Scientific Software Development at Democritos

Scientific Software Development at Democritos

Paolo Giannozzi

Democritos National Simulation Center & Scuola Normale Superiore di Pisa

July 12, 2005

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

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

d eGir o n co li@s is s a .it

Re d u c e d c e ria s u rfac e s

Ce

Ce

Neutral surface evolved for 1.6 ps Surface with ex cess electron evolved for 2.4 ps

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

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

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

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.

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

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.

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)

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

11/ 07/ 05 2

11/ 07/ 05 1

Cl assi cal MD: DLPROTEIN- 2:

Pa ck ge t o cr e a t e a n d

s im u la t e (MD)

b io m o le cu les : p r o t e in s

s t a r t in g p o in t :

DL_POLY

L

L

fr o m Da r e s b u r y La b s

De ve lo p e d b y S.

Melch ion n a + S.Co z z in i

Re p lica t e d Da t a

p a r a lle lis m

Ob je ct b a s ed a p p r o a ch

u s in g F9 0 / 9 5

Cu r r e n t ve r s io n : 2 .1 r 2

To p o lo gy

Bu ild e r

Ut ilit ie s

M.D.

“En gin e”

DLP

L

L ROTEIN

PACKA

K

K GE

11/ 07/ 05 3

Dl p r ot ei n :

Th e good :

To n s o f d iffe r en t MD- e n s e m b le s

“go o d a n d u n d er co n t r o l” MD e n gin e

No “b la ck b o x” s yn d r om e

A p ack age t o eas ily m od ify an d im p lem en t you r own p iece of s oft war e

Fu lly o p e n - s o u r ce

Th e b ad :

Sca la b ilit y cou ld b e a n is s u e

Pe r fo r m a n ce co u ld b e p o o r wit h r e s p e ct t o “b la ck b o x”

p a ck a ges (Am b er et c.)

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