Metadata Management in the MoSGrid Science Gateway - Evaluation and the Expansion of Quantum Chemistry Support

Science gateways are employed to hide increasingly complex IT infrastructures from users via easy-to-use graphical interfaces while enabling IT-driven research not possible before. The science gateway MoSGrid (Molecular Simulation Grid) is a valuable and user-friendly workbench to submit and process molecular simulation studies on a large scale. With regard to the needs of the users, we focus on the interoperability of simulations using two prominent quantum chemical codes, Gaussian09 and NWChem. At a first glimpse, the definition of functionals and basis sets seems to be sufficient to evoke the same type of calculation in both codes using the quantum chemical workflows in MoSGrid. In more detail, this is not true and more aspects such as integration grids, convergence criteria and basis set dimensions have to be well defined in order to obtain a trustworthy comparability between quantum chemical codes. In previous work, these details have not been defined and included in the MSML (Molecular Simulation Markup Language) implementation within MoSGrid. After the investigation presented here, all these details can be integrated to extend the quantum chemical workflows in MoSGrid. Furthermore, a performance evaluation of the underlying metadata management is performed to investigate its suitability and scalability to the MSML extension.

[1]  Sonja Herres-Pawlis,et al.  Geometrical and optical benchmarking of copper guanidine–quinoline complexes: Insights from TD‐DFT and many‐body perturbation theory† , 2014, J. Comput. Chem..

[2]  Giovanni Scalmani,et al.  Gaussian 09W, revision A. 02 , 2009 .

[3]  Richard Grunzke,et al.  Architectural Implications for Exascale based on Big Data Workflow Requirements , 2014, High Performance Computing Workshop.

[4]  Thomas Steinke,et al.  Standards‐based metadata management for molecular simulations , 2014, Concurr. Comput. Pract. Exp..

[5]  Ugo Becciani,et al.  Science gateway technologies for the astrophysics community , 2015, Concurr. Comput. Pract. Exp..

[6]  Péter Kacsuk,et al.  Remote Storage Resource Management in WS-PGRADE/gUSE , 2014, Science Gateways for Distributed Computing Infrastructures.

[7]  Stefan Markov The Globus Striped GridFTP Framework and Server , 2006 .

[8]  Thomas Steinke,et al.  A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics , 2012, Journal of Grid Computing.

[9]  Ugo Becciani,et al.  VisIVO Gateway and VisIVO Mobile for the Astrophysics Community , 2014, Science Gateways for Distributed Computing Infrastructures.

[10]  Alexander Hoffmann,et al.  Hiking on the potential energy surface of a functional tyrosinase model--implications of singlet, broken-symmetry and triplet description. , 2014, Chemical communications.

[11]  Edward I. Solomon,et al.  Computational inorganic and bioinorganic chemistry , 2009 .

[12]  John Shalf,et al.  The International Exascale Software Project roadmap , 2011, Int. J. High Perform. Comput. Appl..

[13]  André Brinkmann,et al.  Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway , 2012, HealthGrid.

[14]  Alexander Hoffmann,et al.  Geometrical and optical benchmarking of copper(II) guanidine–quinoline complexes: Insights from TD‐DFT and many‐body perturbation theory (part II) , 2014, J. Comput. Chem..

[15]  Henry S. Rzepa,et al.  Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles , 1999, J. Chem. Inf. Comput. Sci..

[16]  Li Tian,et al.  Copper active sites in biology. , 2014, Chemical reviews.

[17]  Tjerk P. Straatsma,et al.  NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations , 2010, Comput. Phys. Commun..

[18]  Richard Grunzke,et al.  Managing Complexity in Distributed Data Life Cycles Enhancing Scientific Discovery , 2015, 2015 IEEE 11th International Conference on e-Science.

[19]  Extreme Science and Engineering Discovery Environment: Gateway to Discovery, XSEDE13, San Diego, CA, USA - July 22 - 25, 2013 , 2013, XSEDE.

[20]  Gábor Terstyánszky,et al.  Parameter Sweep Workflows for Modelling Carbohydrate Recognition , 2010, Journal of Grid Computing.

[21]  Ákos Balaskó Workflow Concept of WS-PGRADE/gUSE , 2014, Science Gateways for Distributed Computing Infrastructures.

[22]  Dirk Habich,et al.  Towards an Industry Data Gateway: An Integrated Platform for the Analysis of Wind Turbine Data , 2015, 2015 7th International Workshop on Science Gateways.

[23]  Miklós Kozlovszky,et al.  DCI Bridge: Executing WS-PGRADE Workflows in Distributed Computing Infrastructures , 2014, Science Gateways for Distributed Computing Infrastructures.

[24]  G. Scuseria,et al.  Climbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solids. , 2003, Physical review letters.

[25]  Ugo Becciani,et al.  An Innovative Science Gateway for the Cherenkov Telescope Array , 2015, Journal of Grid Computing.

[26]  Richard Grunzke,et al.  Expansion of Quantum Chemical Metadata for Workflows in the MoSGrid Science Gateway , 2014, 2014 6th International Workshop on Science Gateways.

[27]  Heinz Decker,et al.  Copper-O2 reactivity of tyrosinase models towards external monophenolic substrates: molecular mechanism and comparison with the enzyme. , 2011, Chemical Society reviews.

[28]  F. Weigend,et al.  Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. , 2005, Physical chemistry chemical physics : PCCP.

[29]  Björn Hagemeier,et al.  UNICORE 6 — Recent and Future Advancements , 2010, Ann. des Télécommunications.

[30]  Mohammad Mahdi Jaghoori,et al.  WS-PGRADE/gUSE-Based Science Gateways in Teaching , 2014, Science Gateways for Distributed Computing Infrastructures.

[31]  Thomas Steinke,et al.  The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations. , 2014, Journal of chemical theory and computation.

[32]  Richard Grunzke,et al.  Insights into the influence of dispersion correction in the theoretical treatment of guanidine‐quinoline copper(I) complexes , 2014, J. Comput. Chem..

[33]  Tibor Gottdank Introduction to the WS-PGRADE/gUSE Science Gateway Framework , 2014, Science Gateways for Distributed Computing Infrastructures.

[34]  M. Orio,et al.  Density functional theory , 2009, Photosynthesis Research.

[35]  Miklós Kozlovszky,et al.  WS-PGRADE/gUSE Generic DCI Gateway Framework for a Large Variety of User Communities , 2012, Journal of Grid Computing.

[36]  Pter Kacsuk,et al.  Science Gateways for Distributed Computing Infrastructures , 2014, Springer International Publishing.

[37]  Péter Kacsuk,et al.  Data Avenue: Remote Storage Resource Management in WS-PGRADE/gUSE , 2014, 2014 6th International Workshop on Science Gateways.

[38]  Mihai V. Putz,et al.  Applications of Density Functional Theory to Biological and Bioinorganic Chemistry , 2013 .

[39]  William E. Allcock,et al.  The Globus Striped GridFTP Framework and Server , 2005, ACM/IEEE SC 2005 Conference (SC'05).

[40]  Antoine H. C. van Kampen,et al.  A Grid-Enabled Gateway for Biomedical Data Analysis , 2012, Journal of Grid Computing.

[41]  Richard Grunzke,et al.  Molecular Simulation Grid (MosGrid): A Science Gateway Tailored to the Molecular Simulation Community , 2014, Science Gateways for Distributed Computing Infrastructures.

[42]  Richard Grunzke,et al.  Towards Generic Metadata Management in Distributed Science Gateway Infrastructures , 2014, 2014 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing.

[43]  Sonja Herres-Pawlis,et al.  Bis‐μ‐oxo and μ‐η2:η2‐peroxo dicopper complexes studied within (time‐dependent) density‐functional and many‐body perturbation theory , 2013, J. Comput. Chem..

[44]  Otis Gospodnetic,et al.  Lucene in Action, Second Edition: Covers Apache Lucene 3.0 , 2010 .

[45]  Richard Grunzke,et al.  Orbital analysis of Oxo and Peroxo Dicopper Complexes via Quantum Chemical Workflows in MoSGrid , 2013, IWSG.