BIFI is one of the most relevant e-science centres in Spain, both as resource providers and as scientific end-users. Mainly composed by engineers and physicists, the Computing Area includes a large range of activities from technology research, user support, applied research, technology transfer and engagement.
BIFI hosts the Supercomputing Centre of Aragón (CESAR), a computing infrastructure covering a wide set of technologies: HPC (Distributed and Shared Memory), Grid, Cloud, Volunteer Computing and Dedicated Computers.
In fact, the Computing Area is structured in four research lines:
The HPC computing resources deliver several millions of CPU hours and hundreds of terabytes of storage per year, to both BIFI’s researchers (and their collaborators) and external users through the Spanish Supercomputing Network, the Hosted Clusters program and other services provided.
Also the grid&cloud infrastructures provide computing resources to a wide range of researches, who have specific or complementary requirements to those offered by the HPC infrastructures. In addition to this, they also serve as a testbed for Spanish and European companies and SMEs, which are willing to adopt these technologies to improve their business model. Therefore, in the last years, we have focused our cloud research and infrastructures in helping SMEs on how to take advantage of these powerful technologies.
In the research line of special purpose computers, we work on the design and construction of machines dedicated to solve very specific problems, like the awarded supercomputer JANUS, based on FPGAs and with relevant scientific results published.
BIFI is an international reference in citizen science activities and leads the volunteer computing project Ibercivis.
Head of the Research Line:
Mari Carmen Ibáñez
Citizen science is a research line that promotes the participation of society in science. The first project that emerged in this framework was Ibercivis, in which citizens may collaborate with basic research by sharing computational resources in their idle computer times.
Among the main objectives of this promising research line are to recognize the potential of citizen science and the role of society, as well as the importance of active participation of citizens in different activities of scientific nature. In recent years, contributions in this regard have been significantly increasing and have a great added value for researchers, in general. BIFI Institute supports and promotes this task, allowing citizens to make use of resources and computational infrastructure through different activities such as data analysis and the development of interesting experiments in diverse scientific fields. In this way, volunteers can engage in research and contribute to science.
Besides developing our own tools, citizen science projects and participatory experiments collaborating with researchers and citizens, the group has coordinated “Socientize”. This project proposed useful policy recommendations as an input for the strategy for Citizen or Public engagement in European science research activities in Horizon 2020. All these proposals are included in the White Paper on Citizen Science for Europe. Several Commission services (including DGs CONNECT, RTD and the JRC) are using this Paper as a reference document.
1.- White Paper on Citizen Science for Europe.
2.- Socientize Consortium 2013. Green Paper on Citizen Science — Citizen Science for Europe: Towards a better society of empowered citizens and enhanced research, November, 2013.
3.- Cell Spotting: Educational and Motivational Outcomes of Cell Biology Citizen Science Project in the Classroom. Cândida G. Silva, António Monteiro, Caroline Manahl, Eduardo Lostal, Teresa Holocher-Ertl, Nazareno Andrade, Francisco Brasileiro, Paulo Gama Mota, Fermín Serrano Sanz, José A. Carrodeguas, Rui M. M. Brito (2015). JCOM – Journal of Science Communication – “Citizen Science” Special Issue (accepted for publication).
4.- SOCIENTIZE participatory experiments, dissemination and networking activities in perspective. Cândida G. Silva, Rui M. M. Brito, António Monteiro, José A. Farias Leal, Adabriand Furtado, Nazareno Andrade, Francisco Brasileiro, Paulo Gama Mota, Caroline Manahl, Teresa Holocher-Ertl, Manuel Pérez Alconchel, Eduardo Lostal Lanza, Carlos Val Gáscon, Francisco Sanz, Fermín Serrano Sanz (2014). Human Computation 1 (2), pp. 119-135.
5.- A Performance/Cost Evaluation for a GPU-Based Drug Discovery Application on Volunteer Computing. D. GUERRERO, Ginés; IMBERNON, Baldomero; PEREZ-SANCHEZ, Horacio; SANZ, Francisco; GARCIA, José M. and CECILIA José M. (2014). BioMed Research International Volume 2014 (2014), Article ID 474219.
6.- Adsorption of probe molecules in pillared interlayered clays: Experiment and computer simulation. A. Gallardo, J.M. Guil, E. Lomba, N.G. Almarza, S.J. Khatib, C. Cabrillo, A. Sanz, y J. Pires (2014). Journal of Chemical Physics 140, 224701.
7.- Heterogeneous networks do not promote cooperation when humans play a Prisoner’s Dilemma. GRACIA LAZÁRO, Carlos, FERRER, Alfredo, RUIZ, Gonzalo, TARANCÓN, Alfonso, CUESTA, José A., SÁNCHEZ, Ángel, MORENO, Yamir (2012). PNAS 109(32), pp. 12922–12926.
8.- Technical Note: An algorithm to calculate the tissue phantom ratio from depth dose in radiosurgery. RAMOS GARCÍA, Luis Isaac, ALMANSA,, Julio F. Medical Phisics, vol. 38, issue 5 (April 2011).
9.- Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods. SIMõES, Carlos J.V., MUKHERJEE, Trishna, BRITO, Rui M. M., JACKSON, Richard M. (2010). J. Chem. Inf. Model. 50 (10), pp 1806–1820.
10.- Searching for Anti-Amyloid Drugs with the Help of Citizens: the ‘AMILOIDE’ Project on the IBERCIVIS Platform. SIMõES, Carlos J.V., RIVERO, Alejandro, BRITO, R. M. M. (2010). ERCIM News 82, pp. 25-26.
3.- Open Digital Science.
4.- EGI Engage.
5.-Citizen Science Observatory.
6.- Science in your Mobile.
7.- Aqua .
Head of the Research Line:
Gonzalo Ruiz, email@example.com
Alfredo Ferrer, firstname.lastname@example.org
The development group belongs to the computing area at BIFI, and it is composed by two experienced computing engineers.
The main goal of this team is to research and support research when software development is involved. To achieve it, one of the most important tasks that we perform is the participation in research projects in which we collaborate with companies and other research groups. These collaborations are focused on different innovative topics such as BigData, Internet analysis, social networks, distributed computing, new technologies in education, etc. The collaboration levels go from small contributions to local companies/research groups to international projects such as FPVII.
The other task that we carry out at BIFI is to support ongoing research through software development improving or optimizing programs that already exist, and consulting for choosing the best technologies and techniques for their development.
1.- Analysis of academic productivity based on Complex Networks. September 2015, R. Álvarez, E. Cahué, J. Clemente-Gallardo, A. Ferrer, D. Íñiguez, X. Mellado, A. Rivero, G. Ruiz, F. Sanz, E. Serrano, A. Tarancón, Y. Vergara. Scientometrics, September 2015, Volume 104, Issue 3, pp 651-672.
2.- RRLab: Remote Reality Laboratory to teach mechanics in schools. November 2013, Elisa Cauhé, Alfredo Ferrer, Gonzalo Ruiz, David Íñiguez, Alfonso Tarancón. Chapter 6 of the book “IT Innovative Practices in Secondary Schools: Remote Experiments”, Published by Deusto in 2013. ISBN: 978-84-15772-01-9
3.- Hadoop Cloud SaaS access via WS-PGRADE adaptation. November 2012, Elisa Cauhé, Arturo Giner, Jaime Ibar, Gonzalo Ruiz, Ruben Vallés. 6th IBERIAN GRID INFRASTRUCTURE CONFERENCE PROCEEDINGS Pages: 161-172 Published: 2013
4.- Heterogeneous networks do not promote cooperation when humans play a Prisoner‘s Dilemma. 8th June 2012, Carlos Gracia-Lázaro, Alfredo Ferrer, Gonzalo Ruiz, Alfonso Tarancón, José A. Cuesta, Angel Sánchez, and Yamir Moreno. PNAS, Vol. 109, no. 32.
5.- OptiWeb: An optimization application for steel cut industries ported to the Grid in the framework of PireGrid project. 5th May 2011, “Proceedings of the 5th IBERGRID. ISBN: 978-84-9745-884-9”
6.- Structural and Dynamical Patterns on Online Social Networks: The Spanish May 15th Movement as a Case Study. 30th July 2011, Javier Borge-Holthoefer, Alejandro Rivero, Íñigo García, Elisa Cauhé, Alfredo Ferrer, Darío Ferrer, David Francos, David Íñiguez, María Pilar Pérez, Gonzalo Ruiz, Francisco Sanz, Fermín Serrano, Cristina Viñas, Alfonso Tarancón, Yamir Moreno . PLoS ONE 6(8): e23883, 2011.
1.- We participated in the project called “Aragón Open Data”, developing the “Social” part, that consists of gathering information from the Internet (social networks, press, etc.) related to Aragon and presenting it in a structured format through an API in order to provide citizens with tools to make their own applications.
2.- Development of the application called Kampal which is a tool that builds and studies networks formed by members of the University of Zaragoza through their research outcomes and projects. The emphasis is on relationships between people, and on the dynamics of the interactions rather than on individual properties.
3.- Development of a platform that includes several interactive teaching units focused on the study of the Solar System using the technology behind Microsoft Kinect device. These units have been developed in collaboration with the local school Juan de Lanuza within the context of its innovation cathedra.
4.- Participation in SEPS, an INNPACTO project which tries to forecast different kinds of possible risks and hazards in electrical networks, and studies the impact they would have if disturbances or failures finally happen. In this project, we collaborate with companies and research organizations such as Gas Natural Fenosa, Telvent, Universidad Carlos III and Universidad de Lérida.
5.- RRLab (Augmented reality lab for physics): this project, also thought to have educational purposes, consists of the creation of a web platform to perform some physics experiments remotely, with the aim that students can compare their theoretical results with the ones obtained in the experiments.
6.- Prisoners dilemma experiment: we developed a web platform that allows to carry out collective experiments involving humans with the aim of studying how people behave in front of strategic scenarios and different kinds of social dilemmas. This platform has been used in two different experiments so far -in one of them 1300 high-school students participated in real time, which is nowadays the largest experiment done of this kind. During the last years we have made several changes and improvements in the platform in order to study different parameters and variables and how they impact human behavior.
7.- Feelicity: it was a project based on Streetrs, developed with TEDxZaragoza people for the geotagging of happy moments of users.
8.- Collaboration in the Ibercivis project carrying out different development tasks (visualization, web development, BOINC client customization, etc.)
9.- Participation in the project called STEREA “Optimización de Recursos Hídricos y Telegestión de Regadío” that consisted of one of the first web applications made to manage the irrigation systems of different fields with the aim of optimizing resources, reducing costs and increasing productivity.
10.- The FPVII project called SCIBUS, that aims to create a generic-purpose gateway technology as a toolset to provide seamless access to major computing, data and networking infrastructures and services in Europe including clusters, supercomputers, grids, desktop grids, academic and commercial clouds.
11.- Study of the Spanish 15M movement using Twitter data. In this case, the group supported different tasks related to the study such as visualization of the dynamics of messages exchange, the creation of a web page and additional data collection.
12.- Optiweb: in the beginning of 2011, this project developed in collaboration with the company Schnell Software, consisted of optimizing one of their software products to allow using a grid computing platform in order to improve its performance.
Head of the Research Line:
The High Performance Computing (HPC) group at BIFI is mainly devoted to:
1.- PrionScan: an online database of predicted prion domains in complete proteomes. Angarica, V.E., Angulo, A., Giner, A., Losilla, G., Ventura, S., and Sancho, J. BMC Genomics. 15: 102. 2014.
1.- Spanish Supercomputing Network (RES): the RES consists of a distributed virtual infrastructure of supercomputers located in different sites, each of which contributes to the total processing power available to users of different R&D groups in Spain or based in another country but developed by with participation of Spanish researchers. Since its establishment in 2007, we host & manage CAESARAUGUSTA, the node of Aragón in the RES.
2.- ETP4HPC: the European Technology Platform (ETP) in the area of High-Performance Computing (HPC), whose main goal is to assist the European Comission in the definition of research priorities and action plans in the area of HPC technology provision.
3.- SCC-Computing: establishing a strategic collaboration with Chinese computer scientists in developing next generation computing systems beyond Tianhe-1A (rated 1st supercomputer in the world in November 2010 top500 ranking).
Head of the Research Line:
Participation in national and international projects related to distributed grid & cloud computing and discussion and integration forums of these technologies from research to companies.
Technical configuration, integration, administration and user support of the Colossus and AraGrid infrastructures, both of them part of the CESAR supercomputing center. They have together more than 4000 computing cores and about 700TB of raw storage.
These infrastructures provide computing resources to a wide range of researches, who have specific or complementary requirements to those which HPC infrastructures offer. In addition to this, they also serve as a testbed for Spanish and European companies and SMEs, which are willing to adopt these technologies to improve their business model. Therefore, in the last years, we have focused our cloud research and infrastructures in helping SMEs on how to take advantage of these powerful technologies and it is one of our main objectives both offering IaaS (Infrastructure as a Service) computing resources and collaborating in the development and cloud integration of their applications.
Furthermore, the infrastructures are shared by the Ibergrid initiative (Spain & Portugal) and also by EGI (European Grid Infrastructure), which is one of the greatest distributed infrastructures of the world.
Teaching and dissemination: Due to the special requirements of Grid and Cloud infrastructures, we provide user support in the migration and adaptation of the applications in order to work within this distributed environments. Our team also actively collaborates in this kind of activities organizing workshops, courses, talks and meetings with companies, as well as the dissemination of all the projects in which we are participating.
4.- FedCloud EGI (Federated Cloud)
5.- CloudSME (Simulation for manufacturing & engineering)
6.- SCI-BUS (Scientific gateway Based User Support)
8.- EGI-InSPIRE ( European Grid Infrastructure )
10.- int.eu.grid (Interactive European Grid)
Head of the Research Line:
Sergio Pérez Gaviro
José Miguel Gil Narvión
Luis Antonio Fernández
Victor Martín Mayor
Juan Jesús Ruíz Lorenzo
Computers have become an essential tool in our quotidian lives. Very simple daily mundane activities as buying a train ticket or sending someone a message require the use of conventional computers. Of course, they also play a very important role in more difficult tasks, such as bank transfers or power grid management for instance. On the other hand, computers have also made possible many advances in Science and nowadays are patently present in a very wide set of different scientific areas. Indeed, many institutions around the World spend a huge amount of money and human effort to build clusters of computers (see for example, www.top500.org/lists/ for a detailed ranked list of the most powerful supercomputers in the World).
For some specific problems, however, conventional computers are not enough. They would spend thousands of years to perform some particular calculations. So in the framework of supercomputing one finds the Special Purpose Computers, which are developed and designed to perform some specific computing-intensive calculation.
The development of this kind of supercomputers is in fact the objective of this research line. So, thanks to a very successful scientific collaboration between researchers from BIFI and the Universidad de Zaragoza, Universidad Complutense de Madrid, Universidad de Extremadura, Università degli Studi di Roma “La Sapienza” and Università di Ferrara, the Janus supercomputer was born in 2008. It is a modular, massively parallel, and reconfigurable FPGA-based computing system for High Performance Scientific Computing. Its reconfigurable architecture would permit Janus to afford different scientific computational applications, as in Physic, in Chemistry or in Biology. So far, the Janus Collaboration focused its efforts on the study and simulation of spin glasses, paradigm of complex systems.
Janus is composed by 16 boards. On each board, a bidimensional 4×4 grid of FPGA-processors is located and linked obeying periodic boundary conditions. Each of these processors is called SP (Simulation Processor) and carries on the simulations. A 17th FPGA is settled in the middle acting as a crossbar and called IOP (Inpu/Output Processor), in charge of all internal connections and external communications. All FPGA modules are Xilinx Virtex4-LX200.
The Janus II Special Purpose Computer is the new generation supercomputer located at BIFI from 2013. Following the same successful Janus philosophy, JanusII is composed again by 16 boards. On each board, 16 latest generation FPGA processors (Xilinx Virtex-7 XC7VX485T FPGA) are located and linked obeying periodic boundary conditions. They are called SP’s from “Simulation Processor”, since they will be in charge of the simulations. All SP’s on each board are controlled by a full fledged computer that we call CP (Control Processor), running the Linux operating system. These CP’s configure all FPGA processors for the simulations, controlling and monitoring their status. The CP uses a commercially available Computer-on-Module system (COM), based on an Intel Core i7 processor; it connects via the PCIe interface to a so-called Input-Output-Processor (IOP) built inside yet another FPGA. The IOP actually manages all connections to all SP’s, controlling the configuration procedure and their operation, and monitoring their status. The Janus II architecture includes also improved communications, permitting the interconnection between all boards, and it enlarges 100 times the memory available.
JanusII was built thanks to FEDER funds: Ministerio de Economía y Competitividad (Gobierno de España), Gobierno de Aragón, European Union.
More info: http://www.janus-computer.com
1.- Janus Collaboration: M. Baity-Jesi, R. A. Baños, A. Cruz, L. A. Fernandez, J. M. Gil-Narvion, A. Gordillo-Guerrero, D. Iñiguez, A. Maiorano, F. Mantovani, E. Marinari, V. Martin-Mayor, J. Monforte-Garcia, A. Muñoz Sudupe, D. Navarro, G. Parisi, S. Perez-Gaviro, M. Pivanti, F. Ricci-Tersenghi, J. J. Ruiz-Lorenzo, S. F. Schifano, B. Seoane, A. Tarancon, R. Tripiccione, D. Yllanes. “Janus II: a new generation application-driven computer for spin-system simulations”. arXiv:1310.1032. Computer Physics Communications 185, 550-559 (2014)
2.- Janus Collaboration: R. A. Banos, A. Cruz, L. A. Fernandez, J. M. Gil-Narvion, A. Gordillo-Guerrero, M. Guidetti, D. Iniguez , A. Maiorano, F. Mantovani, E. Marinari , V. Martin-Mayor, J. Monforte-Garcia, A. Munoz Sudupe, D. Navarro, G. Parisi, M. Pivanti, S. Perez- Gaviro, F. Ricci-Tersenghi, J. J. Ruiz-Lorenzo, S. F. Schifano, B. Seoane, A. Tarancon, R. Tripiccione, D. Yllanes. “An FPGA-based supercomputer for statistical physics: the ‘weird’ case of Janus”. Book Chapter in: “High-Performance Computing using FPGAs”, pp. 481-506 (2013), University of Glasgow, Publisher: Springer.
3.- Janus Collaboration: M. Baity-Jesi, R. A. Banos, A. Cruz, L. A. Fernandez, J. M. Gil-Narvion, A. Gordillo-Guerrero, M. Guidetti, D. Iniguez, A. Maiorano, F. Mantovani, E. Marinari, V. Martin-Mayor, J. Monforte-Garcia, A. Munoz Sudupe, D. Navarro, G. Parisi, M. Pivanti, Perez-Gaviro, F. Ricci-Tersenghi, J. J. Ruiz-Lorenzo, S. F. Schifano, B. Seoane, A. Tarancon, P. Tellez, R. Tripiccione, D. Yllanes. “Reconfigurable computing for Monte Carlo simulations: results and prospects of the Janus project”. arXiv:1204.4134, The European Physical Journal Special Topics 210, 33 (2012).
4.- Janus Collaboration: F. Belletti, M. Cotallo, A. Cruz, L. A. Fernandez, A. Gordillo, A. Maiorano, F. Mantovani, E. Marinari, V. Martin-Mayor, A. Muñoz-Sudupe, D. Navarro, S. Perez-Gaviro, M. Rossi, J. J. Ruiz-Lorenzo, S. F. Schifano, D. Sciretti, A. Tarancon, R. Tripiccione, J. L. Velasco. “JANUS: an FPGA-based System for High Performance Scientific Computing”. arXiv:0710.3535v2, Computing in Science & Engineering 11-1, 48-58 (2009).
5.- Janus Collaboration: F. Belletti, M. Cotallo, A. Cruz, L. A. Fernandez, A. Gordillo, A. Maiorano, F. Mantovani, E. Marinari, V. Martin-Mayor, A. Muñoz-Sudupe, D. Navarro, S. Perez-Gaviro, J. J. Ruiz-Lorenzo, S. F. Schifano, D. Sciretti, A. Tarancon, R. Tripiccione, J. L. Velasco. “Simulating spin systems on IANUS, an FPGA-based computer.” arXiv:0704.3573, Computer Physics Communications 178 (3), p.208-216, (2008).
6.- Janus Collaboration: F. Belletti, I. Campos, A. Cruz, L. A. Fernandez, S. Jimenez, A. Maiorano, F. Mantovani, E. Marinari, V. Martin- Mayor, D. Navarro, A. Muñoz-Sudupe, S. Perez Gaviro, G. Poli, J. J. Ruiz-Lorenzo, F. Schifano, D. Sciretti, A. Tarancon, P. Tellez, R. Tripiccione, J. L. Velasco. “Ianus: an Adaptative FPGA Computer.” arXiv:0507270, Computing in Science & Engineering, January/February 2006, Volume 8, N 1, p. 41.
7.- Janus Collaboration: M. Baity-Jesi, R.A. Baños, A. Cruz, L.A. Fernandez, J.M. Gil-Narvion, A. Gordillo-Guerrero, M. Guidetti, D. Iñiguez, A. Maiorano, F. Mantovani, E. Marinari, V. Martin-Mayor, J. Monforte-Garcia, A. Muñoz-Sudupe, D. Navarro, G. Parisi, S. Perez-Gaviro, M. Pivanti, F. Ricci-Tersenghi, J. Ruiz-Lorenzo, S.F. Schifano, B. Seoane, A. Tarancon, P. Tellez, R. Tripiccione , D. Yllanes. “Spin glass simulations on the Janus architecture: A desperate quest for strong scaling”. Parallel Processing Workshops, Euro-Par 2012, LNCS Volume 7640 LNCS, 2013, Pages 528-537
8.- Janus Collaboration: M. Baity-Jesi, R. A. Banos, A. Cruz, L. A. Fernandez, J. M. Gil-Narvion, A. Gordillo-Guerrero, M. Guidetti, D. Iniguez, Maiorano, F. Mantovani, E. Marinari, V. Martin-Mayor, J. Monforte-Garcia, A. Munoz Sudupe, D. Navarro, G. Parisi, M. Pivanti, S. Perez- Gaviro, F. Ricci-Tersenghi, J. J. Ruiz-Lorenzo, S. F. Schifano, B. Seoane, A. Tarancon, P. Tellez, R. Tripiccione, D. Yllanes. “Janus2: an FPGA-based Supercomputer for Spin Glass Simulations”. ICS12 Workshop proceedings (http://hpc.pnl.gov/conf/ICS2012/)
9.- Janus Collaboration: Belletti, F; Cruz, A; Fernandez, LA; Gordillo-Guerrero, A; Guidetti, M; Maiorano, A; Mantovani, F; Marinari, E; Martin- Mayor, V; Sudupe, AM; Navarro, D; Parisi, G; Perez-Gaviro, S; Ruiz-Lorenzo, JJ; Schifano, SF; Sciretti, D; Tarancon, A; Tripiccione, R; Yllanes,D. “Nonequilibrium spin glass dynamics with Janus”. AIP Conference Proceedings 1091 (2009) 228-230.
10.- Janus Collaboration: Belletti, F; Cotallo, M; Cruz, A; Fernandez, LA; Gordillo-Guerrero, A; Guidetti, M; Maiorano, A; Mantovani, F; Marinari, E; Martin-Mayor, V; Sudupe, AM; Navarro, D; Parisi, G; Perez-Gaviro, S; Rossi, M; Ruiz-Lorenzo, JJ; Saenz-Lorenzo, JF; Schifano, SF; Sciretti, D; Tarancon, A; Tripiccione, R; Velasco, JL; Yllanes, D; Zanier, G. “Monte Carlo simulations for statistical physics: Janus”. Proceedings Paper: Nuovo Cimento B 123 (2008) 972-974
11.- Janus Collaboration: F. Belletti, M. Cotallo, A. Cruz, L. A. Fernández, A. Gordillo, A. Maiorano, F. Mantovani, E. Marinari, V. Martín-Mayor, A. Muñoz-Sudupe, D. Navarro, S. Perez-Gaviro, M. Rossi, J. J. Ruiz-Lorenzo, S. F. Schifano, D. Sciretti, A. Tarancón, R. Tripiccione, J. L. Velasco. “IANUS: Scientific Computing on an FPGA-Based Architecture”. Parallel Computing: Architectures, Algorithms and Applications, Proceedings of the International Conference ParCo 2007 (C. Bishof, M. Buecker, P. Gibbon, G. Joubert, T. Lippert, B. Mohr, F. Peters editors), Publication Series of the John Von Neumann Institute for Computing, 38 (2007) 553-560. Reprinted in: Advances in Parallel Computing, 15 (2008), 553-560.