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

Multiway Software Dissemination

As software is tested in these real-world environments and used in multiple applications, ways of disseminating software is needed. In the case of Ninf-G, we have successfully developed a procedure that allowed it to be integrated into the US NMI software stack for version 8 and subsequent releases. This was the first instance of a non-US code being introduced into that stack. Another dissemination vehicle we are using is the Rocks Rolls mechanism (i.e. RPM packages configured for automatic (re)deployment to Rocks-based clusters). PRAGMA partners also released codes with changes, and Rocks was localized by the partners at the Korea Institute for Science and Technology Information (KISTI) to allow for easier access and use by the Korean Grid community 27. And with broader dissemination comes broader use. In one case this led to a set of standards proposed in GGF for remote procedure calls 28.

Finally, as the broader community produces new codes or standards, PRAGMA will adopt them. Examples include the CA from Naregi29 or the PMA lead by AIST, which then are used by the broader PRAGMA community.

Building a Community

PRAGMA itself focuses on a grass roots approach in an effort to enable new communities to form and assemble expertise not available at any single institution Some global issues require the ability to rapidly form international teams. Responses to epidemics such as SARS (PRAGMA played a crucial role in helping to pull together an international team to aid Taiwan in their efforts to combat the disease) 30 and emerging threats like Avian Flu often require teams to assemble in hours or days. Other groups with a small set of geographically dispersed experts simply do not have the personnel resources to independently build a complete cyberinfrastructure. In this model, PRAGMA has played a leading role in catalyzing GLEON31, the Global Lake Ecological Observatory Network, a grassroots network of limnologists, information technology experts, and engineers with a common goal of building a scalable, persistent network of lake ecology observatories. Data from these observatories will help this community to better understand key processes such as the effects of climate and land use change on lake function, the role of episodic events such as typhoons in resetting lake dynamics, and carbon cycling within lakes. These teams are, by nature and expertise, international in scope.

We have built a community by focusing on concrete projects to build trust and on an on-going series of semi-annual working meetings. The meetings rotate among PRAGMA member sites to engage a broader group of researchers at each site and to allow the PRAGMA community to appreciate its members’ cultural richness.

Students are an essential component of the PRAGMA community. Pacific Rim Undergraduate Experiences (PRIME)32 provides UCSD undergraduate students summer research experiences at four PRAGMA sites; Osaka, Monash, NCHC, and the Computer Network Information Center of the Chinese Academy of Sciences (CNIC). The students conduct research and contribute to the infrastructure. Further, they have helped expand the collaborations between scientists at the institutions. In addition, the Japanese government has awarded Osaka University funds to create Pacific Rim International UniverSities (PRIUS), a program designed to improve education for graduate students interested in grid technology by supporting a series of activities, including exchanges. Both PRIME and PRIUS build on and enhance the PRAGMA community and would not exist without PRAGMA.

Final Comments

PRAGMA is both a multifaceted organization and an experiment. It is open to institutions who wish to actively participate in projects and contribute and share resources, middleware, applications and expertise with other members. The value of the structure is that it allows for transfer of technology among institutions, allowing in some cases for rapid start ups by acquiring technology, and in other cases for user feedback on technologies that have been developed. The structure also allows for a transfer of technologies between disciplines where, for example, control of an instrument is being moved from neuroscience and a microscope to ecology and a sensor.

Collectively, we have built a human network that allows for new activities to begin. We have built a stable, persistent grass-roots grid testbed on which codes can be tested and science conducted. We have shared our experiences via publications and the improved codes via a variety of software dissemination vehicles, allowing the broader community to benefit. Finally, we have used the structure to build a legacy where researchers will work, collaborate, and educate internationally.

Each of the authors would like to acknowledge support from NSF INT-0314015 for our participation in PRAGMA and for OCI 0505520, for integrating Ninf-G into the NMI stack. We also acknowledge NSF INT-0407508, Calit2 and GEON for their support of PRIME. We wish to thank NSF current and former program officers for their strong partnership and encouragement to “take advantage of the geographical location of San Diego, on the pacific rim” and build the community.
We also note that NSF funds helped leverage resources from PRAGMA partners and their funding agencies. Without partnership involvement, we would not exist.
Finally, we wish to acknowledge the support of NIH P41 RR08605 which supports tools for the biomedical community, the Betty and Gordon Moore Foundation for the launch of GLEON, and NSF NEON 0446802 for tools in GLEON.
1 Large Hadron Collider - lhc.web.cern.ch/lhc/
2 Baldridge, K.K., Sudholt, W., Greenberg, J.P., Amoreira, C., Potier, Y., Altintas, I., Birnbaum, A.. Abramson, D.. Enticott, C.. Slavisa, G. Cluster and Grid Infrastructure for Computational Chemistry and Biochemistry. In Parallel Computing for Bioinformatics (Invited Book Chapter), A. Y. Zomaya (Ed.), John Wiley & Sons, 2005, In press.
3 Sudholt, W., Baldridge, K. K., Abramson, D., Enticott, C., Garic, S. Parameter Scan of an Effective Group Difference Pseudopotential Using Grid Computing. New Generation Computing, Vol.22 No 2 (Special Feature Grid Systems for Life Sciences). February 2004.
4 Sudholt, W., Baldridge, K., Abramson, D., Enticott, C., Garic, S., Applying Grid Computing to the Parameter Sweep of a Group Difference Potential, The International Conference on Computational Sciences, ICCS04, Krakow Poland, June 6 - 9, 2004.
5 The chemistry codes are GAMESS, a community code for quantum mechanics calculations, APBS – Adaptive Poisson Boltzmann Solver (apbs.sourceforge.net/), with an integrated framework for connecting grid resources, GEMSTONE 5a, with parameter sweeps middleware (Nimrod) over a grid.
5a Baldridge, K. K., Bhatia, K., Greenberg, J.P., Stearn, B., Mock, S., Sudholt, W., Krishnan, S., Bowne, A., Amoreira, C., Potier, Y. GEMSTONE: Grid-Enabled Molecular Science through Online Networked Environments. Invited paper: LSGRID Proceedings, 2005, in press
6 Sudholt, W., Baldridge, K., Abramson, D., Enticott, C., Garic, S., Kondric, C., Nguyen, D. Application of Grid Computing to Parameter Sweeps and Optimizations in Molecular Modeling. Future Generation Computer Systems (Invited), 2005. 21, 27-35.
7 Abramson, D., Lynch, A., Takemiya, H., Tanimura, Y., Date, S., Nakamura, H., Jeong, K., Lee, H., Wang, C., Shih, HL., Molina, T., Baldrdige, K., Li, W., Arzberger, P. Deploying Scientific Application on the PRAGMA Grid Testbed: Ways, Means and Lessons. Accepted CCgrid 2006
8 Hey, A., Trefethen, A. Cyberinfrastructure for e-Science, Science 2005 308: 817-821.
9 A 21st Century National Team Science Infrastructure - www.calit2.net/newsroom/release.php?id=660
10 Pacific Rim Application and Grid Middleware Assembly - www.pragma-grid.net
11 Global Grid Forum - www.ggf.org
12 Telescience Portal - telescience.ucsd.edu
13 Nimrod - www.csse.monash.edu.au/~davida/nimrod/
14 Gfarm - datafarm.apgrid.org/. a global parallel file system developed by AIST in collection with KEK, University of Tokyo and Titech.
15 Multiple Organization Grid Accounting System - www2.ntu.edu.sg/SCERN/Dec2004/art1.htm, pragma-goc.rocksclusters.org/softdepot/ntu_acct.html, ntu-cg.ntu.edu.sg/pragma/index.jsp
16 NPACI Rocks - www.rocksclusters.org/
17 Ninf-G - ninf.apgrid.org
18 Zheng, C., Abramson, D., Arzberger, P., Ayuub, S., Enticott, C., Garic, S., Katz, M., Kwak, J., Papadopoulos, P., Phatanapherom, S., Sriprayoonsakul, S., Tanaka, Y., Tanimura, Y., Tatebe, O., Uthayopas, P. The PRAGMA Testbed: Building a Multi-Application International Grid 2005. CCGrid 2006 (submitted).
19 Li, W.W., Byrnes, R.W., Hayes, J., Birnbaum, A., Reyes, V.M., Shahab, A., Mosley, C., Pekurovsky, D., Quinn, G.B., Shindyalov, I.N., Casanova, H., Ang, L., Berman, F., Arzberger, P.W., Miller, M.A., Bourne, P.E. The Encyclopedia of Life Project: Grid Software and Deployment. New Generation Computing, Vol.22 No 2 pp 127-136 (Special Feature Grid Systems for Life Sciences). February 2004. www.ohmsha.co.jp/ngc/ngc2202.htm
20 Tatebe, O., Ogawa, H., Kodama, Y., Kudoh, T., Sekiguchi, Matsuoka, S., Aida, K., Boku, T., Sato, M., Morita, Y., Kitatsuji, Y., Williams, J., Hicks, J., The Second Trans-Pacific Grid Datafarm Testbed and Experiments for SC2003, Proceedings of 2004 International Symposium on Applications and the Internet - Workshops (SAINT 2004 Workshops), 26-30 January 2004, Tokyo, Japan
21 Wei, X., Li, W. W., Tatebe, O., Xu, G., Liang, H., Ju, J. Implementing data aware scheduling in Gfarm using LSFTM scheduler plugin mechanism. Proceedings of the 2005 International Conference on Grid Computing and Applications (GCA'05). Las Vegas. 2005. In press.
22 Lee, D., Lin, A.W., Hutton, T., Akiyama, T., Shinji, S., Lin, F.P., Peltier, S., Ellisman, M.H. Global Telescience Featuring IPv6 at iGrid2002. Future Generation of Computer Systems, 19(6): 103139. 2003.
23 EcoGrid - ecogrid.nchc.org.tw/
24 Recent workshops were hosted by the PRAGMA members Bioinformatics Institution and the National Grid Office Singapore (May 2005), University of Hyderabad (October 2005). Future workshops will be hosted by University of Queensland and the Australian Partnership for Advanced Computing (March 2006), Osaka University (October 2006), National Electronics and Computer Technology Center and Kasetsart University (Spring 2007), National Center for Supercomputing Applications (Fall 2007), and NCHC (Spring 2008).
25 Scalable Cluster Management System Wed - www.opensce.org/components/SCMSWeb/
26 Lee, B-S., Tang, M., Zhang, J., Soon, O.Y., Zheng, C., Arzberger, P. Analysis of Jobs on a Multi-Organizational Grid Test-bed. CCGrid 2006 (accepted).
27 KROCK - rocks.cluster.or.kr
28 Tanimura, Y., Ikegami, T., Nakada, H., Tanaka, Y., Sekiguchi, S., Proceedings of the Workshop on Grid Applications: from Early Adopters to Mainstream Users, GGF Documents, 2005.
29 National Research Grid Initiative - www.naregi.org/index_e.html
30National Science Foundation FY2003 Performance Highlights (NSF-04-011) [See page “From the Director” and page 14] www.nsf.gov/pubs/2004/nsf04011/
31 Global Lake Ecological Observatory Network - gleon.org
32 Pacific Rim Undergraduate Experiences - prime.ucsd.edu

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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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