Universidad de Málaga - Picasso Node

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Overview

The Picasso Supercomputer
Picasso is a RES node located in the Bio-Innovation Building of the University of Málaga (UMA) at the Technological Park of Andalusia (PTA), close to the city of Málaga. It is managed by the SCBI (Supercomputing and Bioinformatics Centre) of the UMA, which runs several integrated computational infrastructures supporting research activities within the University and in the Andalusian region. These include a 7 node cluster of 80 cores and 2TB RAM computers, 32 nodes with 16 cores, 41 nodes with 24 cores and 16 nodes with 2 GPUs each, totalling 63 TFLOP/s. All these resources share computer room, cooling, power and fire extinguishing systems.

Other resources include a virtual infrastructure belonging to the Bioinformatics Platform of Andalusia, which hosts all its servers and desktop systems as virtual machines running on a cluster of VMWare ESX servers.

Organisational Structure

SCBI team at Málaga (left to right): Rafael Larrosa, Darío Guerrero


The SCBI draws on 15 years of experience of the Computational Laboratory of the University of Málaga in running production supercomputers to support scientific research in several fields. It also incorporates a multidisciplinary research infrastructure, the Bioinformatics Platform of Andalusia, whose mission is to provide computational resources and commercial software licenses, and to transfer knowledge and experience on bioinformatics research to the scientific community in Andalusia.

The SCBI is an independent service with its own staff dedicated to administration of machines and user support, but also giving higher level support to researchers in the development of computational solutions for problems in several areas, especially biological research.

There is also strong cooperation with the Computer Architecture Department of the UMA whose main research areas are analysis, design, and evaluation of high performance architectures, from the application level to the lower hardware levels.

Technical and Scientific Highlights 2014

The left half of the Picasso Supercomputer

In 2014 new computer resources were made available to users, with more cores, more disk space and a wider selection of systems. Four different systems are offered, from a cluster of big memory computers with 2TB of RAM each, to a cluster of computers with GPUs, all under the control of the same queue manager, thereby enabling users to select the one which best matches their research needs.

The right half of the Picasso Supercomputer



Biocomputation was one of the main areas that used most of the node´s resources, taking special advantage of the bigmem cluster for the assembly of genomes, and using the rest of the system for other processes. Quantum mechanics, protein folding and custom simulations, where users write their own code, were also heavy users of the system, as can be seen in the publications list.


Key Publications 2014

Articles

  • 3GPP QoS Based Scheduling Framework for LTE. Pablo Ameigeiras, Jorge Navarro-Ortiz, Juan M. Lopez-Soler et al. 2014 - International Journal of Communications Systems
  • A combined MD/QM and experimental exploration of conformational richness in branched oligothiophenes. Jonas Sjöqvist, Rafael Carlos González-Cano, Juan T. López Navarrete et al. 2014 - Physical Chemistry Chemical Physics
  • A Histogram Transform for Probability Density Function Estimation. Ezequiel Lopez-Rubio. 2014 - IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
  • A Performance/Cost Evaluation for a GPU-Based Drug Discovery Application on Volunteer Computing. Ginés D. Guerrero, Baldomero Imbernón, Horacio Pérez-Sánchez et al. 2014 - BioMed Research International
  • Accelerating GWAS Epistatic Interaction Analysis Methods. Upton A, Orue P, Trelles O. 2014 - Proc. XII Symp. Bioinformatics
  • Alkoxy-Functionalized Thienyl-Vinylene Polymers for Field-Effect Transistors and All-Polymer Solar Cells. Hui Huang, Nanjia Zhou, Rocio Ponce Ortiz et al. 2014 - Advanced Functional Materials
  • An adaptive system for compressed video deblocking. Ezequiel López-Rubio, Rafael Marcos Luque-Baena. 2014 - Signal Processing.
  • An Efficient Solvent Accessible Surface Area calculation applied in Ab Initio Protein Structure Prediction. D. Bonetti, H. Pérez-Sánchez, A. Delbem. 2014 - IWBBIO 2014
  • Antiaromatic Bisindeno-[n]thienoacenes With Small Singlet Biradical Characters: Syntheses, Structures and Chain Length Dependent Physical Properties Xueliang Shi, Paula Mayorga Burrezo, Sangsu Lee et al. 2014 - Chemical Science
  • Application of parallel blind docking with BINDSURF for the study of platinum derived compounds as anticancer drugs. J. P. Cerón-Carrasco, J. Cerezo, J. Zúñiga et al. 2014 - IWBBIO 2014
  • BREGMAN DIVERGENCES FOR GROWING HIERARCHICAL SELF-ORGANIZING NETWORKS. EZEQUIEL LOPEZ-RUBIO, ESTEBAN JOSE PALOMO and ENRIQUE DOMINGUEZ. 2014 - International Journal of Neural Systems
  • Chameleon-like behaviour of cyclo[n]paraphenylenes in complexes with C70: on their impressive electronic and structural adaptability as probed by Raman spectroscopy. Miriam Peña Alvarez, Paula Mayorga Burrezo, Takahiro Iwamoto et al. 2014 - Faraday Discussions
  • Compositions of fungal secretomes indicate a greater impact of phylogenetic history than lifestyle adaptation. Krijger J-J, Thon MR, Deising HB et al. 2014 - BMC Genomics
  • De novo assembly characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes. Integration in a database and design of a microarray. Hicham Benzekri, Paula Armesto, Xavier Cousin et al. 2014 - BMC Genomics
  • Diradicals acting through diamagnetic phenylene vinylene bridges: Raman spectroscopy as a probe to characterize spin delocalization. Sandra Rodríguez González, Belén Nieto-Ortega, Rafael C González Cano et al. 2014 - The Journal of Chemical Physics
  • Draft Genome Sequence of Colletotrichum acutatum sensu lato (Colletotrichum fioriniae). Baroncelli R, Sreenivasaprasad S, Sukno SA et al. 2014 - Genome Announc
  • Draft Genome Sequence of Colletotrichum sublineola: a destructive pathogen of cultivated sorghum. Baroncelli R, Sanz-Martín JM, Rech GE et al. 2014 - Genome Announcements
  • Dynamic Deployment of Small Cells in TV White Spaces. Pablo Ameigeiras, David M. Gutierrez-Estevez, Jorge Navarro-Ortiz. 2014 - IEEE Transactions on Vehicular Technology
  • Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves. Leyva M.O., Valverde-Corredor A., Valderrama R. et al. 2014 - DNA Research
  • EDOT-Based Copolymers with Pendant Anthraquinone Units: Analysis of Their Optoelectronic Properties within the Double-Cable Context. Daniel Herrero-Carvajal, Alejandro de la Peña, Rafael C. González Cano et al. 2014 - Israel Journal of Chemistry
  • Energy of marine currents in the Strait of Gibraltar and its potential as a renewable energy resource. María Concepción Calero, Jesús García Lafuente, José Carlos Sánchez Garrido et al. 2014 - Under review in Renewal and Sustainable Energy Reviews
  • Experimental and numerical characterization of harbor oscillations in the Port of Málaga, Spain. Simone Sammartino, José Sánchez Garrido, Javier Delgado et al. 2014 - Ocean Engineering
  • Genetic and physical mapping of the QTLAR3 controlling blight resistance in chickpea (Cicer rietinum L). E. Madrid; P. Seoane; M.G. Claros et al. 2014 - Euphytica
  • Grid topologies for the self-organizing map. Ezequiel López-Rubio, Antonio Díaz Ramos. 2014 - Neural Networks.
  • Huge Energy Gain in Metal-to-Molecule Charge Transfer Processes: A Combined Effect of an Electrical Capacitive Enhancement in Nanometer-Size Hot Spots and the Electronic Structure of the Surface Complex. Jessica Roman-Perez, Cristina Ruano, Silvia P. Centeno et al. 2014 - JOURNAL OF PHYSICAL CHEMISTRY
  • Increasing the Efficiency of Minimal Key Enumeration Methods by Means of Parallelism. Fernando Benito Picazo, Pablo Cordero, Manuel Enciso et al. 2014 - ICSOFT EA
  • Meteorologically-driven circulation and flushing times of the Bay of Algeciras, Strait of Gibraltar. José C. Sánchez-Garrido, Jesús García Lafuente, Simone Sammartino et al. 2014 - Marine Pollution Bulletin
  • Mode Robustness in Raman Optical Activity. Matteo Tommasini, Giovanna Longhi, Giuseppe Mazzeo et al. 2014 - Journal of Chemical Theory and Computation
  • Multistep Dimerization of Tetrakis(n-decyl)heptathienoacene Radical Cations: A Combined Experimental and Theoretical Study. Ferrón CC, Capdevila-Cortada M, Balster R et al. 2014 - Chem. Eur. J.
  • Natural selection on coding and non-coding DNA sequences is associated with virulence genes in a plant pathogenic fungus. Rech GE, Sanz-Martín JM, Anisimova M et al. 2014 - Genome Biol Evol
  • Numerical and experimental study of a HVAC wall diffuser. J.J. Martinez-Almansaa, A. Fernandez-Gutierrezc, L. Parrasa et al. 2014 - Science Direct
  • On the dual character of charged metal-molecule hybrids and the opposite behaviour of the forward and reverse CT processes. Jessica Roman-Perez, Silvia P. Centeno, Maria Rosa López-Ramírez et al. 2014 - CHEMISTRY CHEMICAL PHYSICS
  • On the regioselectivity of the mononuclear copper-catalyzed cycloaddition of azide and alkynes (CuAAC). A quantum chemical topological study. Calvo-Losada, Pino MS, Quirante JJ. 2014 - J Mol Model
  • Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi. J. Fang, A. Lucia Varbanescu, B. Imbernón et al. 2014 - IWBBIO 2014
  • PEGylated aza-BODIPY derivatives as NIR probes for cellular imaging. Daniel Collado, Yolanda Vida, Francisco Najera and Ezequiel Perez-Inestrosa. 2014 - RSC Advances
  • Phenyl- and Thienyl-Ended Symmetric Azomethines and Azines as Model Compounds for n-Channel Organic Field-Effect Transistors: An Electrochemical and Computational Study. Barbara Vercelli, Mariacecilia Pasini, Anna Berlin et al. 2014 - The Journal of Physical Chemistry
  • Predicting induced activity in the Havar foils of the 18F production targets of a PET cyclotron and derived radiological risk. J. Javier Martínez-Serrano and A. Díez de los Ríos. 2014 - Health Physics
  • Properties of Sizeable [n]Cycloparaphenylenes as Molecular Models of Single-Wall Carbon Nanotubes Elucidated by Raman Spectroscopy: Structural and Electron-Transfer Responses under Mechanical Stress. Miriam Peña Alvarez, Paula Mayorga Burrezo, Miklos Kertesz et al. 2014 - Angewandte Chemie International Edition in English
  • Raman Spectroscopic Characterization of Polyselenophenes and Poly(3,4-ethylenenedioxyselenophene)s. Cristina Capel Ferrón, Yana Sheynin, Mao Li et al. 2014 - Isr. J. Chem
  • Rationalizing the Catalytic Activity of Copper in the Cycloaddition of Azide and Alkynes (CuAAC) with the Topology of ∇2ρ(r) and ∇∇2ρ(r). Saturnino Calvo-Losada,† María Soledad Pino-Gonzá lez,‡ and José Joaquín Quirante. 2014 - The Journal of Physical Chemistry
  • Robust gene signatures from microarray data using genetic algorithms enriched with biological pathway keywords. R.M. Luque Baena; D. Urda; M.G. Claros et al.. 2014 - J Biomed Inform
  • Selected ABCB1, ABCB4 and ABCC2 polymorphisms do not enhance the risk of drug-induced hepatotoxicity in a Spanish cohort. Ulzurrun E, Stephens C, Ruiz-Cabello F et al. 2014 - Plos one
  • Sma3s: a three-step modular annotator for large sequence datasets. A. Muñoz-Mérida, E. Viguera, M.G. Claros et al. 2014 - DNA Research
  • Symmetry Lowering in Triindoles: Impact on the Electronic and Photophysical Properties. Constanza Ruiz, Eva M. García-Frutos, Demetrio A. da Silva Filho et al. 2014 - J. Phys. Chem. C
  • The role of High Performance Computing in Bioinformatics. H. Peréz-Sánchez, J. M. Cecilia, I. Merelli. 2014 - IWBBIO 2014
  • The unusual electronic structure of ambipolar dicyanovinyl-substituted diketopyrrolopyrrole derivatives. Alberto Riaño, P. Mayorga Burrezo, M. J. Mancheño et al. 2014 - Journal of Materials Chemistry
  • Turning on the biradical state of tetracyano-perylene and quaterrylenequinodimethanes by incorporation of additional thiophene rings. Zebing Zeng, Sangsu Lee, José L. Zafra et al. 2014 - Chemical Science
  • Zethrene biradicals: How pro-aromaticity is expressed in the ground electronic state and in the lowest energy singlet, triplet, and ionic states. José Luis Zafra, Rafael C González Cano, M Carmen Ruiz Delgado et al. 2014 - The Journal of Chemical Physics
  • Improvement of Virtual Screening predictions using Computational Intelligence methods,G. Cano, J. García, H. Pérez-Sánchez, 2014, Letters in Drug Design & Discovery, 11(1), 33-39.
  • Ligand Induced Change of β2 Adrenergic Receptor from Active to Inactive Conformation and Its Implication with Close and Open of Water Channel: Insight from Molecular Dynamics Simulation, Free Energy Calculation and Markov State Model Analysis, Q. Bai, H. Pérez-Sánchez, Y. Zhang, Y. Shao, D. Shi, H. Liu, X. Yao, (2014) Physical Chemistry Chemical Physics, 16(30), 15874-85.
  • Descubrimiento de Fármacos basado en Cribado Virtual Refinado con Enfoques Neuronales Paralelos,H. Pérez-Sánchez, G. Cano, J. García-Rodríguez, (2014), Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería, DOI:10.1016/j.rimni.2014.06.004.
  • Labelling Herceptin with a novel oxaliplatin derivative: A computational approach towards the selective drug delivery, J.P. Cerón-Carrasco, J. Cerezo, A. Requena, J. Zúñiga, J.Contreras-García, S. Chavan, M. Manrubia-Cobo, H. Pérez-Sánchez, (2014) Journal of Molecular Modeling, DOI:10.1007/s00894-014-2401-7.

Seminars and conferences

  • Cold response in Olive tree; A RNAseq Study. Leyva-Pérez M.O., Valverde A., Jiménez-Ruiz J. et al. 2014 - CONGRESS: 5TH WORKSHOP OF COST ACTION.
  • La respuesta a estrés por frío en el olivo (Olea europea L.) se produce mediante cambios transitorios de la expresión génica a la vez que por cambios adaptativos estables durante la persistencia del ESTRÉS. María de la O Leyva-Pérez, Antonio Valverde, Jaime Jiménez-Ruiz et al. 2014 - CONGRESS: XXXIX CONGRESO DE LA SOCIEDAD ESPAÑOLA DE GENÉTICA
  • Un gen marcador de la infección por Verticillium dahliae del olivo cultivado (Olea europaea L.). Leyva M.O., Schilirò E., Jiménez-Ruiz J. et al. 2014 - CONGRESS - XII REUNIÓN DE BIOLOGÍA MOLECULAR DE PLANTAS
  • Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi, J. Fang, A. Lucia Varbanescu, B. Imbernón, J. M. Cecilia, H. Pérez-Sánchez, (2014) , International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014, 579-588.
  • Application of parallel blind docking with BINDSURF for the study of platinum derived compounds as anticancer drugs, J. P. Cerón-Carrasco, J. Cerezo, J. Zúñiga, A. Requena, J. Contreras-García, S. Chavan, M. Manrubia-Cobo, B. Imbernón, J. M. Cecilia, H. Pérez-Sánchez, (2014) , International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014, 972-976.
  • The role of High Performance Computing in Bioinformatics, H. Pérez-Sánchez, J. M. Cecilia, I. Merelli, (2014), In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014, 494-506.


Key Projects 2014

2014 was a highly productive year, with numerous publications and very interesting research.

Physical oceanography research

The physical oceanography research group [1] of the University of Malaga conducted a simulation of the circulation and renew times of the water in the Bay of Algeciras. The evolution of possible oil spills, taking into account currents and meteorological forces, is studied, with the objective of optimising interventions in case disaster strikes. The Bay is a place of singular complexity. The clash between Atlantic and Mediterranean water flows that develop in the adjacent Strait of Gibraltar, and its study is of particular interest to the scientific oceanographic[2] community.


Experimental and numerical characterisations of harbour oscillations in the port of Málaga were also done. The harbour is characterised by abnormal oscillations of the sea level. Its trigger seems to be the resonance between high-frequency oscillations of the sea level induced by the atmospheric fronts and the harbour structure. With this research the effect of future expansions can be studied and design optimised in order to avoid such problems.[3]

Panel (a) map of the Province of Málaga. Weather stations are represented in white circles. The main rivers and geographical structures cited are indicated. Panel (b) map of the Port of Málaga. The two tide gauges analysed are represented in white triangles.

Panel (a) finite element discretisation grid used to solve the eigenvalue problem. Panel (b) and (c) amplitudes of the first and the second modes, respectively. Amplitude is expressed in normalized units.

An adaptive system for compressed video deblocking

The icai research group of the University of Málaga icai developed a video deblocking system which is based on the properties of the DCT. Many state of the art methods for video compression rely on the Discrete Cosine Transform (DCT) and the quantization of its coefficients. Hence it is suitable for MPEG-2 compressed videos, since the MPEG-2 standard belongs to this class of compression formats. The system carries out an online analysis of the video in order to adapt its operation to the characteristics of the incoming video frames. Experiments with benchmark real videos are shown, which demonstrate the performance of our proposal both in quantitative and qualitative terms.

File:decomp_videos_qual.jpg

In the above figure three different performance metrics are applied over the akiyo sequence with a bitrate of 310.2 kbits/s. (a) MSE comparison; the lower the signal the better the method. (b) SSIM comparison; the closer to 1 the index, the better the method. (c) Blockiness comparison; the closer to the dotted line, the fewer amount of blocking artefacts the method yields.

HVAC simulation

The fluid mechanics group of the University of Málaga fluidmal inside the general research of flows, jets, vortices, etc. analysed the work of a HVAC diffuser, developing a Micro/Macro Level Approach (MMLA) method to model a conventional diffuser. This procedure reduces the number of points in order to solve the airflow in a room. This can be seen as a numerical box method, and it provides a number of variables at the inlet of the room (outlet of the diffuser) which are difficult to obtain experimentally, e.g. turbulent properties. Flow visualizations were carried out to determine the shape of the plume. These qualitative experimental data are also compared with numerical temperature fields for sufficiently high Reynolds numbers and give accurate results. In addition, we report the throw and drop of the diffuser for different flow rates. Finally, the pressure drop of the terminal device was obtained experimentally, and it is also shown that numerical results can predict it accurately. A discussion of two different methods to compute the pressure drop is given, showing the differences in relation to the airflow characteristics near the outlet of the diffuser.

File:Hvac_habitacion.jpg

Sketch of the experimental setup.

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