February 2006
International Cyberinfrastructure: Activities Around the Globe
Peter Arzberger, University of California, San Diego
Philip Papadopoulos, San Diego Supercomputer Center and University of California, San Diego

Collaborative Science-driven Teams

PRAGMA brings multidisciplinary, multi-institutional teams together, driven by application needs. In addition to the computational chemistry application described above, another team of researchers from the US, Japan, China, and Singapore, integrated a protein annotation pipeline (iGAP 19) developed at UCSD, a distributed file system (Gfarm 20) developed at the National Institute for Advanced Industrial Science and Technology (AIST), and a metascheduler (CSF) being extended by researchers at Jilin University in China to schedule iGAP testing 21. This software/middleware synthesis effort has led to improvements of Gfarm. In particular, the metadata server design is changed to meet the requirements of high throughput file creation and registration. Automatic replication of data and deployment of applications to remote sites become fully supported for most common architectures 7. Finally, a successful annotation of the bacteria, Burkholderia mallei, a known bioterrorism agent, has been conducted with this infrastructure and the PRAGMA testbed (the annotation will be publicly available pending publication of analysis results).

A final example integrates expertise of IPv6 networking at the Cybermedia Center of Osaka University, remote control of a microscope at UCSD, and use of a computational grid to build tomographic reconstructions of subcellular structures, and the development of visualization modules from the National Center of High-performance Computing (NCHC), to provide an enhanced suite of tools for researchers to use 22. Not only did the team benefit, but each group did as well. UCSD researchers were able to better access the machine in Japan and distributed compute resources at the three sites. Osaka researchers were able to control the machines and make codes available to their users, and NCHC colleagues were able to take the concept and knowledge of remote control of a microscope and retarget the application to that of sensors in the environment, creating EcoGrid 23 in Taiwan.

Each of these international science and technology teams has shared technology and experience to significantly enhance their research agendas. The structure of PRAGMA, with its culture of openness to new ideas and technologies coupled with a recurring series of focused workshops24, provided the essential glue for these teams. Each of these accomplishments has resulted in ongoing collaborations that now span years.

Routine Use Grids

These and other examples 7 have driven the use of PRAGMA’s evolving grass-root grid testbed. The overall goal of the PRAGMA testbed is to provide a stable platform to allow these and other application/middleware codes to be tested, and to understand how to make applications run on a routine basis without the superhuman efforts that many of these examples currently require.

The current testbed consists of resources and participants from 19 institutions from five continents and 13 countries. It is an instantiation of a useful, interoperable, and consistently available grid system that is neither dedicated to the needs of a single science domain nor funded by a single national agency. This testbed is heterogeneous in equipment and connectivity (bandwidth as well as persistence) between machines, reflecting both funding realities and the future global cyber-infrastructure.

The testbed has been grown using a minimum set of requirements. The initial software stack comprised of Globus plus local scheduling software. Additional middleware is added based on the needs of the applications. For example, a remote procedure call middleware, Ninf-G developed at AIST, became part of the testbed since it was required by two applications being used in PRAGMA: one is a time dependent density functional theory calculation; the other a Quantum Mechanical / Molecular Dynamics (QM/MD) code 7.

These routine use experiments have produced results through strong feedback between application and middleware developers. Codes have had to be improved to operate in a network environment where connections fail, in particular to be more fault tolerant. The testbed development is being driven by many application areas, allowing examination of different requirements. In addition, a richer monitoring set (SCMSWeb)25 developed at Kasetsart University and accounting tools (MOGAS) 26 of the Nanyang Technological University were introduced to the testbed.

PRAGMA has demonstrated that these grids can be very useful to improve codes and to conduct meaningful and otherwise unachievable science.

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Reference this article
Arzberger, P., Papadopoulos, P. "PRAGMA: Example of Grass-Roots Grid Promoting Collaborative e-Science Teams," CTWatch Quarterly, Volume 2, Number 1, February 2006. http://www.ctwatch.org/quarterly/articles/2006/02/pragma-example-of-grass-roots-grid-promoting-collaborative-e-science-teams/

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