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F. Boulahya, I. Dubus, F. Dupros, P. Lombard EGEE User Forum, May 9 th -11 th , Manchester

FOOTPRINT@work, a computing framework for large scale parametric simulations : application to pesticide risk assessment and management. F. Boulahya, I. Dubus, F. Dupros, P. Lombard EGEE User Forum, May 9 th -11 th , Manchester. Outline. FOOTPRINT presentation FOOTPRINT@work architecture

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F. Boulahya, I. Dubus, F. Dupros, P. Lombard EGEE User Forum, May 9 th -11 th , Manchester

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  1. FOOTPRINT@work,a computing framework for large scale parametric simulations : application to pesticide risk assessment and management F. Boulahya, I. Dubus, F. Dupros, P. Lombard EGEE User Forum, May 9th-11th, Manchester

  2. Outline • FOOTPRINT presentation • FOOTPRINT@work architecture • PRZM and MACRO Models • FOOTPRINT@work and EGEE EGEE User Forum, May 9th-11th, Manchester

  3. Outline • FOOTPRINT presentation • FOOTPRINT@work architecture • PRZM and MACRO Models • FOOTPRINT@work and EGEE EGEE User Forum, May 9th-11th, Manchester

  4. FOOTPRINT presentation • 3year EU-funded project • Part of the 6th Framework Program (FP6) • Started in January 2006 • Objective : • Develop functional tools to identify pathways and sources of pesticides contamination in the agricultural landscape • Help decision makers to choose strategies to reduce pesticides contamination of water ressources at different scale • Local/Farm • Catchments • National/EU • How : • Based on meta-modelling i.e. based on a large number of precomputed scenarios • http://www.eu-footprint.org • Huge requirement of computing power EGEE User Forum, May 9th-11th, Manchester

  5. Outline • FOOTPRINT presentation • FOOTPRINT@work architecture • What is FOOTPRINT@work? • ComputeMode • OAR/CIGRI • PRZM and MACRO Models • FOOTPRINT@work and EGEE EGEE User Forum, May 9th-11th, Manchester

  6. FOOTPRINT@work architecture • What is FOOTPRINT@work? • Relies on a French national Grid initiative IGGI • Infrastructure for Grids, Cluster and Intranet • Partners : BRGM, INRIA, Mandriva • Allow access and gather the whole computing resources spread over the intranet of a company • The ability to use desktop PC coming from the BRGM administrative staff and researchers to perform large scale pesticide simulations EGEE User Forum, May 9th-11th, Manchester

  7. Outline • FOOTPRINT presentation • FOOTPRINT@work architecture • What is FOOTPRINT@work? • ComputeMode • OAR/CIGRI • PRZM and MACRO Models • FOOTPRINT@work and EGEE EGEE User Forum, May 9th-11th, Manchester

  8. FOOTPRINT@work architecture • ComputeMode • Provides a seamless Linux cluster infrastructure within an Intranet • Aggregates idle user machine to a virtual computing cluster • Is based on : • PXE boot with DHCP and Wake-on-LAN • NFS accesses • PostgreSQL database linked to an Apache server for an easy to use web interface • http://www.computemode.org/ EGEE User Forum, May 9th-11th, Manchester

  9. FOOTPRINT@work architecture • ComputeMode Avantages • An almost homogeneous environment • Every nodes boot a same diskless Linux flavor • The only sources of heterogeneity are the difference in CPU powers and the RAM available • A safe environment • Due to a diskless operating system • Logging on a node is only allowed through an ssh coming from the ComputeMode server or through an interactive job reservation EGEE User Forum, May 9th-11th, Manchester

  10. FOOTPRINT@work architecture • ComputeMode : how does it work? • Each cluster node has to be registered • A hostname attached to its MAC address • A booting schedule : describes when this machine will work “locally” and when it will take part of the cluster • Properties are added (location,type,…) which are exported to the job manager • Standard schedule : from 6pm until 8am from Monday to Friday and the whole Saturday and Sunday • During a computing period, possibility to halt the PC by hitting 'Alt-Ctl-Del' • To get some more availability, users may inform the system that they will be out of office for the next few days thanks to a simplified web page • Including vacations, nights and weekend a single PC could be used 4.5 days in a week for grid computations EGEE User Forum, May 9th-11th, Manchester

  11. FOOTPRINT@work architecture • ComputeMode : Shedule EGEE User Forum, May 9th-11th, Manchester

  12. Outline • FOOTPRINT presentation • FOOTPRINT@work architecture • What is FOOTPRINT@work? • ComputeMode • OAR/CIGRI • PRZM and MACRO Models • FOOTPRINT@work and EGEE EGEE User Forum, May 9th-11th, Manchester

  13. FOOTPRINT@work architecture • OAR • Batch sceduler • Developed by the ID-IMAG laboratory • Is written in Perl and is based on a MYSQL relational database • One example of users: the French national Grid Grid5000, http://www.grid5000.fr • available free of charge under an Open Source license http://oar.imag.fr/ EGEE User Forum, May 9th-11th, Manchester

  14. FOOTPRINT@work architecture • CIGRI • a campaign manager for parametric job • based on a MySQL database and a web interface • written in Perl • acts as a meta-scheduler and uses OAR and ssh to successfully handle the campaigns (task and job scheduling, multi-cluster support). • several thousand parameters can be manipulated • indicates where jobs are executed at what time • indicates what happens on the Grid platform and what are errors related to their campaigns • available free of charge under an Open Source license: http://cigri.imag.fr/ EGEE User Forum, May 9th-11th, Manchester

  15. FOOTPRINT@work architecture • CIGRI web interface to manage campaigns EGEE User Forum, May 9th-11th, Manchester

  16. Outline • FOOTPRINT presentation • FOOTPRINT@work architecture • PRZM and MACRO Models • Models descriptions • Emulation • Management of parametric campaigns • FOOTPRINT@work and EGEE EGEE User Forum, May 9th-11th, Manchester

  17. PRZM and MACRO Models • MACRO • A physically-based, one-dimensional, numerical model of water flow and reactive solute transport in field soils (Jarvis, 1994) • Calculates coupled unsaturated-saturated water flow in cropped soil and can also deal with saturated flow to field drainage systems • Richards' equation and the convection-dispersion equation are used to model soil water flow and solute transport in the soil micropores, while a simplified capacitance type-approach is used to calculate fluxes in the macropores EGEE User Forum, May 9th-11th, Manchester

  18. PRZM and MACRO Models • PRZM (Pesticide Root Zone Model) • Based on a one-dimensional finite-difference code • Consists of hydrologic (flow) and chemical transport components to simulate runoff, erosion, plant uptake, leaching, decay, foliar washoff, and volatilisation • Pesticide transport and fate processes include advection, dispersion, molecular diffusion, and soil sorption • Includes soil temperature effects, volatilisation and vapour phase transport in soils, irrigation simulation and a method of characteristics algorithm to eliminate numerical dispersion • Predictions can be made for daily, monthly or annual output EGEE User Forum, May 9th-11th, Manchester

  19. Outline • FOOTPRINT presentation • FOOTPRINT@work architecture • PRZM and MACRO Models • Models descriptions • Emulation • Management of parametric campaigns • FOOTPRINT@work and EGEE EGEE User Forum, May 9th-11th, Manchester

  20. PRZM and MACRO Models • MACRO and PRZM are based on Windows operating system whereas computing nodes are under Linux. • Homologation requires Windows version of these models • the FOOTPRINT@work software includes emulation facilities to run these two codes on Linux platforms • The tools used • For PRZM : Wine (emulation) and Xvfb ( redirection of output events) • For MACRO : a patched version of DOSEMU • NB: Because the sources of MACRO code are available in FOOTPRINT context, this level will be given up as soon as the Linux version is validated EGEE User Forum, May 9th-11th, Manchester

  21. Outline • FOOTPRINT presentation • FOOTPRINT@work architecture • PRZM and MACRO Models • Models descriptions • Emulation • Management of parametric campaigns • FOOTPRINT@work and EGEE EGEE User Forum, May 9th-11th, Manchester

  22. PRZM and MACRO Models • several shell and perl tools have been written to mimic SENSAN package functionalities • What is SENSAN? • A model-independent sensitivity analyser • Communicates with the model through its input and output (no need to adapt the simulations) • Example1 : • Identifies parameters in the input files • The user provides different sets of parameters values • SENSAN runs the model for each set of parameter values • Records input and output values in a spreadsheet format • Example2 : • Offers the possibility to add a system command (renaming output files, moving them,…) EGEE User Forum, May 9th-11th, Manchester

  23. PRZM and MACRO Models • Input data: Two modes are allowed for input data: • one file per individual run • a template file as well as a variable file where a line correspond to a set of parameters (this mimics SENSAN package functionality). • A number of job is associated to each simulation • Output data: • Renamed according to the number of the simulation. • Because of the amount of data that could be generated, two functionalities have been added: • specify a perl script to filter output files during their generation only to preserve “sections” of interest data. • specify a filter script using the same syntax as SENSAN to extract several values. (a merger script is used to aggregate these information to create a table of results) EGEE User Forum, May 9th-11th, Manchester

  24. Outline • FOOTPRINT presentation • FOOTPRINT@work architecture • PRZM and MACRO Models • FOOTPRINT@work and EGEE EGEE User Forum, May 9th-11th, Manchester

  25. FOOTPRINT@work and EGEE • Challenge • Around 12 thousands of agro environmental scenarios (crop x soil x climate) • 100 different pesticides and for each 10 possible application dates • Several millions of runs of MACRO and PRZM • Several Terabytes of data • Internal BRGM Grid capabilities • 500 PC that could be used during idle period (4.5 days per week) • Storage Means in discussion EGEE User Forum, May 9th-11th, Manchester

  26. FOOTPRINT@work and EGEE • EGEE • Because of the computing time (more than 2700 years of running on a single PC) and the amount of storage data (around 20To), FOOTPRINT clearly calls for Grid capabilities such as EGEE infrastructure. • Virtual Organisation Earth Science Research • Needed in FOOTPRINT and available in EGEE infrastructure : • Huge number of available CPUs • Possibility to manage parametric campaigns (functionality of gLite) • Management of files • But needs MACRO to be ported on Linux (current) EGEE User Forum, May 9th-11th, Manchester

  27. Acknowledgements The funding of the FOOTPRINT project by the European Commission through its Sixth Framework Programme is gratefully acknowledged www.eu-footprint.org i.dubus@brgm.fr EGEE User Forum, May 9th-11th, Manchester

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