HP-SEE Wiki
From HP-SEE Wiki
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=== Core Services === | === Core Services === | ||
* [http://hpseewiki.ipb.ac.rs/index.php/Resource_management_system Resource management system] | * [http://hpseewiki.ipb.ac.rs/index.php/Resource_management_system Resource management system] | ||
+ | * [http://hpseewiki.ipb.ac.rs/index.php/LDAP HP-SEE central LDAP] | ||
=== Monitoring Tools === | === Monitoring Tools === |
Revision as of 14:37, 30 March 2012
Upcoming Events
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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
- Porting between 32 and 64 bit addressing
- Adapting code to network topology
- Adapting code to memory architecture
- Porting between different processor architectures
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
- Resource centre BG
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Core Services
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Software Stack and Technology Watch
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Dissemination and Training
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