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Conserving bio-diversity at Peru's CIP

Feature - Conserving bio-diversity at Peru's CIP

A few of the many varieties of potatoes. CIP maintains the world's largest genetic bank of potatoes, including 1500 samples of 100 wild species collected in eight Latin American countries, as well as samples of 3800 traditional Andean cultivated potatoes. The collection is maintained under the auspices of the UN's Food and Agricultural Organization, and is available to plant breeders worldwide free upon request. (Click to enlarge.) Image courtesy International Potato Center

What do the objects at right have in common?

They're all potatoes.

And their continuing variety will be partly because of the grid.

The International Potato Center (known by its Spanish acronym, CIP) seeks to ensure the genetic diversity of this staple food crop. The organization also seeks to reduce poverty and achieve food security on a sustained basis in developing countries through scientific research and related activities - not just on the potato, but on other root and tuber crops as well.

In addition, CIP research includes protecting potato seed, studying better methods of pest management, managing mountain agro-ecosystems, and using genetic resources to improve crops, among other activities.

To help accomplish all this, the CIP installed the first cluster/grid high performance computing system in Peru at its Lima Headquarters in 2004, in collaboration with the International Rice Research Institute (IRRI) in the Philippines and the International Crops Research Institute for the Semi-Arid tropics (ICRISAT) in India, which together act as infrastructure for the bioinformatics research platform of the global Generation Challenge Program (GCP).

A wall mural showing the ancient Inca "God of the Potato" above two researchers at the International Potato Center. Even now, traditional farmers make offerings to the gods on All Souls' Day (1 November), in which coca leaves, llama fat and other items are buried in the ground with a seed potato, in hopes that "Pachamama" (Mother Earth) will grant a bountiful harvest the next year. Image courtesy CIP

Getting to the root of the problem

CIP, IRRI and ICRISAT are the first three of 15 CGIAR (Consultative Group on International Agricultural Research) agricultural research centers setting up pools of expertise for bioinformatics program and platform development.

Since then, CIP has managed the cluster/grid platform based upon the Rocks Linux cluster architecture, with AMD Opteron 64-bit CPUs continuously used (but now overdue for an upgrade).

Due to capital investment constraints, CIP has started exploring more economical alternative systems for high performance computing, including BOINC-style volunteer computing. The principle advantage of a BOINC grid is the ability to exploit under-used PC resources.

Thus, CIP started a pilot project in 2008 to perform the evaluation and benchmark testing of BOINC, targeting the running of long, generalized jobs. Having successfully tested a pilot system consisting of 450 heterogeneous Windows PCs on their corporate headquarter's network, CIP is embarking on a large-scale version in 2009.

CIP selected Jarifa, a tool developed at the University of Extremadura, Spain, by the GEA research group, as the project and resource manager for its Windows-based BOINC grid. The main advantage of Jarifa is the ability to manage grid resources by assigning projects to specific groups of PCs. Such groups may be defined according to user load, times available, or CPU power. In this way, the resources of a BOINC grid may be managed to achieve the most effective and efficient throughput for multiple projects while ensuring the minimum of user intrusion.

Our current goal is to evaluate the potential impact of collaboration within a Boinc Grid upon PC users both within and beyond their basic working day, and to see the computational efficiency of the system in a heterogeneous Windows PC environment.

-Arturo Pacheco (CIP) and Daniel Lombraña González (Jarifa) for iSGTW

For further information, please contact Anthony Collins, Head of Information Technology, at a.collins@cgiar.org, who is managing CIP grid projects together with LINUX systems engineer Arturo Pacheco

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