Bozic, S.

Kondov, I.

Meded, V.

Wenzel, W.

English

KITopen

Multiscale Materials Modelling  on High Performance Computer Architectures The project MMM@HPC is funded by the 7th Framework Programme of the European Commission within the Research Infrastructures with grant agreement number RI-261594. Multiscale simulations of complex materials basing on UNICORE workflows Stefan Bozic Ivan Kondov, Velimir Meded and Wolfgang Wenzel Karlsruhe Institute of Technology, Germany Outline  The Challenges  Project MMM@HPC overview  Approach based on UNICORE middleware  GridBeans  Workflows  Data flow management and Licensing Issues  OpenMOLGrid as Application Wrapper  Proof of Principle: Simulation of Organic Light Emitting Diodes (OLEDs)  Live Demo  Conclusions and outlook  29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 2 The challenges 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 3 Reusability Data complexity Solution for licensing issues Security & Reliability Capacity & Capability  Integration on different size and time scales to address real-life problems in nano-materials science  Develop an easy to use solution for non- experts: industrial and experimental groups MMM@HPC project overview 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 4 www.multiscale-modelling.eu  HPC centres: CINECA, CSC, KIT and KIST (Korea)  Modelling and code developing groups: University Mons, CEA, CSC, STFC, University Patras, KIT  Industrial partners and users: CEA, SONY, KIT, project MINOTOR  Cooperating projects: PRACE, MINOTOR, D-Grid and NGI-DE Can we meet these challenges? 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 5 • GridBeans • UNICORE Workflows Reusability • Chemical Mark-up Language (CML) • OpenMolGRID Data complexity • UNICORE: UVOS/SAML/VOMS • Open Source Licenses Solution for licensing issues • UNICORE • Grid Security Infrastructure (GSI) Security & Reliability • High Performance Computing (PRACE) • Distributed resources (D-Grid, EGI) Capacity & Capability YES! What is UNICORE?  UNICORE: UNiform Interface to COmputing Resources  Grid computing technology (grid middleware) supported by EMI  Seamless, secure, and intuitive access to distributed grid resources  Used in daily production at several supercomputer centres worldwide  Open source under BSD license   Implements standards from the Open Grid Forum (OGF) 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 6 A. Streit et al., UNICORE 6 - Recent and Future Advancements Annals of Telecommunications 65 (11-12), 757-762 (2010) . UNICORE three-layer architecture 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 7 http://www.unicore.eu/unicore/architecture.php UNICORE  Client UNICORE Services UNICORE  System Integration Concept: UNICORE 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 8 Application Protocols → Workflows UNICORE Client Application interfaces → GridBeans UNICORE Services UNICORE System  Provision of simulation tools and services that can be combined in many different application workflows  Adaptable, reusable and extendable interfaces & workflows based on UNICORE  Access to distributed HPC/HTC resources via UNICORE services Application interfaces: GridBeans 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 9  Provides a way to use scientific application on HPC resources (even by non experts)  Designed to decouple scientific applications from the underlying (changing) grid protocols (UNICORE, Globus, Portals)  Different simulation workflows can re-use the same GridBean  Different GridBeans can be employed for the same workflow step R. Ratering et al., "GridBeans: Support e-Science and Grid Applications", Proceedings of the Second IEEE International Conference on e-Science and Grid Computing (e-Science'06), p. 45, IEEE 2006 The GUI of DEPOSIT GridBean developed in MMM@HPC UNICORE Client layer UNICORE Rich Client and Workflows 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 10 UNICORE Rich Client Workflow DEPOSIT GridBean GUI Embedded visualisation with Jmol Control flow: Example 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 11 Data Flow: Example 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 12 OLED: Simulation protocol 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 13 continuum model (FEA) coarse-grained model (CG) Atomistic model (MM) QM model (QM) Elmer ToFeT (KMC) DEPOSIT MOPAC FEAP End-bridging MC LAMMPS TURBOMOLE Transporter DL_POLY BigDFT molecular scale electronic scale  macroscopic scale ~ 10-10 m ~ 10-6 m ~ 10-8 m Workflow  Film deposition (or MD)  Generate disordered film morphologies  QM calculations of hopping sites  Calculate HOMO, LUMO, LUMO+1 etc energies.    Electronic couplings reorganization energies  Calculate charge hopping rates  Kinetic Monte Carlo (KMC)  Calculate charge  (electron-hole) mobility  Calculate current density  OLED: charge transport in Alq3 disordered films Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 14 J. J. Kwiatkowski, J. Nelson, H. Li,  J. L. Bredas, W. Wenzel, and C. Lennartz, Phys. Chem. Chem. Phys., 2008, 10, 1852–1858. 29/02/2012 Realization: GridBeans and Workflow Reused GridBeans:  MOPAC  Gaussian  Amber Newly developed GridBeans:  DEPOSIT  TURBOMOLE  OpenBabel  PairFinder 29/02/2012 15 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 Kondov, I. et al., UNICORE-Based Integrated Application Services for Multiscale Materials Modelling , In: Romberg, M. et al. (Eds.) „UNICORE Summit 2011 Proceedings, 7–8 July 2011, Torun, Poland“, IAS Series, vol. 9 (2011), pp. 1-10, FZJ Jülich. Data exchange and licensing issues  Chemical Markup Language (CML)  Data flow management with the OpenMolGRID library  S. Sild et al., LNCS 3470, 464, Springer (2005);  S. Sild et al., J. Chem. Inf. Model., 46, 953 (2006).  Read, write and convert chemical file format  Provides a data model   Application Wrapper  Further data models are being evaluated  MEMOPS (UML based) R. Fogh et al., J. Integr. Bioinf. 7, 123 (2010).  License management  OpenSource and Commercial applications in simulations  VOMS with UNICORE (UVOS and SAML) is being evaluated 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 16 Application Wrapper: OpenMOLGrid 29/02/2012 17 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 Application Wrapper Lifecycle 1. Preprocessing: Validation of App. Parameter, Generation of App. specific Input Files 2. Execution: Run App(s) in seperate Process(es), Monitoring of stdout/stderr (allows interaction with the application) 3. Postprocessing: Error Handling, Parsing App Output, Creation of Workflow Data Current OLED workflow 29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 18 MOPAC GridBean DEPOSIT GridBean Pairfinder GridBean PairwiseQM GridBean BABEL GridBean  CML CML PDB CML CML Pair Pair Pair Reduction GridBean Edge Edge Edge CML CML Edge 1 Molecule n Molecules MM: Film depostion QM: Geometry Optimization CG: Compute Charge mobility MM: Determination of Site pairs QM: Pairwise QM calculations J (eV), DE (eV) FEA: Calculate Current Density Simulation protocol UNICORE Workflow Demonstration 29/02/2012 19 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 Demo Conclusions and Outlook  With UNICORE we provide an optimal low-effort/low-cost solution for multiscale modelling  GridBeans → App Interfaces  Workflows → Simulation protocol  Data Exchange in WFs between applications handled with CML and OpenMOLGrid  Proof of Principle: Workflow for simulation of OLEDs  Current work  Integration of the CG and FEA steps into the OLED workflow  Elmer, DL_POLY and BigDFT GridBeans  Simulation of whole OLED devices  Deployment and test operation of the workflow  MMM@HPC Development Kit (Virtual Box)    29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 20 Acknowledgments  All consortium partners in MMM@HPC  Funding from the EC      Partner projects, supporting infrastructures and software  29/02/2012 Stefan Bozic – ISGC, Academia Sinica Taipei, February 29, 2012 21 

Multiscale simulations of complex materials basing on UNICORE workflows

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Multiscale simulations of complex materials basing on UNICORE workflows

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