualization tools (VMD, VirtualGL/TurboVNC) as well as one application from the PRACE community code repository: Quantum Espresso or Siesta.

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Timeline Profiling

The use of Python in HPC is increasing as many programmers start to realise that they need not write their entire software stack in a traditional high performance language like C or Fortran. Instead, the high-level control constructs are written in Python and the computationally intensive parts of the code are pushed down into a compiled language.

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Multi-Platform Parallel Code Coverage

CP2K ( is a widely-used program for atomistic simulation using a wide range of methods including Forcefields, Density Functional Theory, Hybrid DFT-Hartree-Fock, and post-HF. It is a large code base, extending to over 800,000 lines of Fortran 95, is open-source (GPL) and has an active community of around 15 developers spread across Europe. The code can be compiled for a range of architectures including GNU/Linux, IBM BlueGene, Intel, can be built either as a serial executable, or use MPI and/or OpenMP for parallelisation and key computational kernels have CUDA implementations for use on GPGPU systems.

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Looking Inside a Crystal Liquid Display

Liquid crystals, as their name suggests, both flow like a liquid and have regular 1D- or 2D-ordering like a crystal. It is the regular ordering which gives them interesting optical properties, and makes them useful in many common consumer electronic devices. Looking at the structure of this crystal ordering is therefore of great interest in itself.

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Dinosaur Racing

This project focuses on visualisation used in the configuration and/or representation of a dinosaur simulation. The simulation will run on HECToR, the UK’s national supercomputing service (hosted by EPCC)

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Bioflow in Coronary Arteries

The aim of this project is the modelling of blood flow within coronary artery and visualization the large data set with Paraview – an open source visualization tool. This project will have two students.

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Task Based Parallelization

The project will consist of the analysis of the potential parallelism of an application with Tareador, its porting to the OmpSs programming model and performance analysis and fine tuning with performances tools.

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Facial Attribute Classifiers

The automatic categorization of a person’s demographic information such as gender, age, or ethnicity represents an invaluable asset for both market analysis and video surveillance. On the one hand, it facilitates accurate real-time statistics about observed market segments in a shop, and makes it possible to dynamically select and display advertisements based on the customer type. On the other hand, labelling all detected faces in a surveilled scene would enable refined search, retrieval and visualization capabilities for surveillance applications.

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Universal Access Layer Reader

Upgrades of the VisIt Universal Access Layer reader plugin Location: University of Ljubljana, Faculty of mechanical engineering (ULFME), Ljubljana, Slovenia Project Abstract: This project is about programming in C++ with XSLT code generation. The aim is to extend existing program (UAL database reader

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Wind Loading on a Solar Tracker

Wind Loading on a Solar Tracker Location: University of Ljubljana, Faculty of mechanical engineering (ULFME), Ljubljana, Slovenia Project Abstract: Solar trackers are usually singly supported slender constructions with large platform on which solar cells for production of electricity are mounted. Sun tracker structure

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Scientific Workflows

This project is about programming in Java. The aim is to extend existing program (actor) running under Kepler workflow engine to be able to control visualizations with VisIt.

Kepler provides graphical user interface (GUI) for describing information flow between computing units called “actors”. An actor can be encapsulated code submitted to HPC/GRID or, in our case, VisIt visualization tool. VisIt provides a session configuration that can facilitate visualization with applied data operators, window positions, ranges, labelling, etc, to be stored/restored for reuse.

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Electronic Structure of C60

Numerical calculations of electronic structure of materials are an important tool in various fields of condensed matter physics, materials science, and engineering. Today’s supercomputers allow accurate ab initio simulations of systems consisting of several thousands of atoms. One of the most successful computational frameworks in electronic structure calculations is Density Functional Theory (DFT). First-principles simulations within DFT are a major consumer of supercomputing resources in many computing centres.

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Electron-Phonon Coupling

Organic semiconductors are materials of great current research interest due to their low production cost and suitability for electronic and optoelectronic devices such as solar cells, light-emitting diodes and transistors. To understand the performance of these devices one needs to understand how electrical current flows in these materials. Particles that carry the current are electrons which throughout their motion in the material interact with atomic vibrations – phonons. Therefore, understanding the strength of electron-phonon interaction is crucial for understanding the material properties.

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Simulations of Plasma Turbulence

Within the present project, we propose to visualise the results of a study of turbulence and magnetic reconnection in space plasmas to the full dimensional 3D-3V phase space configuration.

Numerical simulations are focused in particular on the analysis of the role of kinetic processes at play in the turbulent cascade in the solar wind, its relationship with explosive magnetic reconnection events and the evolution of the distribution of particle velocities.

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Visualising OpenFOAM Models

The use of HPC resources is allowing for finer resolutions in CFD simulations, which, in turn, produce larger and larger datasets. Such datasets cannot be easily visualised on desktop workstations and in numerous cases, cannot be visualised on the machines they were produced on. This is a memory issue.

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Hybrid Molecular Dynamics

The DL POLY application has been parallelised using a domain decomposition approach, employing the Message Passing Interface (MPI) library for inter-process communication. More recently, the code has been“hybridised” to exploit multi-core shared memory architectures as well as Graphics Processing Units. The existing parallel implementation of DL POLY is highly efficient and scales well to many thousands of CPU cores.

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K-Means Clustering in Astrophysics

Particle-In-Cell (PIC) models have gained widespread use in astrophysics as a means to understand detailed plasma dynamics, particularly in collisionless plasmas, where non-linear instabilities can play a crucial role for launching plasma waves and accelerating particles. PIC models employ often hundreds of billions of computational ‘particles’ to represent the astrophysical plasma, for example electrons, ions and photons.

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Accelerate Routines in CCSM4

The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth’s past, present, and future climate states. In order to improve the simulations, the resolution and complexity of the model is constantly increased, which in turn increases the computational demand of the model.

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Visualisation of CFD

The aim of this project is to address an issue with visualization of large data sets which are results of CFD simulations on HPC systems.
This project will use CFD simulation performed on HPC system using open source code OpenFOAM and visualize results using another open source code Paraview.

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Air Pollution Models

This project addresses an issue of visualizing results of a new air pollution model which is under development at our university. We expect that simulations of air pollution models will be very large and hardware demanding, and therefore, the usage of HPC capabilities will be necessary.

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