Bratislava: Chapter 2 out of 3

How to MPI So… In order to face the segmentation fault, Katerina performed changes in the allocations .. But not only in the makefiles, but into the input files too.. And that defeated the segmenation fault. But now she should

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Finding the fireball

A legend says that there was once a warm sunny day in Scotland. I have started my quest to find out if the myth was true, but I was not the only one. A group of scientists from the UK

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Development of sample application in PyCOMPSs/COMPSs

COMPSs is a programming model and runtime that aims at parallelizing sequential applications written in sequential programming languages (Java, Python, C/C++). The paradigm used to parallelize is the data-dependence tasks: the application developer selects the parts of the code (methods, functions) that will become tasks and indicates the directionality of the arguments of the tasks. With this information, the COMPSs runtime builds a data-dependence task graph, where the concurrenty of the applications at task level is inherent. The tasks are then executed in distributed resources (nodes in a cluster or a cloud). The runtime implement other features such as data transfer between nodes or elasticity in the cloud.

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The Fast Multipole Method: A Coulomb solver for the masses

There is time for laughs and there is also time for being serious and getting things done. In this blog post I would like to summarize what I have learned about the Fast Multipole Method during this programme. This theoretical

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How to thrive at Jülich in a nutshell

If you are here because you have survived to one hard month at the JSC, A.K.A. Jail for Students of Computer Science. You should be proud, but now it is not the time for bragging, you are still at the

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All good things must come to an end

It has been a fantastic couple of weeks, but all good things must come to an end. The time has come for the preparation of the final report and the video presentation. My project has reached a satisfactory position and

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15 degrees, rain and HPC: Summer in Edinburgh (week 3)

The first and probably most important task due for our third week in Edinburgh was the Week 3 report. It’s not only about presenting our project after about two weeks of work but also updating the time schedule and preparing

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15 degrees, rain and HPC: Summer in Edinburgh (week 1)

The first week of our stay consisted of many introductions. Introductions to our site coordinator Catherine, to our project mentors Toni and Neelofer, to EPCC and King’s Buildings in general, to Edinburgh and of course to our projects. EPCC is

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Visualization tool for olfactory bulb data

A clear understanding of the spatio-temporal dynamics of olfactory bulb mitral cells in representing an odor input is very difficult to achieve experimentally; for this reason, the activity-dependent effects of olfactory bulb network self-organization generated by the mitral-granule cell microcircuits remain poorly understood. To deal with this problem, we have constructed olfactory bulb microcircuits using realistic three dimensional (3D) inputs, cell morphologies, and network connectivity.

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Exploring Mars Surface – 3D Visualization of post processed MARSIS data

MARSIS is a radar carried by the European Space Agency spacecraft Mars Express, and probing the interior of Mars to look for ice and water. To validate identification of echoes from subsurface structures, electromagnetic scattering from the Martian surface was simulated using HPC. Simulations will make it possible to use automated procedures to detect subsurface interfaces, or to study the correlation between real and simulated surface echo strengths to detect unusual surface properties.

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Interactive Manipulation of Weather Regimes during Continuous Climate Simulations

The vision for this project is to create an interactive visualisation application that demonstrate how the particular weather and climate regime that we experience here on earth is just one manifestation of infinitely many other possible regimes, and how those regimes are determined by basic physical parameters like gravity, planetary tilt, the universal gas constant, and others. This will be done through interactive simulations of the atmospheric circulation on a rotating planet whose major physical properties can be changed arbitrarily. The application user can “play God” by moving sliders on a scale on the monitor with the mouse (with a slider for each adjustable physical parameter), and then immediately see the effect of their changes by viewing the resulting flow-field. The connection between each basic parameter and the way it determines the atmospheric circulation can be immediately visualised.

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Enabling Real-Time Visualisations of Molecular Dynamics Properties in DL_POLY_4 (Proof of Concept)

This project has the goal of extending the widely used DL_POLY_4 molecular dynamics software package to enable 3D visualisations of molecular simulations in real-time, representing a significant advance for the DL_POLY code. The project will involve extending the DL_POLY_4 source code and will see the exploitation of state-of-the-art visualization toolkits.

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Optimal deflation in the linear solver for lattice QCD

The student(s) will work in the Lattice QCD group of Prof. C. Alexandrou at CaSToRC in Cyprus.The task of the student will be to optimize deflation in the open source twisted mass code tmLQCD (https://github.com/etmc/tmLQCD) for the Blue Gene architecture.The student will write an interface so the eigenvectors produced using the tmLQCD code are written and reused for further computation. The student will investigate ways to optimise reading and writing (I/O) time, e.g. using compression or reduced precision.

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Making Quarks phli further

Simulations of Lattice Quantum Chromodynamics (the theory of quarks and gluons) are used to study properties of strongly interacting matter and can, e.g., be used to calculate properties of the quark-gluon plasma, a phase of matter that existed a few milliseconds after the Big Bang (at temperatures larger than a trillion degrees Celsius). Such simulations take up a large fraction of the available supercomputing resources worldwide.

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A Fast Multipole Toolbox for GPU cluster

Modern multi- and many-core hardware architectures provide a huge amount of floating point operations (FLOPs). To harvest these FLOPs efficiently a lot of parallelism in the examined algorithm needs to be uncovered and exploited. Performance boosts are well hidden in low-level hardware features of the CPUs or GPUs. The great diversity and short life cycle of todays HPC hardware does not allow for hand-written, well-optimized assembly kernels anymore. This begs the question if we can utilize the hidden performance from high-level languages with greater abstraction possibilities like C++.

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Visualization and CPU Performance Analysis of PRACE Material Science Community Code: Siesta

Siesta is density-functional based packages for electronic-structure calculations Both codes enables the calculation of nano scale structures at the atomic level. The packages are written in Fortran and utilize MPI for parallel communication. Students have to compile and optimize each code as well as write job scripts for the scheduler. They will run some selected examples, from small molecules to large bulk systems to measure and check scalability and determine the optimal resource requirement. They will visualize input and output data with VMD as well as plot scalability graphs for performance analysis.

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Graphical interface for real time monitoring, automatic event detection, and alert triggering in HPC parallel software

Large HPC physics simulations can create local signs of failure or success long before a global signature is observed. If these signs go unnoticed valuable computer resources could be spared. We have created a system that monitors software in real time looking for predefined signatures of problems. When one is detected, the software can create a fast automatic rendering of the problem area and send an alert to the user, who can evaluate the seriousness of the issue and decide whether to cancel the computation early.

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Collaborative interface for in-situ visualization and steering of HPC molecular dynamics simulations

HPC software tends to work in batch modes, where simulations are submitted to supercomputer queues, and results are collected and analyzed only after they have finished computing. We are developing an infrastructure for real time visualization, analysis, and steering of HPC code. In particular we are focusing on PELE, an efficient molecular dynamics simulation software. The architecture is: PELE runs on HPC hardware while connected to a server that preprocesses data and streams 3D renderings of the molecules to a GUI, where the end user can tweak simulation parameters which are then sent in real time to PELE. The interface we are developing includes state-of-the-art interaction design and is prepared to run on many platforms (including touch, motion, and voice input), and can be used simultaneously and collaboratively through many devices. The summer project will be dedicated to implementing one feature of the end GUI.

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Using open source CFD (OpenFOAM) for turbulence modelling of different wall-bounded flow regimes

Development of the high performance computers (HPC) has made possible conducting numerical simulation of fluid flow of practical interest. Turbulent separated bluff body flows are of great importance for the CFD community. Many turbulence models are developed to properly capture, with some success, the mechanisms found in the flow separation behind a bluff body.
This project aims in testing the ability of the current turbulence models found in the open source CFD (OpenFOAM) for high Reynolds number flows. Unsteady Reynolds Navier-Stokes (URANS) approach will be used for modelling the turbulent separated flows. The work will be done using the HPC resources offered at ULFS. Also, visualization of the results will be carried using ParaView.

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Parallel boundary point method

Semidefinite programming problems are optimization problems where we look for a symmetric matrix that satisfies certain set of linear equations, is positive semi definite (has all eigenvalues non-negative) and yields maximum value of given linear objective function (see e.g. http://en.wikipedia.org/wiki/Semidefinite_programming) .

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Visualization and GPU Performance Analysis of PRACE Material Science Community Code: Quantum Espresso

Quantum Espresso is density-functional based packages for electronic-structure calculations Both codes enables the calculation of nano scale structures at the atomic level. The packages are written in Fortran and utilize MPI for parallel communication. Students have to compile and optimize each code as well as write job scripts for the scheduler. They will run some selected examples, from small molecules to large bulk systems to measure and check scalability and determine the optimal resource requirement. They will visualize input and output data with VMD as well as plot scalability graphs for performance analysis.

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Medical image segmentation and visualization

Project will focus on rapid prototyping and testing of different algorithms for image segmentation as well as visualization of 3D data. In a first stage implementation and testing of suitable image segmentation techniques for medical image segmentation will be done. As an input data for image segmentation the consecutive series of CT or MRI medical images will be used. After the segmentation visualization of the obtained 3D data will be performed.

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ESPRESO API for ParaView Catalyst to perform In situ Analysis

The main goal of this project is to develop a workflow for parallel “In situ” analysis using ESPRESO solver and ParaView Catalyst. During the stay the student will cooperate directly with developers of the ESPRESO library to implement the API for ‘”In situ” visualization of the transient finite element analysis using ParaView Catalyst.

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Modelling of Wi-Fi signal propagation using the boundary element method

The main goal of this project is to develop a workflow for parallel modelling of the Wi-Fi signal propagation in buildings using the boundary element method (BEM). For this purpose the student will use the parallel boundary element software BEM4I developed at IT4Innovations National Supercomputing Centre.

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Implementing MPI parallelisation in a the Fluctuating Finite Element Analysis (FFEA) tool

FFEA uses a continuum mechanics description of soft macromolecules and is specifically designed to take advantage of emerging low resolution experimental data, such as protein structural maps from the Electron Microscopy Data Base. The model is a Finite Element algorithm which has been generalised to include thermal fluctuations, enabling the simulation of large protein complexes within their cellular environment, and therefore provides acces to the elusive mesoscale regime between 10 and 500nm that is too computationally expensive for atomistic molecular dynamics, but too small for conventional macroscopic simulation techniques to be applicable.

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