The Grid road of a small research unit.

The CEMCC experience.

Juan Pablo Abarza, Gustavo Lacoste

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.


2
Servidor SGI ALTIX 450: 10 processors Intel Itanium 2
Montecito Dual- Core (20 cores) 1.4Ghz/12MB cach; 40 Gb
memory (10x4Gb); 6 SATA Disks of750GB 7200 rpm (4.5TB).

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