CLARA - HPC cluster
About the CLARA project
High-performance computing system CLARA@UNIBA.SK (CLustered Academic Research Appliance) is one of the latest additions to the portfolio of services of the Centre of Information Technologies (CIT CU). It is provided in the SAaOS form (Software As an Optimised Service) since January 15, 2020, for research teams across the Comenius University. The cluster is prepared for theoretical-chemical and theoretical-physical computing, utilizing massive parallelized matrix operations, often used in chemistry, pharmacy and biology.
The CLARA system consists of interconnected clustered computing nodes, system and application package. It was implemented, configured and optimized for permanent high load operation and computing power by professionals at CIT CU in late 2019. With its relatively low energy consumption, CLARA also meets the standards of green computing.
Basic technical information - CLARA@UK
| Manufacturer | Supermicro |
|---|---|
| Hardware | SYSF619P2-RT/ X11DPFR |
| CPU type | 2xCPU – Intel Xeon Silver 4216 |
| CPU parameters | 2.1GHz, 16C/32T, AVX-512 FMA |
| Interconnectivity | 56G InfiniBand + 2x10G Ethernet |
| Number of modules (dimensional factor 4U) | 1 |
| Number of computing nodes | 8 |
| Number of CPU sockets | 16 |
| Number of interconnecting devices InfiniBand | 1 |
| Current configuration round-up | 256 cCPU, RAM 2,5TB, SDD 38TB |
| Current installed computing power for Double Precision aritmethic | 8 TFLOPS |
| Current energy consumption | <2kW |
| Installed system software | CentOS 7.4, Sun Grid Engine SGE v.8.1, Open MPI v.2.1, gcc / gfortran v.4.8 |
| Optimized mathematical libraries | OpenBLAS v.0.3.8, ATLAS v.3.10.3 LAPACK v.3.9.0 |
Key quantitative usage parameters - March 15, 2020
| Parameter | Value | Units |
|---|---|---|
| users total | 32 | researchers |
| number of finished tasks | 4622 | pcs |
| average task duration | 13325 | seconds |
| "virtual" CPU** time total | 4637 | days |
| number of I/O operations (read/write bytes) | 40,7 | PB |
| **=reduction to 1 physical core, how long would the computing process take | ||
| APPLICATIONS | Number of tasks | % |
| DIRAC | 637 | 14 |
| GAUSSIAN | 2576 | 56 |
| Open MOLCAS | 1200 | 26 |
| NWCHEM | 32 | 1 |
| SCHRODINGER | 177 | 4 |
| CFOUR | ||
| GROMACS | ||
| MRCC |
Research projects with top usage of computing resources CLARA@UK
Lead researcher: Doc. Pavel Neogrády, DrSc.
Research project: Referenčné výpočty vlastností, interakcií a reaktivity chemických systémov.
Field of research: Theoretical and Computational Chemistry
Lead researcher: Prof. Ivan Černušák, DrSc.
Research project: Eurofusion WPHCD-2020-ENR Computational modelling of Cs-Mo and impurities interactions in NBI sources
Field of research: Materials chemistry / Dissertation - Mgr. Silvia Kozáková
Lead researcher: Prof. Ivan Černušák, DrSc. a Dr. Florent Louis (Univ. Lille)
Research project: Chemical reactivity of halogens in troposphere (bilateral cooperation CU and UL)
Field of research: Atmospheric Chemistry
Lead researcher: Florent Louis (Associate Professor)
Participants : Florent Louis (Associate Professor), Sonia Taamalli (Research Engineer), Zainab Srour (Master 2 student in Atmospheric Environment)
Address : PhysicoChimie des Processus de Combustion et de l’Atmosphère (PC2A), UMR CNRS/Université de Lille 8522, Université de Lille, Bât. C11, 59655 Villeneuve d’Ascq, France
Research project: Atmospheric chemistry of halogenated species
Field of research: Computational Chemistry
Lead researcher: Dr. Michal Májek
Research project: Project PECaN (H2020) – Photo-electro catalysis: new paradigm in organic molecule activation. Computing of photochemical and electrochemical properties of organic compounds and study of their reactivity utilizing DFT methods.
Field of research: Organic Chemistry, Organic Photochemistry and Electrochemistry
Lead researcher: Doc. Ing. Vladimir Frecer, DrSc.
Research project: APVV-17-0239 Computer-aided design, synthesis, activity-testing and disposition of inhibitors of neuraminidases of influenza A virus as potential antiviral compounds
Field of research: Molecular Modeling and Antimicrobial Agent Design
Lead researcher: Doc. Ing. Vladimir Frecer, DrSc.
Research project: VEGA 1/0228/17 Research of antimicrobial compounds and their effects on model cellular membranes
Field of research: Molecular Modeling and Anti-viral Agent Design
Lead researcher: Doc. Ing. Vladimir Frecer, DrSc.
Research project: Modeling of structure-function relationships of mutant proteins of patients with genetic degeneration of retina
Field of research: Rigorous thesis, Mgr. Adam Hotra, PhD.
Lead researcher: Doc. Ing. Vladimir Frecer, DrSc.
Research project: QSAR and research of antimicrobial peptidomimetics
Field of research: Rigorous thesis, Mgr. Peter Polonec
Lead researcher: Doc. Ing. Vladimir Frecer, DrSc.
Research project: QSAR and design of new antiviral compounds
Field of research: Master's theses Michal Talapka
Lead researcher: RNDr. Lukas Felix Pasteka PhD.
Research project: Theoretical spectroscopy of selected molecules and their suitability for laser
Field of research: Dissertation, Andrej Hurajt
Lead researcher: prof. RNDr. Miroslav Urban, DrSc.
Research project: CCSD(T) benchmarks for DFT modeling of covalent and dispersion interactions in polyethylene cross-linked by metal atoms
Field of research: Materials Chemistry
Lead researcher: Radovan Šebesta; other researchers: Mgr. Patrícia Čmelová (doctoral student)
Research project: Hybrid peptide – tiourea catalysts (topic within project APVV-18-0242, Asymmetric multicatalysis for effective synthesis of chiral carbocyclic and heterocyclic compounds)
Field of research: Organic chemistry (asymmetric calatysis)
Lead researcher: Radovan Šebesta; other researchers: Mgr. Dominika Krištofíková (doctoral student)
Research project: Stereoselective domino reactions with mechanical activation (topic within project VEGA 1/0332/19, Mechanochemistry – a tool for effective asymmetric catalysis)
Field of research: Organic chemistry (asymmetric calatysis)
Extent of utilization of cluster resources - 24 hours
