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Virtual Research Communities

Computational Chemistry VRC

Overview

Computational chemistry and material science is one of the highlighted research areas in computational science and a typical heavy user of HPC resources. The computational technologies are an indispensable tool for investigations in domains like quantum molecular dynamics, molecular modelling, nano-technology and design of new materials. Considering the size of the problems to be studied, the required calculations are extremely computationally intensive. Thus HPC would greatly facilitate the proposed work allowing the researchers to deal not only with “pilot” or model systems but to work on big and complicated real systems, which are physically and technologically more significant and challenging. These studies will extend understanding of some fundamental science issues and are of practical importance for pharmaceutical industry, nanotechnology, biomedicine, and many others.

Initially Computational Chemistry VRC supports 7 applications with main developers in 6 SEE countries, collaborating with scientists from more than 20 advanced research centers in Europe.

Computational Chemistry Applications

Acronym Application Name Main developer Stage
CFDOF CFD Analysis of Combustion Faculty of Mech. Engineering, University of Banja Luka (UoBL), Bosnia - Herzegovina testing 09.2011
CompChem Quantum Mechanical, Molecular Mechanics, and Molecular Dynamics computation in chemistry Univeristy of Belgrade, Faculty of Chemistry, Republic of Serbia production 09.2011
FMD-PA Design of fullerene and metal-diothiolene-based materials for photonic applications Computational Chemistry Group of NHRF, Greece production 08.2011
HC-MD-QM-CS Hybrid Classical/Quantum Molecular Dynamics – Quantum Mechanical Computer Simulation of Condensed Phases UKIM, Institute of Chemistry, Faculty of Natural Science and Mathematics, FYROM production 08.2011
ISyMAB Integrated System for Modeling and data Analysis of complex Biomolecules IFIN-HH/DPETI, Romania beta 09.2011
MDCisplatin Molecular Design of Platinum Group Metal Complexes as Potential Non-classical Cisplatin Analogues Acad. Roumen Tsanev Institute of Molecular Biology-BAS, Bulgaria beta 09.2011
PCACIC Principal component analysis of the conformational interconversions in large-ring cyclodextrins IOCCP-BAS, Bulgaria production 08.2011


Computational Physics VRC

Overview

Computational Physics is nowadays the main beneficiary of the scientific HPC, large-scale numerical computations being necessary whenever the complexity of the physical systems investigated does not allow the derivation of an analytical solution. The main objective of the Computational Physics VRC is to join together the various physics research teams from the SEE area and to provide them access to a powerful HPC infrastructure and tools which will make possible their participation in multidisciplinary and international collaborations. For this purpose, software developers from 7 countries (Albania, Bosnia and Herzegovina, Bulgaria, FYR of Macedonia, Republic of Moldova, Romania, Serbia) contributed with 12 applications in the fields of High Energy and Particle Physics, Plasma Physics, Physics of Condensed Matter, Atomic Physics, and Computational Fluid Dynamics. The application range extends from nanoelectronics, micro-devices optimization and the modeling of robotic devices for biomedicine, to improved means for feature detection in satellite images, which leads to better mapping, localization and search services.

Computational Physics Applications

Acronym Application Name Main developer Stage
AMR_PAR Parallel algorithm and program for the solving of continuum mechanics equations using Adaptive Mesh Refinement Institute of Mathematics and Computer Science, Laboratory of Mathematical Modelling, Republic of Moldova production 09.2011
EagleEye Feature Extraction from Satellite Images Using a Hybrid Computing Architecture University Politehnica of Bucharest / Computer Science and Engineering, Romania production 08.2011
FAMAD Fractal Algorithms for MAss Distribution Institute for Space Sciences, Romania testing 07.2011
FuzzyCmeans Parallel Fuzzy C Means for classification/Feature detection category West University of Timisoara/Computer Science Department, Romania production 08.2011
GENETATOMICS Genetic algorithms in atomic collisions Institute of Physics, Faculty of Natural Science and Mathematics, UKIM, FYROM production 09.2011
GIM Geophysical Inversion Modeling Polytechnic University of Tirana, Albania testing 05.2011
HAG High energy physics Algorithms on GPU Institute for Space Sciences, Romania testing 09.2011
HMLQCD Hadron Masses from Lattice QCD University of Tirana, Albania production 07.2011
NUQG Numerical study of ultra-cold quantum gases Scientific Computing Laboratory, Institute of Physics Belgrade, Serbia production 08.2011
SET Simulation of electron transport Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, Bulgaria production 08.2011
SFHG Self Avoiding Hamiltonian Walk on Gaskets Faculty of Mechanical Engineering, Dept. of Thermomechanics, University of Banja Luka, Bosnia and Herzegovina 2012
SIMPLE-TS_2D Finite Volume Method for calculation of 2D gas-microflows using standard MPI Kiril Stoyanov Shterev and Stefan Kanchev Stefanov, Institute of Mechanics – BAS / Department of “Complex and multiphase Flows”, Bulgaria production 08.2011


Life Sciences VRC

Overview

Life Sciences depend heavily on the use of HPC for both data mining and data integration as well as for the simulation of biological systems. HPC technologies are essential for research areas such genome analysis, expression profiling, -omics analysis and biological simulations, whereby a vast amount of experimental data needs to be analyzed and synthesized into reasonable hypothesis. Thus HPC would greatly facilitate the various applications described in this project, enabling the respective research teams to study questions that have thus far been intractable due to their high computational complexity. The use of HPC in the Life Sciences applications with help further our understanding of basic problems in the fields of DNA sequence analysis, comparative genomics, and brain modeling among others and can be of great importance for the health sector.

The Life Sciences VRC supports 7 applications with main developers in 5 SEE countries (Greece, Hungary, Montenegro, Armenia, Georgia) working in the areas of computational biology, computational biophysics, DNA sequence analysis and computational genomics. The various projects involve collaborations with numerous scientists both in Europe and the U.S. and will foster the development of new collaborations among the participant SEE countries.

Life Sciences Applications

Acronym Application Name Main developer Stage
CMSLTM Computational Models of Short and Long Term Memory George Kastellakis, IMBB-FORTH, Greece production 09.2011
DeepAligner Deep sequencing for short fragment alignment Windisch Gergely, Márton Judit,Obuda University (OU), John von Neumann Faculty of Informatics, Biotech Group, Hungary production 02.2012
DiseaseGene In-silico Disease Gene Mapper Windisch Gergely, MártonJudit, Obuda University (OU), John von Neumann Faculty of Informatics, Biotech Group, Hungary deployable 02.2012
DNAMA DNA Multicore Analysis School of Computer & Communication Sciences, Laboratory for Computational Biology and Bioinformatics, RAxML software, Montenegro production 11.2011
MDSCS Molecular Dynamics Study of Complex systems Dr. Armen Poghosyan, Dr. Hrachya Astsatryan, National Academy of Sciences of the Republic of Armenia production 07.2011
miRs Searching for novel miRNA genes and their targets Anastasis Oulas, IMBB/FORTH, Greece production 05.2011
MSBP Modeling of some biochemical processes with the purpose of realization of their thin and purposeful synthesis Jumber Kereselidze, Tbilisi State University Department of Natural Science, Georgia testing 08.2011

User Guidelines

Getting Access to HP-SEE Infrastructure

Porting Support

Supporting Tools

Developer Guidelines

HPC programming techniques

Code programming and optimization

Architecture-specific optimization

Setting up the software environment

Choice and usage of libraries and application tools

Compiler-level optimization

Using development tools

Input/Output methodologies

Usage of job submission systems

Scalability testing and optimization

Benchmarking

HPC Infrastructure Operations

HPC Centers

Core Services

Monitoring Tools

Network Operations

Software Stack and Technology Watch

Dissemination and Training

HPC Initiatives, Procurement and Organization Guidelines

National HPC task-force modeling and organizational guidelines

Templates

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