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Grid computing appears as a viable promise for dealing with problems that need availability of computing power, by using a coordinated mesh of computational resources geographically distributed in a planetary scale. In Latin America the question has to be raised, whether grid deployments and developments have some use for o comparatively small number of users at local level.
Grid computing appears as a viable promise for dealing with problems that need availability of computing power, by using a coordinated mesh of computational resources geographically distributed in a planetary scale. In Latin America the question has to be raised, whether grid deployments and developments have some use for o comparatively small number of users at local level.
Grid computing appears as a viable promise for dealing with problems that need availability of computing power, by using a coordinated mesh of computational resources geographically distributed in a planetary scale. In Latin America the question has to be raised, whether grid deployments and developments have some use for o comparatively small number of users at local level.
Centro de Excelencia de Modelacin y Computacin Cientfica Facultad de Ingeniera, Ciencia y Administracin, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, Chile.
Key Words Grid computing, shared resources, resource-planning. Abstract: A survey of the road towards Grid computing taken at CEMCC of Universidad de La Frontera is depicted. Valuable experience and development of emerging scientific bonds and areas of research are gained, a process that is described as well as a view of possible tendences for the near future.
1. INTRODUCTION
The present technological expansion, together with the accelerated growth in computing resources for high performance scientific computation have increased the necessity for correct design, scheduling and use of the infrastructure allocated for that purpose. In this paradigm of global nature, cluster/cloud/distributed computing arises naturally as a viable alternative in parallel and distributed computing environments. Although it ist not widely recognized as powerfull enough, it is currently subject of strong international fostering and further development, grid computing appears as a viable promise for dealing with problems that need availability of computing power, by using a coordinated mesh of computational resources geographically distributed in a planetary scale, which are connected via commercial or academic advanced nets.
Thus, a set of middleware tools have been developed meaning a layer between different users and the applications and software tools envisaged as to provide transparent access to the grid to any potential user.
Of these, a special mention should be made to globus, or gLite, developed by EGEE 1 , each footing on a different conception of how this transparent layer has to be developed and with differents scientific applications in mind, having grid potential. In Latin America the question has to be raised, whether grid deployments and developments have some use for o comparatively small number of users at local level, considering the associated costs, mainly during the first implementation levels and most importantl a lack of experience in this field.
1 Enabling Grids for E-sciencE, http://public.eu-egee.org/ Be as it may be, the fact is that grid computing is already on the global table and small communities are faced to set the roots of their future integration to the developments that are being made now, in a rapidly growing field, with sustainable outputs in a number of scientific applications with consequences in sustainable development. So, for example, the number of downloads of Globus toolkit from year 2000 up to now has experienced a 100-fold increase: from 100 to 25.000 downloads/month.
2. EXPERIENCE
The Centre of Excellence in Modelling and Scientific Computation (Centro de Excelencia de Modelacin y Computacin Cientfica (CEMCC)) of Universidad de La Frontera, is a unit anchored to the Facultad de Ingeniera, Ciencias y Administracin, and has the mission of contributing to the expansion of scientific knowledge, its transmission to society by technological applications, in a frame of interdisciplinarity aimed at providing solutions to complex problems requiring advanced mathematical modelling and high performance scientific computation.
The CEMCC has shown presence at chilean level through active participation at a number of initiatives toward grid computing, most of them headed by the consortium REUNA, Red Universitaria Nacional, or National Universities Net, as in GRID workshops, GRID Schools and so on, via projects granted by the Chilean Agency CONICYT (Programa Bicentenario de Ciencia y Tecnologa, PBCT).
It is an active member of the consortium CLGRID, collaborating in a number of workshops on High Performance Computing (HPC) and has scientific bonds with a number of academic institutions.
In this report we comment on two areas of developments since 2005, namely, Physics and Bioinformatics.
a) 3-D spin glasses time series simulations. The main subject of research in this area consist in finding suitable techniques for assessment of the critical temperatures at which phase transitions occur in 3-D lattices, a well known fact in solid state physics. Techniques used so far use the autocorrelation of a parameter q characterizing spin ordering and Montecarlo simulations.
b) Bioinformatics/molecular dynamics: a number of systems with high impact potential have been studied and are currently under development, as is the case in the study of the beta amyloid peptide (A), whose behavior in different environments is simulated, or the structural analysis of a fraction of the venom of a spder (Latrodectus mactans). Valuable experience has been gained in the alignment of sequences with Blast and MPIBlast.
3. LOCAL REALITY
The CEMCC has modest resources with which small/medium size computations can be performed and a multidisciplinary team. Hardware infrastructure is available under two different artchitectures: An SGI Altix server 450(Nahuelbuta) 2 and a parallel Cluster Beowulf (Troquil) 3 with distributed memory. With these equipments we can test the required infrastructure for different problems as pilots, with expansion capacity (scalable models).
4. TESTING The first experience with clustering and distributed computing was gained in 2005. Globus (Fig. 1) and Unicore. A number of jobs were sent among different machines/architectures. As a result, it was observed that Globus was more flexible in configuring as well as possessing better support, since it was a standard, while Unicore was more friendly since it showed a better graphical set of tools.
3 Cluster Beowulf: Master Mother board Intel D845EBG2L; Processor Pentium IV 2.0 Ghz; integrated net plus secondary net 3COM; HD Maxtor 80GB; 512MB DDR.. Nodes Motherboard Intel D845EBG2L; Processor Pentium IV 2.0 Ghz; Integrated net; HD Maxtor 40GB 7200rpm ATA100: 512MB DDR.
Fg. 1 Reference: Installation Manual Globus 4.0 Version 0.8 Daniel Escobar Caldern - 28 de Julio 2005
Globus is considered a standard and is used as a base platform, allowing different components of the grid to interact in a unified environment. Unicore instead offers more easy of usage and installations (although with some limitations), see Fig. 2 and 3.
Fig. 2 Installation ans client-server testing.
Fig. 3 gridbeans developments for Unicore Presently some graphical user oriented applications are under development, based on Unicore infrastructure support. With new users coming from molecular dynamics, this work has acquired new relevance, in interaction with Universidad de Concepcin. The problem of data transfer speed became relevant, with low performances in the transmission of the initial configurations and the
reception of the outputs. Data obtained has to be interpreted graphically by the users. Again, the tendence points out to Grid developments, since a single image contains huge amounts of information. It is much faster to send a single image that thousands of Megabytes integrated in a log file. Thus, a visualization application developed on Unicore was envisaged.
5. PROJECTIONS
5.1. CEMCC We aim at fostering potential developments in this emergent areas that will enable us to step forward in the scientific and technological development. Strategies in formation of the required human resources are being analized and implemented, with e-science developments and focus in sight, thus converging towards Grid computing, the isntallation, configuration and administration of Grid infrastructures and the use of these infrastructures in the technological solutions of a number of scientific problems the assesment of protein structure conformation, which in itself, is a challenge for Bioinformatics. Phenomena as in secondary structure formations, subunits-folding, etc., are part of the many interrogants that arise that need extensive computations and considerable backup memory (storage).
5.2. At grid level
From the experience gained in these experiments we conclude that we are able to notably improve the performance. We envisage the following structure:
1. A Census of actual requirements and availability of infrastructure. 2. Group necessities in computing power into categories based on demand and requirements. 3. For each task, adequate available tools for performance optimization.
As an example, in a physical system of many particles, or a specific particle physics experiment, the best option should be an assignment into a shared memory whetherenvironment and. Provided infrastructure is available, migrate the software used to OpenMP.
6. CONCLUSIONS
Based on our experience and observations, we conclude that costs for high performance computations become neglectible, if taking into account the simplicity and transparency of the Grid at user level. Moreover, this very fact stimulates integration of new researchers into a team (e-science paradigm) allowing generation of new knowledge, a supportive collaborative environment and a rational use of resources.
ACKNOWLEDGEMENTS
The authors would like to thank Drs. Andrs vila and Julio Lpez, researchers at Centro de Excelencia de Modelacin y Computacin Cientfica, Universidad de La Frontera Chile for their continuing support.
REFERENCES
1. Manual Instalacin Globus 4.0 Version 0.8 Daniel Escobar Caldern - 28 de Julio 2005. 2. Globus toolkit History, Globus project 3. http://public.eu-egee.org/ 4. www.unicore.eu
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