Scientific Software Development at Democritos

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1 Scientific Software Development at Democritos Paolo Giannozzi Democritos National Simulation Center & Scuola Normale Superiore di Pisa July 12, 2005 Typeset by FoilTEX

2 What is Democritos? Democritos (Democritos Modeling Center for Research in Atomistic Simulations) is a National Laboratory of Italian INFM (National Institute for the Physics of Matter) Democritos is based at SISSA Trieste; researchers from various Universities are also associated with Democritos Democritos activities: Research in Atomistic Simulations of materials Hardware and Software tools for computation Educational and Outreach

Italian INFM (National Institute for the Physics of Matter) Democritos is based at SISSA Trieste;

3 Research areas at Democritos Materials modeling at the nano-scale Computer modeling of bio-molecular systems Quantum fluids in confined geometries Theory and simulation of strongly correlated and disordered systems Information technology for molecular modeling and computation

confined geometries Theory and simulation of strongly correlated and

4 Reduced ceria s urfaces Ce 3+ Ce 4+ Ce 3+ d [email protected]

5 Methane to Methanol pathway on Rh(111)

6 Neutral surface evolved for 1.6 ps Surface with ex cess electron evolved for 2.4 ps Additional dangling OH

7 Information Technology at Democritos: activity lines Software for Atomistic Simulations The Quantum-ESPRESSO distribution: electronic structure calculations using plane waves and pseudopotentials with density-functional theory DLPROTEIN: Classical Molecular Dynamics simulations XCrysDen: Graphical Tool for Molecular Modeling Cluster Computing / Grid Computing OpenMosix development, testing, benchmarking Design and implementation of beowulf clusters for high-performance scientific computing

Classical Molecular Dynamics simulations XCrysDen: Graphical Tool for Molecular Modeling Cluster Computing / Grid Computing

8 Scientific Software at Democritos: goals Provide software tools for the wide range of research topics performed at Democritos Provide high-quality scientific software under a free (open-source) license to the entire scientific community (not only for specialists) Maintain and improve the current expertise in scientific software that characterises Democritos researchers, in view of new algorithmic and methodological developments

entire scientific community (not only for specialists) Maintain and improve the current expertise in

9 Scientific Software at Democritos: goals (2) More technical goals: Provide a framework for easy testing and addition of new developments Provide a collaborative framework in which everybody can contribute to/benefit from new developments Needed: Good programming practice, documentation, tools for distributed programming Free/Open-Source License

which everybody can contribute to/benefit from new developments Needed: Good

10 Democritos and Software License Most Democritos software is released under the terms of the GNU (Gnu s Not Unix) General Public License (GPL). Basically: The source code is available. You can do whatever you want with the sources, but if you distribute any derived work, you have to distribute under the GPL the sources of the derived work. Advantages: Everybody including commercial entities can contribute. Nobody can steal the code and give nothing back to the community.

You can do whatever you want with the sources, but if you distribute any derived work, you have to distribute under

11 The Quantum-ESPRESSO distribution The Quantum-ESPRESSO (Open-Source Package for Research in Electronic Structure, Simulation, and Optimization) distribution contains three main packages: PWscf (Trieste, Lausanne): self-consistent electronic structure, structural relaxation, dynamics, linear-response CP (Lausanne, Princeton): variable-cell Car-Parrinello molecular dynamics with ultrasoft pseudopotentials FPMD (Bologna, Trieste): variable-cell Car-Parrinello molecular dynamics The three packages share a common installation method, input format, pseudopotential format, data output format, parts of basic code

linear-response CP (Lausanne, Princeton): variable-cell Car-Parrinello molecular dynamics with ultrasoft pseudopotentials FPMD (Bologna, Trieste):

12 The Quantum-ESPRESSO distribution (2) A Graphical User Interface and a pseudopotential generation code are a part of the distribution Highly portable codes, effective and well tested parallel algorithms, mostly written in Fortran-90 The distribution is maintained as a single CVS (Concurrent Version System) tree. Available to everyone anytime via anonymous (read-only) access. web site:

written in Fortran-90 The distribution is maintained as a single CVS (Concurrent Version System) tree.

13 Quantum-ESPRESSO outreach Collaborations: CINECA, Bologna MIT, Dept. of Materials Science and Engineering Princeton University University of Minnesota (VLAB Project) Targacept Tutorials held: Trieste, January 2003 (with ICTP) Bologna, March 2004 (with CINECA) Beijing, July 2004 (with ICTP and ICTS) Esfahan (April 2005), (with ICTP and ISMO IUT) Next: Cagliari (September 2005), Bengalore (december 2006)

Targacept Tutorials held: Trieste, January 2003 (with ICTP) Bologna, March 2004 (with CINECA)

14 Perspectives and future developments Straightforward: better documentation better-structured code new algorithmic and methodological developments More difficult but most important: interoperability with other packages (pseudopotentials, data exchange, etc) inclusion of more packages used by the Democritos community into a larger and more diverse software repository

most important: interoperability with other packages (pseudopotentials, data exchange, etc)

15 Ads 11/ 07/ 05 2

16 Classical MD: DLPROTEIN- 2: Pack ge to create an d sim u late (MD) biom olecu les: p rotein s starting p oin t: DL_POLYL from Daresbu ry Labs Develop ed by S. Melch ion n a + S.Coz z in i Rep licated Dat a p arallelism Object based ap p roach u sin g F90/ 95 Cu rren t version : 2.1r2 Top ology Bu ild er Utilities DLP ROTEIN PACKA GE M.D. Engine http :/ / cm / DLPROTEIN 11/ 07/ 05 1

Coz z in i Rep licated Dat a p arallelism Object based ap p roach u sin g F90/ 95 Cu rren t version

17 Dlprotein: The good : Ton s of d ifferen t MD- en sem bles good an d u n d er con trol MD en gin e No black box syn d rom e A p ackage to easily m od ify and im p lem ent your own p iece of software Fu lly op en - sou rce The bad : Scalabilit y cou ld be an issu e Perform an ce cou ld be p oor with resp ect to black box p ackages (Am ber et c.) 11/ 07/ 05 3

p iece of software Fu lly op en - sou rce The bad : Scalabilit y cou ld be an issu e

18 XCrysDen in action (from

19 XCrysDen in action (2)

20 Credits D. Alfe, F. Antoniella, G. Ballabio, S. Baroni, M. Boero, N. Bonini, C. Bungaro, R. Car, C. Cavazzoni, P. Cazzato, D. Ceresoli, G. Cipriani, M. Cococcioni, I. Dabo, A. Dal Corso, A. Debernardi, G. Deinzer, O. Dieguez, S. Fabris, R. Gebauer, S. de Gironcoli, M. Hilgeman, Y. Kanai, A. Kohlmeyer, A. Kokalj, K. Kudin, M. Lazzeri, K. Maeder, N. Marzari, F. Mauri, N. Mounet, A. Mosca Conte, A. Pasquarello, P. Pavone, M. Profeta, G. Roma, Manu, C. Sbraccia, A. Smogunov, K. Stokbro, P. Thibaudeau, A. Tilocca, P. Umari, R. Wentzcovitch, Y. Wu, X. Wang, S. Zilberman

Kanai, A. Kohlmeyer, A. Kokalj, K. Kudin, M. Lazzeri, K. Maeder, N. Marzari, F. Mauri, N. Mounet, A. Mosca Conte, A. Pasquarello, P. Pavone, M.

The Quantum ESPRESSO Software Distribution

The Quantum ESPRESSO Software Distribution The DEMOCRITOS center of Italian INFM is dedicated to atomistic simulations of materials, with a strong emphasis on the development of high-quality scientific