SPIRALES «Soutien aux Projets Informatiques dans les Equipes Scientifiques»

Transcription

1 Direction du Système d'information Service Informatique scientifique et Appui aux Partenaire du Sud Formulaire de demande DSI-SPIRALES 2012 SPIRALES «Soutien aux Projets Informatiques dans les Equipes Scientifiques» Appel à projets 2013 Date de clôture: 31 décembre 2012 La mise en œuvre de l appel à projets est réalisée par la DSI de l IRD Contact spirales@ird.fr I.R.D (Institut Recherche Développement) Siège social : Le sextant-44, boulevard de Dunkerque-Marseille

2 1 Nature du projet 1.1 Titre du projet Implementation of a cluster of PCs at Geophysical Institute of Peru 1.2 Résumé du projet proposé (5 lignes maximum) This project is the continuation of a SPIRALES project funded last year that allowed implementing a 2-nodes cluster at IGP (see Appendix A4 for report of 2012 activities). The current project is aimed at meeting the initial objective of a 4-nodes PC cluster in order to support on-going and emerging scientific activities related to regional climate variability, estuarine ecosystem dynamics, hydrological extreme events and solid earth physics/seismology. Four UMRs are participating and the project fits with needs of two LMIs (DISCOH and Paleotraces). 1.3 Type de projet Etude de faisabilité Nouveau projet x Continuum (préciser année de démarrage : 2012) 2 Porteur(s) et collaborateur(s) du projet 2.1 Unité x UMRs UMI LMI N 5566 Nom : Boris Dewitte 2.2 Département x Environnement & Ressources Santé Sociétés 2.3 Statut et coordonnées du porteur de projet Prénom Nom Statut / Catégorie Localisation géographique Téléphone Fax Boris Dewitte - DR2 IRD LEGOS, 14 av. Edouard Belin, Toulouse Tel : Fax : bxd@legos.obs-mip.fr 2.4 Nom et coordonnées du Directeur d'unité (si différent) Nom prénom - Statut / Catégorie Localisation géographique Téléphone Fax Yves Morel - IRD LEGOS, 14 av. Edouard Belin, Toulouse Tel : Fax : yves.morel@legos.obs-mip.fr 2.5 Avis du directeur d'unité (obligatoire) Je me porte garant sur le personnel et pourcentage de temps impartis pour réaliser ce projet qui s inscrit dans les priorités du LEGOS. Nicholas Hall (Directeur Adjoint du LEGOS) pour Yves Morel (Directeur du LEGOS) (voir aussi Appendix A0 pour les avis des directeurs pour la première année du projet) Page 2 sur 13

3 2.6 Site(s) de déroulement du projet Geophysical Institute of Peru (Instituto Geofísico del Perú, IGP) Calle Badajoz 169 Mayorazgo IV Etapa, Ate-Vitarte, Lima, Perú 2.7 Site administratif à partir duquel se feront les dépenses budgétaires Représentation de l IRD au Pérou Casilla Lima 18 Pérou 2.8 Liste des unités (ou organismes partenaires) du projet Organisme (laboratoire/unité) Directeur - Localisation géographique Laboratoire d Etudes en Géophysique et Océanographie Spatiales - UMR5566 Yves Morel Toulouse Institut des Sciences de la Terre ISTerre - UMR 5275 Philippe Cardin Grenoble Laboratoire d Aéorologie UMR5560 Franck Roux Toulouse Geoscience Environnement Toulouse UMR5563 Patrick Seyler Toulouse (cf. Appendix A0 for letters of support from each director in 2011) 2.9 Liste des intervenants impliqués de manière effective dans la réalisation du projet Prénom Nom - Statut / Catégorie Organisme (unité/laboratoire) - Localisation géographique - Contribution en % de temps homme ou en jours*homme (ETP total ou pour une période) Boris Dewitte - DR2 IRD (LEGOS/UMR5566) Toulouse bxd@legos.obs-mip.fr forte disponibilité - 50% sur la durée du projet Ken Takahashi DR (IGP) Lima - ken.takahashi@igp.gob.pe forte disponibilité - 50% sur la durée du projet Didier Gazen - IR CNRS (LA/UMR5060) Toulouse didier.gazen@aero.obs-mip.fr forte disponibilité - 40% sur la durée du projet Huber Gilt IR (IGP) - Lima - huber.gilt@igp,gob.pe forte disponibilité 60% sur la durée du projet Berlin Segura IE (IGP) - Lima - berlin.seguro@igp.gob.pe forte disponibilité 50% sur la durée du projet Gildas Cambon - IR IRD (LEGOS/UMR5566) Toulouse gildas.cambon@legos.obs-mip.fr disponibilité moyenne - 20% sur la durée du projet Séréna Illig CR2 IRD (LEGOS/UMR5566) Lima/Toulouse serena.illig@legos.obs-mip.fr disponibilité moyenne - 20% sur la durée du projet Florent Lyard - DR2 CNRS (LEGOS/UMR5566) Toulouse florent.lyard@legos.obs-mip.fr disponibilité faible - 10% sur la durée du projet Sebastien Carretier DR2 IRD (GET/UMR5563 Toulouse Sebastien.carretier@get.obs-mip.fr disponibilité faible 10% sur la durée du projet Patrick Marchesiello - DR2 IRD (LEGOS/UMR5566) Toulouse patrick.marchesiello@legos.obs-mip.fr disponibilité faible - 10% sur la durée du projet Serge Prieur - DR CNRS (LA/UMR5060) Toulouse serge.prieur@aero.obs-mip.fr disponibilité faible - 10% Page 3 sur 13

4 sur la durée du projet 3 Moyens / appuis demandés à la DSI 3.1 Soutien demandé à la DSI pour 2012 Soutien demandé : soutien en accompagnement: à la préparation du projet informatique (cahier des charges, gestion appel d offre) à la réalisation du projet informatique (spécifications, développement, tests) à la rédaction du volet informatique d un dossier de financement à la rédaction d un cahier des charges pour la recherche d un opérateur informatique soutien pour l hébergement: de l applicatif scientifique sur une machine virtuelle (accès root autorisé) d un serveur physique (cas particulier où une machine virtuelle ne conviendrait pas) soutien pour obtenir des outils/licences: SVN 1 (un serveur peut être mis à disposition de l équipe de développement pour partager le code source) PowerAMC 2 ArcView, ArcEditor, ArcInfo 3 X soutien financier (pour un besoin différent des soutiens précédents): HT X justification: This amount covers the price of an additional computing nodes which will allow meeting the initial objective of 5 nodes (4 computing node and 1 master node) (see estimate from Dell Peru in Appendix A1). The project will also benefit from support from IGP which will buy a 4 th computing node in 2013 (see letter from Ken Takahashi, head of the climate research group at the Geophysical Institute of Peru (Instituto Geofísico del Perú; IGP) and coordinator of the Work Package on Physics of the LMI DISCOH Appendix A2) 3.2 Montant(s) précédemment attribué(s) par la DSI - en euros HT Montants attribués ( HT) Moyens affectés au projet et Cofinancements acquis hors SPIRALES ( HT) Autres sources de financements (interne ou externe IRD) acquis pour ce projet (ex. ANR, ): IGP Mangrove project (cf. letter from IGP in Appendix A2). Montant ( HT): euros (this will cover expenses for a 4 th computing node) from IGP (see Appendix A1 for invoice). 1 Système libre de gestion de versions ( Page 4 sur 13

5 4 Description des besoins et du projet 4.1 Objectifs scientifiques (en précisant les aspects innovants) There are four main scientific objectives for which this project SPIRALES is motivated: 1) Understand the processes of air-sea-land interaction in the South-Eastern Pacific, 2) Understand the interaction between the regional ocean circulation and the mangrove hydrodynamics in northern Peru and 3) Understanding and modelling of the key parameters (multiscale) controlling the relationship building frequency vs soil frequency and 4) relocalization of earthquakes Peruvian series in order to precise the active tectonic structures and their geometry. 1) Processes of air-sea-land interaction in the South Eastern Pacific: The role of local air-sea-land modes in modulating the climate variability and change in the eastern boundary current systems is presently unclear. Possible mechanisms include wind-upwelling- sea surface temperature (SST) gradient, SST-low clouds, wind-sst-low clouds, wind-evaporation-sst, SST-PBL turbulence-wind. The study of these mechanisms and their role in climate variability and change would greatly benefit from the development and experimentation with a regional coupled ocean-atmosphere model. Our objectives are to: - Characterise the relationship between the coastal atmospheric circulation and coastal SST and oceanic circulation. - Implement, validate and test sensitivities of a regional coupled ocean-atmosphere model for the southeast Pacific. - Characterise air-sea coupled mechanisms and their impact on the regional climate through coupled and uncoupled numerical experimentation. This issue fits perfectly within the scientific objectives of the subprogram of the special agreement between IGP and IRD entitled Ocean-atmosphere coupling at regional scale in the Southeastern Pacific and its relation with the equatorial variability (PIs: Ken Takahashi (IGP) and Boris Dewitte (IRD)) (cf. Appendix A3). It is also complementary to the scientific objectives of the LMI DISCOH for which the IGP PI of the SPIRALES project (Ken Takahashi) is coordinating the activities dedicated to physics and ocean and atmospheric modelling. This project also benefits from on-going activities within the ECOLA team (Lead: Florent Lyard) dedicated to the development of a coupled model platform based on the models ROMS and WRF. During a recent stay of Dr. Ken Takahashi at LEGOS (Oct. 2010) a first version of the coupled model was developed and run on the CALMIP computing facilities (CALMIP - Calcul en Midi Pyrennées - is providing to the scientific community in Toulouse a cluster of 352 nodes with a power of 33 Teraflops). This configuration was tested on the PC cluster of Laboratoire d Aérologie to verify that the proposed cluster configuration is well suited for running the regional coupled model. 2) Impacts of climate variability and change in the northern Peru mangrove ecosystem project: The Peruvian mangrove ecosystem is located just to the north of the equatorial front, the boundary between the cool Humboldt system and tropical conditions. This region is strongly affected by El Niño events, particularly through coastal warming, extremely high rainfall and river discharges, the latter of which produces flooding and strong sediment transports. IGP is leading an interdisciplinary and multi-institutional project focused on the impact of climate variability and change on the mangroves and one of the key activities in this project is the characterization and modeling of the hydrodynamics of the mangroves. The model that is being used for this purpose is T-UGOm 2D, developed at LEGOS. This model has the advantage of being able to use an unstructured grid that can represent an ample range of scales, which for the mangroves is from kilometers to meters, and also due to the capability of representing wetting and drying, which is useful for simulating the irrigating effects of the tides that is key for the ecosystem. For this purpose, a collaboration between IGP (Ken Takahashi) and LEGOS (Florent Lyard) has been established, within which the first step will be setting up a working version of T-UGOm 2D in the cluster that will be set up at IGP through the present SPIRALES proposal. Additionally, the influence of equatorial oceanic waves (e.g. Kelvin) will be assessed with high-resolution 3D oceanic modeling based on ROMS, which will also be implemented in the cluster. 3) Extreme hydrometeorological events in Peru This activity is framed within the new scientific program for IGP-IRD collaboration, included in the update to the IGP-IRD agreement in Among the objectives of this program, we have studying the atmospheric processes associated with such extreme events; studying the interaction between orography and climate, particularly through the rainfall-erosion-orogeny feedback process; c) assessing the predictability and future climate change effects on extreme events; d) studying the hydrological processes leading to erosion and sediment transport. For these objectives, high resolution atmospheric and hydrological modeling is a key component and the proposed cluster would provide a basic system for this purpose. Specific atmospheric models to be used are the MM5 and WRF models, as well as the two-way nested IPSL (global)/lmdz (regional) model. Hydrological and Page 5 sur 13

6 erosion models to be used are included in the code CIDRE (Carretier et al., Carretier, S., B. Poisson, R. Vassallo, E. Pepin, and M. Farias (2009), Tectonic interpretation of transient stage erosion rates at different spatial scales in an uplifting block, J. Geophys. Res., 114, F02003, doi: /2008jf001080). This program is coordinated by Dr. Jhan Carlo Espinoza (IGP) and Dr. Sébastien Carretier (IRD, LMTG/GET). 4) Solid earth physics/seismology: Although IGP and IRD have a strong collaboration in solid earth physics/seismology, dynamical numerical modelling is a topic that is yet to be developed in this context. With this respect, IGP is interested in developing 3D multi-scale numerical tectonic models, from the 3D-local soil dynamic behavior (including non linearity) to the 3D dynamics of the plate subduction and Andean orogeny. This will provide a strong tool for the interpretation of the observational data and for hypothesis testing. It will be also a key element of the study of the relationship between climate and orogeny, using the atmospheric and tectonic models. 4-1) Multi-scale modelling of soil-structure dynamic parameters Actually, in the seismological risk point of view, the coincidence between soil and structure frequencies is considered as a very bad configuration, leading to excessive solicitation of the structure when shaking by an earthquake (Caracas 1967, Mexico 1985, Pujili 1996). We propose, through heavy computing to explore the different effect of this frequency coincidence. This approach will be developed on theoretical model by sending synthetic and real accelerometers (magnitude, main frequency, peak ground acceleration). Geologically, these models will be initially simple and progressively complicated, to check the robustness of the results. The soil will be modelled as a half space horizontally stratified (thickness, shear wave velocity, Rayleigh velocity, damping ), possibly with a non-linear behavior below strong solicitation, and the building as an oscillator at one or more degrees of freedom (natural frequency, rupture an ultimate capacities). This modelling should lead to the construction of capacity curves that will define the impact of an earthquake on a statistical building sample. The code yet developed will be easily installed on the cluster. 4-2) Relocalization of the Peruvian earthquake catalogue The actual methods for earthquake localization use only the data as they have been digitized (P and S waves time arrival). In the frame of atypical use of these data, the developed method (VarP_S code) allows to play on the quality of the time arrival, leading for each station (P and S arrival time) to 16 possibilities (4 qualities for each P and S time). As earthquake location need at least 5 stations, the possibilities of the total parameter space is 16 5 possibilities (close to one million), leading to a too heavy number of possibilities when the earthquake is recorded on 20 stations (16 20 possibilities). In a first step, the goal is to map (on numerical and real data) the whole space parameter to find the key parameters that can lead finally to the development of an inversion process to explore the whole space by a Monte-Carlo or a Neighborhood method to minimize the processing time. 5) Development of parallel computing capabilities Recently, the engineers at IGP's Jicamarca Radio Observatory (JRO) have implemented a small cluster of computers based on Linux and open-source software (MPI, Torque, and Maui) that allowed to develop and test parallel computing algorithms for aeronomy and signal-processing radar applications, like the development of a Monte Carlo method to study the effects of Coulomb collisions on waves in ionospheric plasmas; and the implementation a parallel computing procedure for a new radio imaging technique developed at JRO. IGP's JRO has also started the development of algorithms using GPUs (graphics processing units), using two NVIDIA Tesla cards in which new parallel processing techniques are been developed and tested. IGP plans to experiment with the application of the high-computing capabilities of the GPU processors to enhance the computing power of the proposed cluster at IGP. The reviewers are also invited to refer to Appendix A3 that presents the three scientific programs of the special agreement between IRD and IGP ( convenio ) that are associated to these projects. The convenio was renovated in April Adéquation du projet avec la philosophie de SPIRALES (cf critères d évaluation dans SPIRALES_Notice.doc ) This SPIRALES project is aimed at supporting four main research activities developed in collaboration between IRD and IGP researchers. These research activities are related to risk managements (climate variability and extreme events, climate change and seismology [earthquakes and buildings]) and are top-priority issues for Peru with a high societal benefit. In that sense the proposed SPIRALES project is highly relevant from a scientific Page 6 sur 13

7 perspective. IGP is not the main partner of any LMIs although it has been instrumental in the definition of the LMI DISCOH in particular for which it is providing the expertise on atmospheric science and climate variability. In particular, within the LMI DISCOH it is now recognized that the development of the projects related to atmospheric and air-sea coupled modelling has to be carried out in close collaboration with IGP. IGP is also informally involved in the activities of the LMI Paleotraces ("Paléoclimatologie tropicale : traceurs et variabilités") through its modelling activities dedicated to the study of the atmospheric circulation near Pisco (central Peru region) and the so-called Paracas events (extreme wind events) that bring dust over the sea in this region and may help interpreting the sediment core collected within the LMI Paleotraces. These LMIs would therefore highly benefit from the development of computing capacities at IGP in collaboration with IRD. Concretely, IGP will coordinate within the LMI DISCOH the runs with WRF, ROMS and/or the coupled WRF-ROMS model so that the configurations provide physical fields that can be used for applications relevant to LMI DISCOH and distribute these results within this community. In particular, the simulations of the ocean-biogeochemical models (either ROMS-PISCES model in collaboration with LOCEAN (Paris) or ROMS-BioBus model in collaboration with LEGOS) will be carried out on the IMARPE cluster (former SPIRALES project started in 2007) using the simulated atmospheric forcing provided by the IGP cluster. We also propose within this project to have a two-day course given at IGP in which the first day will be dedicated to the basics of parallel computing and the second day will be dedicated to users training (job administration, queueing, etc.). In addition to IGP scientists, interested researchers associated with the LMI DISCOH could attend. In summary, the present proposal aims at improving the coordination of the scientific activities dedicated to modelling within the LMI DISCOH by sharing efforts and expertises in a more systematic way. It is important to note that the coordinator of this project Boris Dewitte (LEGOS/IRD) was also the coordinator of a SPIRALES project dedicated to the implementation of a PC cluster at IMARPE in This cluster has permitted the successful development of the collaborative modelling projects (ANRs PCCC ( ) and PEPS ( )) between IRD and IMARPE and has been instrumental for the definition of the LMI DISCOH. It is still the main platform for the on-going projects dedicated to modelling of the ocean circulation and its coupling with biogeochemistry within the LMI DISCOH and is now maintained and administrated by the IMARPE team (CIMOBP). As the coordinator of one of the special agreement between IRD and IGP (Appendix A3) and as part of its modelling activities within the LMI DISCOH, Boris Dewitte in close collaboration with Ken Takahashi (IGP) will ensure that the development of the proposed SPIRALES project be successful. Boris Dewitte has in particular applied for a long-term stay in Peru (expatriation) from 2013 after realizing two missions of two months at IGP in Ken Takahashi, as the head of the IGP department dealing with climate studies and as the coordinator of the Work Package 2 ( Physics ) of the LMI DISCOH will also provide a strong support for the installation of the further equipments at IGP as well as for the compilation and running of the different models (ROMS, WRF, T-UGO..). The cluster ressources will be also used in 2013 by two Postdocs funded by IRD (Clémentine Juncas (LSCE) and Katerina Goubanova (LEGOS). Overall the project is timely and benefits from a very favourable environment from both a scientific and organizational perspective. Although IGP is already benefiting from substantial computing capabilities, the use of them is currently devoted to atmospheric prediction and monitoring. The SPIRALES project would allow developing the aforementioned specific projects (section 4.1) that cannot be carried out within the current computing system at IGP. In particular, the development of a regional coupled model requires a specific environment that has been tested on similar PC cluster than the one proposed in the current project. The tools developed by the IRD and CNRS teams (ROMS, ROMS/WRF coupler, T_UGO, others) would be directly fitted to the computing environment of the cluster, which will considerably ease the collaboration and the advancement of the research. The newly implemented 2-nodes cluster is already permitting the development of model configurations. Once implemented and tuned these models will be run for extensive periods of time requiring the full capabilities of a 4-nodes cluster. As Peru, and more especially Lima, is one of the countries with the higher possibilities of strong earthquake in the future decades, the SPIRALES project would allow helping for a best evaluation of the seismic/tsunami risk at the country and city scale. The tools developed with the help of the cluster would be applied worldwide as the thematic is more extensive than the only Peru (application in Algeria, Liban, Ecuador ). Further increasing of the cluster potential will be of strong benefit for the seismic thematic, leading to more intensive computing concerning the soil performance, especially in the non-linear domain. Since such platform is becoming widely used, the development realized in collaboration with IGP could be more easily transposed to others regions within different collaborative initiatives. Considering the on-going scientific IRD activities in South America on issues dedicated to extreme events and their projection in a warming climate, the current SPIRALES project is benefiting from a very favourable environment and it is planned to have the cluster capabilities incremented in the future, which the proposed technical configuration is allowing. In that sense the present SPIRALES project is aimed at providing a preliminary computing platform allowing for the leverage that is necessary for tackling with the scientific issues of the IRD-IGP special agreement (convenio) and the LMI DISCOH. Page 7 sur 13

8 4.3 Description de l'existant (moyens outils compétences) IGP has a 4-core HP rx6600 workstation that is used for high-resolution atmospheric modeling with MM5 running in parallel with OpenMP. MPI has been successfully used at IGP with WRF atmospheric model. At Jicamarca, local engineers have implemented a small cluster of computers based on Linux and open-source software (MPI, Torque and Maui) Experience at Jicamarca in parallel programming using MPI and/or CUDA for upper-atmosphere problems such as signal processing of radar images and Monte-Carlo simulations of Coulomb collisions in plasmas. Experience in climate group with parallel computing using atmospheric model (WRF, MM5) and oceanic (ROMS) models. Existence of a group at IGP dedicated to computional support ("Telemática"). 4.4 Nom de votre outil (dans le cas d un développement d application) 4.5 Calendrier du projet (diagramme de Gant souhaité) The schedule of activities for 2012 are given in the Appendix A4 ( Rapport d activité 2012 ). Here will provide a schedule for activities planned in 2013, including scientific and technical J F M A M J J A S O N D Installing WRF on cluster and carry out x performance tests Installing MM5 on cluster and carry out x x performance tests Installing OASIS (coupler) and test x ROMS_OASIS_WRF Test performance of cluster for x x x ROMS_OASIS_WRF (comparison with CALMIP cluster) Buying and adding compute nodes to cluster Installing FVCOM model for estuarine modeling x x x Installing and carry out tsunami modelling x x x (TUNAMI-N2) and test performance (FUNWAVE). Installing trajectory calculation for dust transport x Installing high resolution KOM on cluster and x x x carry out tests Installing and running TUGO model (Mangrove x x project) Installing SPEEDY global atmospheric model x x Testing ROMS_OASIS_SPEEDY x x Installing GMT and GAMIT (for GPS data processing) Initial tests with the implementation of GFDL AM2.1 global atmospheric model Reporting x x Page 8 sur 13

9 4.6 Décrire l architecture envisagée pour votre outil (un schéma sera apprécié) The cluster consists of two head nodes and a set of compute nodes (see schematic below) One head node referred as the "Administration Node" (or "Admin Node" for short) will handle the PXE boot and monitoring of compute nodes with DHCP/TFTP services and open source tools based on BProc project ( The Admin Node does not need to be powerful : a simple dual-core, 8GB RAM, 1Gb/s network card, and two hard disks (< 250GB) in a Raid 1 (mirroring) setup are sufficient. This node is only accessed by the cluster administrators. It uses OpenSuSE 11.4 linux distribution as the operationg system with linux kernel and runs the bpmaster daemon (BProc) that communicates with the bpslave daemon launched at boot on every compute node. Each compute node will receive when booting a copy of a linux kernel from the admin node. The second head node referred as the "Head node" contains eight 2.4 GHz Intel Xeon Nehalem processors (two quad-core sockets), 24 GB RAM, a 1Gb/s network card and all disk space areas needed for system and users data (10TB, RAID 6). It is configured as any linux workstation with for example an OpenSuSE 11.4 distribution that provides all libraries, binaries and development tools needed by users. It is accessible from the public network and is the only cluster access point for users. It runs an NFS server to share the working environment (libraries, binaries, home and data directories) with the compute nodes which are accessible on a private network through an ethernet switch (up to 48 ports x 1Gb/s). Users can edit and compile their codes on the head node before submitting compute jobs via the SLURM resource manager (slurmctld daemon). Compute nodes are dedicated to user jobs execution (either sequential or parallel codes). Each one contains eight 2.4 GHz Intel Xeon Nehalem processors (two quad-core sockets), 24 GB RAM, a 1Gb/s network card and one 40Gb/s Infiniband host control adapter. A local disk space is available on each compute node used for fast temporary local storage (/workdir), swap et system /tmp. Every job that is very disk-intensive should be set up to read and write its scratch files to /workdir rather than the Head Node NFS-mounted home. Because no ssh daemon is running on a compute node, the only way for a user to get access to it is via the batch submission system SLURM (slurmd daemon). Compute nodes are connected to a a high bandwidth/low latency Infiniband Network switch (36 ports 40Gb/s) : this high performance network is dedicated to Message-Passing (MPI) for applications that support it (like WRF and ROMS). Schematic: IGP/IRD SPIRALES cluster configuration Page 9 sur 13

10 4.7 Lister les méthodes/référentiels, langages de programmation - Libraries and Software : exclusively open-source and free software - Compilers : gnu compilers (gcc, g++, gfortran), Intel compilers (icc, ifort) - Scientific Libraries : Open-MPI, netcdf, lapack, blas... - Bproc Admin tools : bpsh, bpctl, bpstat to remotely set up a computer node. Page 10 sur 13

11 - Resource manager : SLURM ( is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters. SLURM has three key functions. First, it allocates exclusive and/or non-exclusive access to resources (compute nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (normally a parallel job) on the set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pending work. - Visualization tools : Ferret, Grads 4.8 Énumérer et décrire les données/méta données de votre outil (thématique, format, volume, ) See section Liste des livrables et documents (spécifications fonctionnelles, techniques, API, manuel utilisation ) Nom du document Date de réception Descriptif du document Two reports will be provided at the end of the years that cover the project (Dec 2012 (see Appendix A4) and Dec 2013). We also plan to write a document ( users s guide type ) that will summarize the main steps of the cluster implementation (technical and computational aspects) and that could serve for other future projects and collaborators. 5 Bénéfices pour le Sud (cf critères d évaluation dans SPIRALES_Notice.doc ) 5.1 Sites de déroulement du projet au Sud Geophysical Institute of Peru, Lima (Peru) 5.2 Liste exhaustive des partenaires au Sud La recherche de synergie ou de partenariat (projet inter-unités impliquant des partenaires du Sud) et la mobilisation de compétences extérieures à l'unité doit être recherchée. Prénom Nom Organisme (laboratoire/unité) Lieu géographique Type de bénéfice Ken Takahashi, Ph. D. IGP Lima - ken.takahashi@igp.gob.pe Head of Climate Variability and Change Research at IGP / ocean-atmospheric modeling and high-resolution coastal hydrodynamical modeling. Edmundo Norabuena, Ph. D. - IGP - Lima - edmundo.norabuena@igp.gob.pe - Head of Spatial Geodesy at IGP / 3D modeling of subduction process Hernando Tavera, Ph. D. - IGP - Lima - hernando.tavera@igp.gob.pe - Head of Seismology at IGP / Inversion calculations for propagation velocities of seismic waves Jhan Carlo Espinoza, Ph.D. - IGP - Lima - jhan-carlo.espinoza@igp.gob.pe - Hydrological modeling Yamina Silva, Ph. D. - IGP - Lima - yamina.silva@igp,gob.pe - High resolution atmospheric modeling Marco Milla, Ph. D. - IGP - Lima - marco.milla@jro.igp.gob.pe - Parallel computation / upper atmosphere modeling Juan Carlos Villegas, M. Sc. - IGP - Lima - juancarlos.villegas@igp.gob.pe - Inversion calculations of GPS data Isabel Bernal, M. Sc. IGP Lima - isabel.bernal@igp.gob.pe - Inversion, dynamic soil parameters, propagation velocities of seismic waves Christian Flores, M. Sc. IGP Lima christian.flores@igp.gob.pe, Microzonation, dynamic soil parameters Bhila Herrera, M. Sc. IGP Lima bhila.herrera@igp.gob.pe, Structure dynamic parameters, soil-structure interaction Sheila Yauri, M.Sc. - IGP - Lima - sheila.yauri@igp.gob.pe - Tsunami modeling Kobi Mosquera, M. Sc. - IGP - Lima - kobi.mosquera@igp.gob.pe - Oceanographic modeling Page 11 sur 13

12 Julio Quijano - IGP - Lima - julio.quijano@igp.gob.pe - Regional ocean-atmosphere modeling Berlin Segura - IGP - Lima - berlin.seguro@igp.gob.pe - Regional ocean-atmosphere modeling Huber Gilt - IGP - Lima - huber.gilt@igp,gob.pe - Parallel computation 5.3 Pérennité du projet Décrire la capacité de pérennité du projet, notamment dans l organisation du projet mise en place avec les partenaires du Sud The IGP and IRD have been collaborating on issues related to seismology since The projects dedicated to climate variability and ocean-atmospheric modelling were launched in In particular, IRD and IGP have been collaborating to the international VOCALS project through the realisation of a regional cruise (VOCALS-Rex, November 2008). A PhD student from IGP is also funded by IRD (Kobi Mosquera). Considering the on-going projects and the history of collaboration, it is more than likely that the SPIRALES project will strengthen the collaboration between both institutions and allows going forward in the development of the research activities. Note also that since the LMI DISCOH and LMI Paleotraces are likely to operate at least until 2014, this makes a time frame favourable for the valorisation of the proposed SPIRALES project. The diversity of the scientific projects (climate variability, climate change and seismology) that the cluster will support is also a strong asset for making the SPIRALES project durable. 5.4 Développement de compétences Lister les actions prévues de transfert de compétences envers les partenaires du Sud Within this SPIRALES project, the future administrators of the cluster at IGP will be trained on the cluster administration and their counterparts at IMARPE will be invited as well. Many researcher and students from IGP will benefit from the cluster capabilities in order to develop their research projects. Close collaboration with IMARPE is expected in LMI DISCOH-related topics, including submission of model runs in the cluster at IGP that will be useful for IMARPE, IGP, and other LMI DISCOH partners. This will include IMARPE personnel visiting IGP to coordinate and setup these runs. Similarly, IGP personnel will also collaborate with IMARPE using their clusters. 6 Valorisation(s) liées au projet Un projet "SPIRALES" ne peut être le projet d une unité ; il a vocation à être valorisé et être réutilisé au sein de l institut, et à l extérieur. Une démarche de capitalisation doit être recherchée. 6.1 Valorisation(s) prévue(s) (données, licence logiciel, capitalisation du logiciel, transfert de compétences ) This cluster involves four UMRs in France, three of them collaborating closely with IGP, so that its use is expected to be intensive and its promotion well acquired. It is planned to increment the PC cluster capabilities as time goes. The choice of its structure is actually motivated by the possibility to reach a more powerful cluster within a few years. This should ensure that there will be more and more interest in maintaining this tool which is aimed at becoming the main instrument of intensive calculation at IGP. In terms of simulated data, the relevant simulations performed on the cluster will be made available to the LMI DISCOH community, in particular to the researchers of the CIMOBP (Modeling center at IMARPE) that specializes in ocean-biogeochemical coupling and will greatly benefit from the availability of realistic atmospheric forcings to force their model. This will be coordinated by the leaders of WP2 of the LMI DISCOH and should ensure a proper and fruitful use of the data produced by the cluster. 6.2 Formations Lieu géographique Date Public ciblé Nombre d intervenants Nombre de personnes formées Page 12 sur 13

13 In 2012, an engineer from IGP has been designated (Huber Gilt) as the cluster administrator and has been given a hands-on in-depth training on cluster administration by a specialist from LA (Didier Gazen) in Lima. The interaction between Didier Gazen and Huber Gilt will continue in 2013 in order to pursue the training and ensure the successful increase in capabilities of the cluster when the two additional nodes will be included. Interactions with the administrator of the IMARPE Cluster (Jorge Ramos) will be also encouraged considering that an interest was expressed during the class on system administration given on the 13 th of December, 2012 (cf. Appendix A4-D) for the SluBK system. 6.3 Publication(s) et communication prévue(s) Various scientific communications should arise from the use of the cluster. In particular it is planned to carry out long-term regional coupled simulations which, for this region, should be the first attempt, and therefore should convey many new scientific results. The research allowed by the cluster on the air-sea coupling issue will be also very beneficial for the LMI DISCOH and LMI PALEOTRACES community providing realistic high-resolution simulations of the Peru region, allowing for a number of downstream studies and publications. Page 13 sur 13

14 Appendix A0: Letters of support from : Laboratoire d Etudes en Géophysique et Océanographie Spatiales (LEGOS) Laboratoire d Aérologie (LA) Laboratoire Mixte International DISCOH Geophysical Institute of Peru (IGP) Institut des Sciences de la Terre (ISTerre) Géosciences Environnement Toulouse (GET)

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19 Grenoble, 15 décembre 2011 à : Direction du système d information, Institut de Recherche pour le Développement Philippe CARDIN Directeur d ISTerre Téléphone: 33(0) Télécopie: 33(0) direction.isterre@ujfgrenoble.fr Unité Mixte de Recherche UJF/CNRS/UdS/IRD/IFSTTAR CNRS 5275 IRD 219 Grenoble : Adresse géographique : 1381, rue de la Piscine Saint-Martin-d Hères Adresse postale : BP Grenoble cedex 9 Chambéry : Université de Savoie Le Bourget du Lac cedex Objet : Soutien au projet «Réalisation d un cluster à l Institut de Géophysique du Pérou (Lima)» en réponse à l appel d offres SPIRALES «Soutien aux Projets Informatiques dans les Equipes Scientifiques» 2012 Madame, Monsieur, Depuis 2000, notre laboratoire ISTerre (anciennement LGIT) est fortement impliqué sur les différentes thématiques que l IGP (Institut Géophysique du Pérou) soutient en Sciences de la Terre, que ce soit au niveau du Risque Volcanique, de la Sismotectonique, de la Géodynamique andine ou plus récemment du Risque Sismique en milieu urbain. Ces recherches sont focalisées sur la dynamique de la structuration andine avec une focalisation sur l impact sociétal des phénomènes catastrophiques (volcan séisme). Les travaux entrepris conjointement entre ISTerre et l IGP se basent sur l utilisation et le développement d outils informatiques adaptés qui seront fortement optimisés par une structure de type cluster. L IGP dispose déjà d un centre de calcul dédié à la modélisation atmosphérique. Le lancement de plusieurs nouveaux projets scientifiques en partenariat, en particulier relatifs aux Sciences de la Terre Solide, focalisés sur des processus d inversion ou de modélisation numérique, bénéficierait grandement de la mise en place d une plateforme de calcul dédiée que ce projet SPIRALE propose de réaliser. Finalement, le développement d un outil de calcul conjointement avec le LEGOS permet d une part de mutualiser le futur cluster et d autre part de soutenir le développement de moyens numériques d un partenaire avec qui l IRD collabore activement sur plusieurs thèmes de recherche qui intéressent la communauté scientifique en Amérique du Sud. Etant donné la qualité des projets scientifiques que ce projet SPIRALE vise à soutenir, je soutiens sans réserve ce projet SPIRALE porté par Boris Dewitte et soutenu par Bertrand Guillier. Philippe Cardin.

20 GEOSCIENCES ENVIRONNEMENT TOULOUSE UMR 5563 CNRS / UR 234 IRD / UPS / CNES Patrick Seyler Directeur adjoint Tel : Fax : Toulouse, le 20 décembre 2011 à : Direction du système d Information, Institut de Recherche pour le Développement Objet : Soutien au projet «Réalisation d un cluster à l Institut de Géophysique du Pérou (Lima)» en réponse à l appel d offres SPIRALES «Informatique en Soutien à la Science et Appui aux partenaires du Sud» 2012 Madame, Monsieur, Depuis une dizaine d années, le GET (Géosciences Environnement Toulouse) est impliqué dans plusieurs programmes scientifiques au Pérou sur les thèmes de l hydrologie des grands bassins versants, les couplages lithosphère-océan-atmosphère et l évolution des surfaces continentales dans un contexte de changement climatique. Ces thématiques ont un impact sociétal direct et très apprécié de nos partenaires institutionnels en terme de gestion de la ressource (l eau) et du risque (crues, glissement de terrain, séismes). Ces programmes rayonnent sur l ensemble du notre partenariat en Amérique du Sud (à la fois au niveau péruvien mais aussi au niveau régional :Equateur, Bolivie, Chili) qui permet la collecte et l analyse d un très grand nombre de données. Ces bases de données uniques à notre connaissance servent à nos partenaires et à nos chercheurs et doctorants à construire des modèles visant par exemple à simuler la répartition pluviométrique dans l espace et dans le temps ou encore à simuler les modifications des réseaux hydrographiques au cours des derniers millénaires. Le projet SPIRALES «Réalisation d un cluster à l Institut de Géophysique du Pérou (Lima)» s inscrit dans le cadre de l ensemble de ces projets. Il permettrait de lever un verrou technique récurrent chez nos partenaires par la mise en place de moyens de calcul rendus absolument nécessaire au développement de ces projets de modélisation. En particulier, nous souhaitons avec l Institut de Géophysique du Pérou ou serait hébergé ce cluster, aidé par d autres instituts (Institut de recherches hydrauliques de Porto Alegre, Brésil et Laboratoire de Météorologie Dynamique, Paris), développer un modèle couplé climat-hydrologie pour l étude des processus d interaction entre pluie, érosion et orogénèse dans la région andine, afin de comprendre la genèse des événements hydrologiques extrêmes dans cette région ou l impact sociétal de tels événements est dramatique. Ce projet SPIRALES rentre complètement dans les objectifs et les priorités du GET déclinées dans son contrat quadriennal et évalué très positivement par l AERES. Il permettrait enfin de mutualiser les moyens entre différentes unités de recherche de l IRD travaillant chez nos partenaires péruviens qui collaborent déjà entres elles sur des thèmes connexes. Aussi j apporte mon soutien sans réserve à ce projet SPIRALES porté par Boris Dewitte (LEGOS). Patrick Seyler