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4. New Thread Migration Strategies for NUMA Systems

Author

Lorenzo, O. G., Becoña, M. L., Pena, T. F., Cabaleiro, J. C., Lorenzo, J. A., and Rivera, F. F.

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Performance
Abstract

Multicore systems present on-board memory hierarchies and communication networks that influence performance when executing shared memory parallel codes. Characterising this influence is complex, and understanding the effect of particular hardware configurations on different codes is of paramount importance. In previous works, monitoring information extracted from hardware counters at runtime has been used to characterise the behaviour of each thread in the parallel code in terms of the number of floating point operations per second, operational intensity, and latency of memory access. We propose to use this information to guide thread migration strategies that improve execution efficiency by increasing locality and affinity. Different configurations of NAS Parallel OpenMP benchmarks on multicores were used to validate the benefits of the proposed thread migration strategies. Our proposed strategies produce up to 70% improvement in scenarios where locality and affinity are low, there being a small degradation in performance for codes with high locality and affinity., Comment: Unpublished work

Published
2018

8. Optimal control of two coupled spinning particles in the Euler-Lagrange picture

Author

Delgado-Téllez, M., Ibort, A., de la Peña, T. Rodríguez, and Salmoni, R.

Subjects
Mathematics - Optimization and Control
Abstract

A family of optimal control problems for a single and two coupled spinning particles in the Euler-Lagrange formalism is discussed. A characteristic of such problems is that the equations controlling the system are implicit and a reduction procedure to deal with them must be carried on. The reduction of the implicit control equations arising in these problems will be discussed in the slightly more general setting of implicit equations defined by invariant one-forms on Lie groups. As an instance, the first order differential equations describing the extremal solutions of an optimal control problem for a single spinning particle, obtained by using Pontryagin's Maximum Principle (PMP), will be found and shown to be completely integrable. Then, using again PMP, solutions for the problem of two coupled spinning particles will be characterised as solutions of a system of coupled non-linear matrix differential equations. The reduction of the implicit system will show that the reduced space for them is the product of the space of states for the independent systems, implying the absence of `entanglement' in this instance. Finally it will be shown that, in the case of identical systems, the degree three matrix polynomial differential equations determined by the optimal feedback law, constitute a completely integrable Hamiltonian system and some of its solutions are described explicitly.

Published
2015
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10. Optimal Control Realizations of Lagrangian Systems with Symmetry

Author

Delgado-Tellez, M., Ibort, A., and de la Peña, T. Rodriguez

Subjects
Mathematics - Optimization and Control
Abstract

A new relation among a class of optimal control systems and Lagrangian systems with symmetry is discussed. It will be shown that a family of solutions of optimal control systems whose control equation are obtained by means of a group action are in correspondence with the solutions of a mechanical Lagrangian system with symmetry. This result also explains the equivalence of the class of Lagrangian systems with symmetry and optimal control problems discussed in \cite{Bl98}, \cite{Bl00}. The explicit realization of this correspondence is obtained by a judicious use of Clebsch variables and Lin constraints, a technique originally developed to provide simple realizations of Lagrangian systems with symmetry. It is noteworthy to point out that this correspondence exchanges the role of state and control variables for control systems with the configuration and Clebsch variables for the corresponding Lagrangian system. These results are illustrated with various simple applications.

Published
2012

12. 57 Bronchoscopy sampling finds that intra-lung bacterial migration contributes to persistent Pseudomonas aeruginosa infection after elexacaftor-tezacaftor-ivacaftor

Author

Durfey, S., primary, Kapnadak, S., additional, Radey, M., additional, Teresi, M., additional, Gambol, T., additional, Hayden, H., additional, Willmering, M., additional, Godwin, J., additional, Boyken, L., additional, Stroik, M., additional, Singh, S., additional, Steele, C., additional, Woods, J., additional, Vo, A., additional, Stoltz, D., additional, Pena, T., additional, Clancy, J., additional, Aitken, M., additional, Feder, A., additional, and Singh, P., additional

Published
2023
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13. WS13.06 Regional bronchoscopy sampling indicates that Pseudomonas aeruginosa infections persist throughout the lung after elexacaftor/tezacaftor/ivacaftor (ETI) due to intra-lung bacterial migration

Author

Durfey, S.L., primary, Kapnadak, S.G., additional, Teresi, M., additional, Gambol, T., additional, Radey, M.C., additional, Hayden, H.S., additional, Willmering, M.M., additional, Godwin, J.D., additional, Boyken, L., additional, Stroik, M., additional, Vo, A., additional, Singh, S.B., additional, Steele, C., additional, Woods, J.C., additional, Stoltz, D., additional, Pena, T., additional, Clancy, J.P., additional, Aitken, M.L., additional, Feder, A.F., additional, and Singh, P.K., additional

Published
2023
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14. WS05.06 Phase 1/2a randomized, double-blind, placebo-controlled study: safety, Pk, and Efficacy outcome measures of inhaled Gallium Citrate (AR-501) in P Aeruginosa infected Cystic Fibrosis patients

Author

Cohen, A., primary, Lechtzin, N., additional, Boas, S., additional, Pena, T., additional, McBennett, K., additional, Gross, J., additional, Dorgan, D., additional, Couch, L., additional, Hoffman, L., additional, Saavedra, M., additional, Hisert, K., additional, Stevens-Brogan, M., additional, Plascencia, C., additional, Deans, L., additional, Kelson, A., additional, Lovalenti, P., additional, Woo, J., additional, Truong, V., additional, and Jafri, H.S., additional

Published
2023
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18. Phosphorylated S6 Ribosomal Protein as an Additional Marker of Antibody-Mediated Rejection in Lung Allografts: A Multicentre Study

Author

Lunardi, F., primary, Vedovelli, L., additional, Pezzuto, F., additional, Pavec, J. Le, additional, Dorfmuller, P., additional, Ivanovic, M., additional, Pena, T., additional, Wassilew, K., additional, Perch, M., additional, Hirschi, S., additional, Chenard, M., additional, Neil, D., additional, Montero-Fernandez, M., additional, Rice, A., additional, Cozzi, E., additional, Rea, F., additional, Levine, D.J., additional, Roux, A., additional, Goddard, M., additional, Fishbein, G.A., additional, and Calabrese, F., additional

Published
2023
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20. Tazarotene and Bexarotene Show Efficacy as In Vitro Therapeutic Agents in Multiple Sulfatase Deficiency.

Author

Schlotawa, L., Matysiak, K., Kettwig, M., Ahrens-Nicklas, R. C., Baud, M., Berulava, T., Brunetti-Pierri, N., Gagne, A., Herbst, Z. M., Maguire, J. A., Monfregola, J., Pena, T., Radhakrishnan, K., Schröder, S., Waxman, E. A., Ballabio, A., Dierks, T., Fischer, A., French, D. L., and Gelb, M. H.

Subjects
SULFATASES, LYSOSOMAL storage diseases, HIGH throughput screening (Drug development), NEURODEGENERATION, RESEARCH personnel, GLYCOGEN storage disease type II
Abstract

The article discusses the potential use of tazarotene and bexarotene as therapeutic agents for multiple sulfatase deficiency (MSD), an ultra-rare neurodegenerative lysosomal disorder. MSD is caused by mutations in the SUMF1 gene, resulting in impaired function of the formylglycine-generating enzyme (FGE) and reduced activity of cellular sulfatases. The researchers conducted a high-throughput screening assay and found that tazarotene and bexarotene increased sulfatase activities, improved cellular markers of disease, and normalized lysosomal size and position in MSD patient-derived cells. These findings suggest that these drugs could be repurposed as a therapy for MSD patients. [Extracted from the article]

Published
2023
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22. Propuesta de Accesibilidad a los Sistemas Integrados de Transporte con Barreras Físicas para Usuarios de Sillas de Ruedas

Author

Miller, I. D. Castro, Peña, T. P. Ortiz, Salazar, O. I. Campo, Folgueras Méndez, José, editor, Aznielle Rodríguez, Tania Y., editor, Calderón Marín, Carlos F., editor, Llanusa Ruiz, Susana Beatriz, editor, Castro Medina, Jorge, editor, Vega Vázquez, Haddid, editor, Carballo Barreda, Maylen, editor, and Rodríguez Rojas, Rafael, editor

Published
2013
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23. A Load Balance Methodology for Highly Compute-Intensive Applications on Grids Based on Computational Modeling

Author

Martínez, D. R., Albín, J. L., Cabaleiro, J. C., Pena, T. F., Rivera, F. F., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Meersman, Robert, editor, Tari, Zahir, editor, and Herrero, Pilar, editor

Published
2005
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24. Modeling Execution Time of Selected Computation and Communication Kernels on Grids

Author

Boullón, M., Cabaleiro, J. C., Doallo, R., González, P., Martínez, D. R., Martín, M., Mouriño, J. C., Pena, T. F., Rivera, F. F., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Sloot, Peter M. A., editor, Hoekstra, Alfons G., editor, Priol, Thierry, editor, Reinefeld, Alexander, editor, and Bubak, Marian, editor

Published
2005
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25. Performance Prediction for Parallel Iterative Solvers

Author

Blanco, V., González, P., Cabaleiro, J. C., Heras, D. B., Pena, T. F., Pombo, J. J., Rivera, F.F, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Sloot, Peter M. A., editor, Hoekstra, Alfons G., editor, Tan, C. J. Kenneth, editor, and Dongarra, Jack J., editor

Published
2002
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26. Desarrollo de adsorbentes de CO2 a partir del residuo sólido de la preparación de horchata

Author

Córdoba, C., Pena, T., Rubiera González, Fernando, and González Plaza, Marta

Subjects
carbón activado, carbonización hidrotermal, captura de CO2, Ensure access to affordable, reliable, sustainable and modern energy for all, activación iónica in situ, adsorción
Abstract

M.G.P. agradece un contrato del programa Ramón y Cajal cofinanciado por el Fondo Social Europeo (RyC-2015-17516). C.C. agradece una beca de Introducción a la Investigación JAE Intro de la Agencia Estatal CSIC (JAEINT_19_01312).

Published
2022

27. Security by Design for Big Data Frameworks Over Cloud Computing

Author

Awaysheh, F. M., Aladwan, M. N., Alazab, M., Alawadi, Sadi, Cabaleiro, J. C., Pena, T. F., Awaysheh, F. M., Aladwan, M. N., Alazab, M., Alawadi, Sadi, Cabaleiro, J. C., and Pena, T. F.

Abstract

Cloud deployment architectures have become a preferable computation model of Big Data (BD) operations. Their scalability, flexibility, and cost-effectiveness motivated this trend. In a such deployment model, the data are no longer physically maintained under the user’s direct control, which raises new security concerns. In this context, BD security plays a decisive role in the widespread adoption of cloud architectures. However, it is challenging to develop a comprehensive security plan unless it is based on a preliminary analysis that ensures a realistic secure assembly and addresses domain-specific vulnerabilities. This article presents a novel security-by-design framework for BD frameworks deployment over cloud computing (BigCloud). In particular, it relies on a systematic security analysis methodology and a completely automated security assessment framework. Our framework enables the mapping of BigCloud security domain knowledge to the best practices in the design phase. We validated the proposed framework by implementing an Apache Hadoop stack use case. The study findings demonstrate its effectiveness in improving awareness of security aspects and reducing security design time. It also evaluates the strengths and limitations of the proposed framework, from which it highlights the main existing and open challenges in the BigCloud-related area., eSSENCE - An eScience Collaboration

Published
2022
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30. Effects of Nod Factors on Plants

Author

Kondorosi, E., Bauer, P., Brown, S., Crespi, M., de la Pena, T. C., Dudits, D., Turk, J. E., Esnault, R., Jurkevitch, E., Magyar, Z., Poiret, M., Savouré, A., Sallaud, C., Staehelin, C., Schultze, M., Kondorosi, A., Daniels, Michael J., editor, Downie, J. Allan, editor, and Osbourn, Anne E., editor

Published
1994
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32. 517: Regional evolution of Pseudomonas aeruginosa in the human host

Author

Durfey, S., primary, Radey, M., additional, Hayden, H., additional, Teresi, M., additional, Kapnadak, S., additional, Godwin, J., additional, Boyken, L., additional, Stroik, M., additional, Vo, A., additional, Singh, S., additional, Stoltz, D., additional, Brewington, J., additional, Pena, T., additional, Aitken, M., additional, and Singh, P., additional

Published
2021
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37. Theoretical structure and vibrational analysis of ethyl methanesulfonate, CH 3SO2OCH2CH3

Author

Tuttolomondo, M.E., Navarro, A., Pena, T., Altabef, Ben A., and Varetti, E.L.

Subjects
Raman spectroscopy -- Research, Chemicals, plastics and rubber industries
Abstract

Ethyl methanesulfonate, CH3SO2OCH2CH3, is well-known as an alkylating agent in mutagenic and cacinogenic processes. The infrared spectra of CH3SO2OCH2CH3 are reported for the liquid and solid states as well as the Raman spectrum of liquid.

Published
2005

42. Impact of Pre-Transplant Anti-Fibrotic Therapy for IPF Upon Lung Transplant Outcomes

Author

Astor, T.L., primary, Goldberg, H.J., additional, Snyder, L., additional, Courtwright, A., additional, Hachem, R., additional, Pena, T., additional, Zaffiri, L., additional, Criner, G.J., additional, Budev, M.M., additional, Thaniyavarn, T., additional, Lazarus, H.M., additional, Bender, S., additional, Barakat, A., additional, Breeze, J., additional, and LaCamera, P., additional

Published
2020
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48. LBMA and IMAR 2 : Weighted lottery based migration strategies for NUMA multiprocessing servers.

Author

Laso, R., Lorenzo, O. G., Rivera, F. F., Cabaleiro, J. C., Pena, T. F., and Lorenzo, J. A.

Subjects
MULTICORE processors, TELECOMMUNICATION systems, LOTTERIES
Abstract

Summary: Multicore NUMA systems present on‐board memory hierarchies and communication networks that influence performance when executing shared memory parallel codes. Characterizing this influence is complex, and understanding the effect of particular hardware configurations on different codes is of paramount importance. In this article, monitoring information extracted from hardware counters at runtime is used to characterize the behavior of each thread for an arbitrary number of multithreaded processes running in a multiprocessing environment. This characterization is given in terms of number of operations per second, operational intensity, and latency of memory accesses. We propose a runtime tool, executed in user space, that uses this information to guide two different thread migration strategies for improving execution efficiency by increasing locality and affinity without requiring any modification in the running codes. Different configurations of NAS Parallel OpenMP benchmarks running concurrently on multicore NUMA systems were used to validate the benefits of our proposal, in which up to four processes are running simultaneously. In more than the 95% of the executions of our tool, results outperform those of the operating system (OS) and produces up to 38% improvement in execution time over the OS for heterogeneous workloads, under different and realistic locality and affinity scenarios. [ABSTRACT FROM AUTHOR]

Published
2021
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50. Effects of Nod Factors on Plants

Author

Kondorosi, E., primary, Bauer, P., additional, Brown, S., additional, Crespi, M., additional, de la Pena, T. C., additional, Dudits, D., additional, Turk, J. E., additional, Esnault, R., additional, Jurkevitch, E., additional, Magyar, Z., additional, Poiret, M., additional, Savouré, A., additional, Sallaud, C., additional, Staehelin, C., additional, Schultze, M., additional, and Kondorosi, A., additional

Published
1994
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