Abstract
The increasing availability of computer power on Grid platforms has promoted the implementation of complex computational codes on distributed systems, while development of appropriate visual interfaces, tools and portals has minimized the skills necessary to carry out massive Grid calculations. In the present work we analyse the procedures adopted to implement on the Italian Grid Infrastructure (IGI) some computational science codes making use of the IGI web portal. The considered applications of interest for the members of the Chemistry, Molecular and Materials Sciences and Technologies community are VENUS (chemical dynamics for classical trajectory simulations), CRYSTAL (ab initio quantum chemistry for calculations on crystals, slabs and polymers) and Quantum Espresso (electronic structure and materials modeling at the nanoscale).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Chemistry, Molecular & Materials Science and Technology (CMMST) community, https://wiki.egi.eu/wiki/Towards_a_CMMST_VRC (last seen February 2014)
IGI (Italian Grid Infrastructure), http://www.italiangrid.it/ (last seen February 2014)
COMPCHEM VO website, https://www3.compchem.unipg.it/compchem/ (last seen February 2014)
IGI MoU, https://www.italiangrid.it/sites/default/files/ (last seen February 2014)
EGI-Inspired project, http://www.egi.eu/about/egi-inspire/ (last seen February 2014)
European Grid Infrastructure, http://www.egi.eu (last seen February 2014)
gLite website, http://glite.web.cern.ch/glite (last seen February 2014)
European Middleware Initiative, http://www.eu-emi.eu (last seen February 2014)
Gervasi, O., Laganà, A.: SIMBEX: a portal for the a priori simulation of crossed beam experiments.. Future Gener. Comput. Syst. 20(5), 703–716 (2004)
Costantini, A., Manuali, C., Faginas Lago, N., Rampino, S., Laganà, A.: COMPCHEM: progress towards GEMS a Grid Empowered Molecular Simulator and beyond. Journal of Grid Computing 8(4), 571–586 (2010)
Hase, W.L., et al.: VENUS96: A general chemical dynamics computer program. QCPE Bull. 16, 671 (1996)
Dovesi, R., Saunders, V.R., Roetti, C., Orlando, R., Zicovich-Wilson, C.M., Pascale, F., Civalleri, B., Doll, K., Harrison, N.M., Bush, I.J., D’Arco, P., Llunell, M., Causá, M., Noël, Y.: CRYSTAL 2014 User’s Manual. University of Torino, Torino (2014)
Giannozzi, P., Baroni, S., Bonini, N., Calandra, M., Car, R., Cavazzoni, C., Ceresoli, D., Chiarotti, G.L., Cococcioni, M., Dabo, I., Dal Corso, A., de Gironcoli, S., Fabris, S., Fratesi, G., Gebauer, R., Gerstmann, U., Gougoussis, C., Kokalj, A., Lazzeri, M., Martin-Samos, L., Marzari, N., Mauri, F., Mazzarello, R., Paolini, S., Pasquarello, A., Paulatto, L., Sbraccia, C., Scandolo, S., Sclauzero, G., Seitsonen, A.P., Smogunov, A., Umari, P., Wentzcovitch, R.M.: Quantum espresso: a modular and open-source software project for quantum simulations of materials. Journal of Physics: Condensed Matter 21(39), 395502 (19pp) (2009)
Liferay technology, http://www.liferay.com (last seen February 2014)
JSR 286 reference, http://www.jcp.org/en/jsr/detail?id=286 (last seen February 2013)
Thain, D., Tannenbaum, T., Livny, M.: Condor and the Grid. In: Berman, F., Fox, G., Hey, T. (eds.) Grid Computing: Making the Global Infrastructure a Reality. John Wiley & Sons Inc. (2002)
Tsaregorodtsev, A., Bargiotti, M., Brook, N., Ramo, A.C., Castellani, G., Charpentier, P., Cio, C., Closier, J., Graciani, R., Kuznetsov, G., Li, Y.Y., Nandakumar, R., Paterson, S., Santinelli, R., Smith, A.C., Miguelez, M.S., Gomez, S.: DIRAC: a community Grid solution. Journal of Physics 119, 062048 (2008)
Kim, K., Jordan, K.D.: Comparison of Density Functional and MP2 Calculations on the Water Monomer and Dimer. J. Phys. Chem. 98(40), 410089–410094 (1994)
Stephens, P.J., Devlin, F., Chabalowski, C.F., Frisch, M.J.: Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem. 98(45), 11623–11627 (1994)
Sipos, G., Kacsuk, P.: Multi-Grid, Multi-User Workflows in the P-GRADE Portal. Journal of Grid Computing 3, 221–238 (2005)
Alfieri, R., Arezzini, S., Barone, G., Becciani, U., Bencivenni, M., Boccia, D., Bottalico, V., Carracciuolo, L., Cesini, D., Ciampa, A., Costantini, A., Cozzini, S., Pietri, R., Drudi, M., Ghiselli, A., Mazzoni, E., Ottani, S., Venturini, A., Veronesi, P.: The HPC Testbed of the Italian Grid Infrastructure. In: Proceedings of 21st Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, vol. 3, pp. 241–248 (2013)
OSG website, http://www.opensciencegrid.org/ (last seen February 2014)
XSEDE website, https://www.xsede.org/home (last seen February 2014)
Academia Sinica website, https://www.sinica.edu.tw/main_e.shtml (last seen February 2014)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer International Publishing Switzerland
About this paper
Cite this paper
Costantini, A. et al. (2014). On the Implementation of Three Popular Computational Chemistry Applications Using the EGI Distributed Computing Infrastructure. In: Murgante, B., et al. Computational Science and Its Applications – ICCSA 2014. ICCSA 2014. Lecture Notes in Computer Science, vol 8579. Springer, Cham. https://doi.org/10.1007/978-3-319-09144-0_41
Download citation
DOI: https://doi.org/10.1007/978-3-319-09144-0_41
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-09143-3
Online ISBN: 978-3-319-09144-0
eBook Packages: Computer ScienceComputer Science (R0)