Opportunities for CyberInfrastructure at the Cornell Nanoscale Facility

1. Opportunities for CyberInfrastructure at the Cornell Nanoscale Facility Garnet Kin-Lic Chan Department of Chemistry and Chemical Biology Cornell University

2. Who I am • Modeling at the Cornell Nanoscale Facility • Opportunities for CyberInfrastructure for Nanoscale modeling • Software Infrastructure • Random ideas about the Web

3. Conjugated Polymers Who am I? • Ab-initio Quantum Chemistry / Electronic Structure theory • Method development for large systems • Renormalization Group methods for multi-scale phenomena • Ab-initio DMRG, Canonical Transformation Theory • Correlated materials problems • Conjugated Polymers, Surface chemistry • Quantum transport in nanoscale structures • User of CCMR and CNF modeling facilities Low-temperature Kondo regime in Metal complexes

4. The Cornell Center for Materials Research and the Cornell Nanoscale Facility • Experimental facilities are not data-intensive • Primary use of computing/cyberinfrastructure is materials modeling • Secondary use is for social aspects e.g. education / communication / documentation

5. Cornell Nanoscale Modeling FacilityThe National Nanostructure Infrastructure Network (http://www.nnin.org) • Computational mission of CNF: Develop modeling resources that complement and expand on the current experimental capabilities. • Development of new computing clusters. • Acquisition of commercial software packages. • Construction of new codes to address user needs. • Expansion and distribution of localized programs to user network. • Web based access – truly remote research Main Computation Nodes Cornell Harvard Stanford University of Texas, Austin University of Michigan Courtesy Derek Stewart

6. Computational Resources available across the country • Computing Power • Cornell Nanoscale Facility • 48 node dual processor Xeon (3.06 GHz) cluster • 16 AMD 64 bit Opteron workstations • Harvard University • 48 node dual processor Xeon (3.06 GHz) cluster • 4 4-way 32 GB Opterons from Sun Microsystems (coming soon!) • University of Texas, Austin • Access to 600 processor Xeon cluster • 224 (1.3 GHz) Power4 processor cluster • Stanford and University of Michigan (resources coming soon!) Duffield Hall

7. A Platform for more than just computation… Services to encourage collaboration and enhance existing tools. • Web based discussion groups that allow new users to learn from existing users. • A conduit for codes developed by localized groups to reach a larger audience (beta testing, optimizing, streamlining) • Creation of input file libraries for different programs

8. How can we use CI for the CNF’s mission? • Develop modeling resources that complement and expand on the current experimental capabilities. • Services to encourage collaboration and enhance existing tools • Software infrastructure • Web-based initiatives

9. Software infrastructure for nanoscale modeling • Multiscale • Inhomogeneous • Neither periodic nor isolated • Multiple energy scales • Electronic, vibrational, electromagnetic • Fundamental algorithms, but also enabling software infrastructure • Interoperable components

10. Interoperabilitiy • Many levels of theory • Each level has multiple algorithms implemented in different packages • Continuum models • Force-field • Tinker, NAMD, Moldy etc. • Kinetic Monte Carlo • Density Functional Theory • ABINIT, SIESTA, PWSCF, DFT++ • Ab-initio quantum chemistry • Gaussian, QCHEM, GAMESS, MOLPRO • Any successful multiscale method cannot adopt a monolithic approach but must reuse components • Scientific issues: different choice of basis • Computer science issues: e.g. conversion of formats

11. Where can we look? • Software industry • CORBA, DCOM, SOAP, XML, RPC • Standard interfaces e.g. BLAS, LAPACK • But - cultural challenges • Scientific modeling companies are notoriously competitive • No motivation for academic scientists • Deciding on an implementation is not enough: it has to be implemented (and free).

12. Example 1: OpenBabel • http://openbabel.sourceforge.net/ • “Open Babel is a community-driven scientific project including both cross-platform programs and a developer library designed to support molecular modeling, chemistry, and many related areas, including interconversion of file formats and data.” • Over 70 different formats • babel [OPTIONS] [-iinput-type] infile [-ooutput-type] outfile • Butonly for structural and geometric information • For true multiscale modeling, require more sophisticated conversion e.g. wavefunctions, orbitals, density matrices, potentials • Data-intensive e.g. many-particle wavefunctions

13. Example 2: EMSL Gaussian Basis Set Order Form (PNNL) • http://www.emsl.pnl.gov/forms/basisform.html • Standardised repository for basis sets for quantum chemistry calculations • Produces outputs for essentially every QC package • Used by 100% of quantum chemists

14. Issues • Where is the boundary between CyberInfrastructure and traditional materials modeling algorithm development?

15. The Web • Web-based frontends (“enhancing existing tools”) • e.g. WebMO frontend to Gaussian / GAMESS • http://www.webmo.net/ • Users draw structures in browser, submit to remote server, used successfully e.g. in Cornell CHEM765 • Essentially Web-mail as opposed to mail-client • Convenient, but really necessary?

16. Social networking (“collaboration”) • The thing of the moment: Flickr, MySpace, Facebook • Set up Facebook for Nanoscale scientists • “Experts” database • But cultural barriers • Virtual conferences? • Useful – but NSF funding?

17. Wikis (“collaboration”) • Accessible web-pages, anyone can edit simply by clicking and typing • Used in my lab for announcements, electronic workbooks, research notes, paper repository • Highly recommended! • Several people have made suggestions already e.g. for material specific wikis

18. Issues: Global vs specific • To what extent should we create specialized sites with a restricted user community? • To what extent should we control the content? • Many of the revolutionary aspects of cyberinfrastructure revolve around a truly global community • E.g. Google – one place to search, do not search by categories as in early engines • Wikipedia, one stop place for all information • Should we make an official contribution to these sites rather than set up our own?