Extending the VEF traces framework to model data center network workloads

Producción CientíficaData centers are a fundamental infrastructure in the Big-Data era, where applications and services demand a high amount of data and minimum response times. The interconnection network is an essential subsystem in the data center, as it must guarantee high communication bandwidth and low latency to the communication operations of applications, otherwise becoming the system bottleneck. Simulation is widely used to model the network functionality and to evaluate its performance under specific workloads. Apart from the network modeling, it is essential to characterize the end-nodes communication pattern, which will help identify bottlenecks and flaws in the network architecture. In previous works, we proposed the VEF traces framework: a set of tools to capture communication traffic of MPI-based applications and generate traffic traces used to feed network simulator tools. In this paper, we extend the VEF traces framework with new communication workloads such as deep-learning training applications and online data-intensive workloads.Ministerio de Ciencia e Innovación y Agencia Estatal de Investigación (MCIN/AEI/10.13039/501100011033) R &D Project Grant (PID2019-109001RA-I00)Publicación en abierto financiada por el Consorcio de Bibliotecas Universitarias de Castilla y León (BUCLE), con cargo al Programa Operativo 2014ES16RFOP009 FEDER 2014-2020 DE CASTILLA Y LEÓN, Actuación:20007-CL - Apoyo Consorcio BUCL

Constructing virtual 5-dimensional tori out of lower-dimensional network cards

[EN] In the Top500 and Graph500 lists of the last years, some of the most powerful systems implement a torus topology to interconnect themillions of computing nodes they include. Some of these torus networks are of five or six dimensions, which implies an additional difficulty as the node degree increases. In previous works, we proposed and evaluated the nD Twin (nDT) torus topology to virtually increase the dimensions a torus is able to implement. We showed that this new topology reduces the distances between nodes, increasing, therefore, global network performance. In this work, we present how to build a 5DT torus network using a specific commercial 6-port network card (EXTOLL card) to interconnect those nodes. We show, using the same number of cards, that the performance of the 5DT torus network we are able to implement using our proposal is higher than the performance of the 3D torus network for the same number of compute nodes.Spanish MINECO; European Commission, Grant/Award Number: TIN2015-66972-C5-1-R and TIN2015-66972-C5-2-R; JCCM, Grant/Award Number: PEII-2014-028-P; Spanish MICINN, Grant/Award Number: FJCI-2015-26080Andújar-Muñoz, FJ.; Villar, JA.; Sanchez Garcia, JL.; Alfaro Cortes, FJ.; Duato Marín, JF.; Fröning, H. (2017). Constructing virtual 5-dimensional tori out of lower-dimensional network cards. Concurrency and Computation Practice and Experience. 1-17. https://doi.org/10.1002/cpe.4361S11

Energy efficient HPC network topologies with on/off links

Producción CientíficaEnergy efficiency is a must in today HPC systems. To achieve this goal, a holistic design based on the use of power-aware components should be performed. One of the key components of an HPC system is the high-speed interconnect. In this paper, we compare and evaluate several design options for the interconnection network of an HPC system, including torus, fat-trees and dragonflies. State of the art low power modes are also used in the interconnection networks. The paper does not only consider energy efficiency at the interconnection network level but also at the system as a whole. The analysis is performed by using a simple yet realistic power model of the system. The model has been adjusted using actual power consumption values measured on a real system. Using this model, realistic multi-job trace-based workloads have been used, obtaining the execution time and energy consumed. The results are presented to ease choosing a system, depending on which parameter, performance or energy consumption, receives the most importance.Ministerio de Economía, Industria y Competitividad (projects PID2019-105903RB-100 and PID2021-123627OB)Junta de Comunidades de Castilla-La Mancha (project SBPLY/21/180501/ 000248

Supporting efficient overlapping of host-device operations for heterogeneous programming with CtrlEvents

Producción CientíficaHeterogeneous systems with several kinds of devices, such as multi-core CPUs, GPUs, FPGAs, among others, are now commonplace. Exploiting all these devices with device-oriented programming models, such as CUDA or OpenCL, requires expertise and knowledge about the underlying hardware to tailor the application to each specific device, thus degrading performance portability. Higher-level proposals simplify the programming of these devices, but their current implementations do not have an efficient support to solve problems that include frequent bursts of computation and communication, or input/output operations. In this work we present CtrlEvents, a new heterogeneous runtime solution which automatically overlaps computation and communication whenever possible, simplifying and improving the efficiency of data-dependency analysis and the coordination of both device computations and host tasks that include generic I/O operations. Our solution outperforms other state-of-the-art implementations for most situations, presenting a good balance between portability, programmability and efficiency.Ministerio de Ciencia e Innovación - FEDER (TIN2017-88614-R)Junta de Castilla y León (VA226P20)Ministerio de Ciencia e Innovación - AEI and European Union NextGenerationEU/PRTR (TED2021–130367B–I00 and MCIN/AEI/10.13039/501100011033

POWAR: Power-Aware Routing in HPC Networks with On/Off Links

[EN] In order to save energy in HPC interconnection networks, one usual proposal is to switch idle links into a low-power mode after a certain time without any transmission, as IEEE Energy Efficient Ethernet standard proposes. Extending the low-power mode mechanism, we propose POWer-Aware Routing (POWAR), a simple power-aware routing and selection function for fat-tree and torus networks. POWAR adapts the amount of network links that can be used, taking into account the network load, and obtaining great energy savings in the network (55%-65%) and the entire system (9%-10%) with negligible performance overhead.This work has been supported by the Spanish MINECO and European Commission (FEDER funds) under project TIN2015-66972-C5-1-R. Francisco J. Andujar has been partially funded by the Spanish MICINN and by the ERDF program of the European Union: PCAS Project (TIN2017-88614-R), CAPAP-H6 (TIN2016-81840-REDT), and Junta de Castilla y Leon FEDER Grant VA082P17 (PROPHET Project).Andújar-Muñoz, FJ.; Coll, S.; Alonso Díaz, M.; López Rodríguez, PJ.; Martínez-Rubio, J. (2019). POWAR: Power-Aware Routing in HPC Networks with On/Off Links. ACM Transactions on Architecture and Code Optimization. 15(4):1-22. https://doi.org/10.1145/3293445S122154Abts, D., Marty, M. R., Wells, P. M., Klausler, P., & Liu, H. (2010). Energy proportional datacenter networks. Proceedings of the 37th annual international symposium on Computer architecture - ISCA ’10. doi:10.1145/1815961.1816004Adiga, N. R., Blumrich, M. A., Chen, D., Coteus, P., Gara, A., Giampapa, M. E., … Vranas, P. (2005). Blue Gene/L torus interconnection network. IBM Journal of Research and Development, 49(2.3), 265-276. doi:10.1147/rd.492.0265M. Alonso S. Coll J. M. Martínez V. Santonja and P. López. 2015. Power consumption management in fat-tree interconnection networks. Parallel Comput. 48 C (Oct. 2015) 59--80. 10.1016/j.parco.2015.03.007 M. Alonso S. Coll J. M. Martínez V. Santonja and P. López. 2015. Power consumption management in fat-tree interconnection networks. Parallel Comput. 48 C (Oct. 2015) 59--80. 10.1016/j.parco.2015.03.007Marina Alonso, Coll, S., Martínez, J.-M., Santonja, V., López, P., & Duato, J. (2010). Power saving in regular interconnection networks. Parallel Computing, 36(12), 696-712. doi:10.1016/j.parco.2010.08.003Bob Alverson Edwin Froese Larry Kaplan and Duncan Roweth. 2012. Cray XC series network. Cray Inc. White Paper WP-Aries01-1112 (2012). Bob Alverson Edwin Froese Larry Kaplan and Duncan Roweth. 2012. Cray XC series network. Cray Inc. White Paper WP-Aries01-1112 (2012).Anderson, T. E., Owicki, S. S., Saxe, J. B., & Thacker, C. P. (1993). High-speed switch scheduling for local-area networks. ACM Transactions on Computer Systems, 11(4), 319-352. doi:10.1145/161541.161736Andujar, F. J., Villar, J. A., Sanchez, J. L., Alfaro, F. J., & Escudero-Sahuquillo, J. (2015). VEF Traces: A Framework for Modelling MPI Traffic in Interconnection Network Simulators. 2015 IEEE International Conference on Cluster Computing. doi:10.1109/cluster.2015.141Barroso, L. A., & Hölzle, U. (2007). The Case for Energy-Proportional Computing. Computer, 40(12), 33-37. doi:10.1109/mc.2007.443Camacho, J., & Flich, J. (2011). HPC-Mesh: A Homogeneous Parallel Concentrated Mesh for Fault-Tolerance and Energy Savings. 2011 ACM/IEEE Seventh Symposium on Architectures for Networking and Communications Systems. doi:10.1109/ancs.2011.17Chen, D., Parker, J. J., Eisley, N. A., Heidelberger, P., Senger, R. M., Sugawara, Y., … Steinmacher-Burow, B. (2011). The IBM Blue Gene/Q interconnection network and message unit. Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis on - SC ’11. doi:10.1145/2063384.2063419Chen, L., & Pinkston, T. M. (2012). NoRD: Node-Router Decoupling for Effective Power-gating of On-Chip Routers. 2012 45th Annual IEEE/ACM International Symposium on Microarchitecture. doi:10.1109/micro.2012.33Christensen, K., Reviriego, P., Nordman, B., Bennett, M., Mostowfi, M., & Maestro, J. (2010). IEEE 802.3az: the road to energy efficient ethernet. IEEE Communications Magazine, 48(11), 50-56. doi:10.1109/mcom.2010.5621967Dally, & Seitz. (1987). Deadlock-Free Message Routing in Multiprocessor Interconnection Networks. IEEE Transactions on Computers, C-36(5), 547-553. doi:10.1109/tc.1987.1676939Das, R., Narayanasamy, S., Satpathy, S. K., & Dreslinski, R. G. (2013). Catnap. Proceedings of the 40th Annual International Symposium on Computer Architecture - ISCA ’13. doi:10.1145/2485922.2485950Derradji, S., Palfer-Sollier, T., Panziera, J.-P., Poudes, A., & Atos, F. W. (2015). The BXI Interconnect Architecture. 2015 IEEE 23rd Annual Symposium on High-Performance Interconnects. doi:10.1109/hoti.2015.15Jack Dongarra Hans W. Meuer and Erich Strohmaier. 2018. TOP500 Supercomputer Sites. Retrieved from https://www.top500.org. Jack Dongarra Hans W. Meuer and Erich Strohmaier. 2018. TOP500 Supercomputer Sites. Retrieved from https://www.top500.org.Duato, J. (1993). A new theory of deadlock-free adaptive routing in wormhole networks. IEEE Transactions on Parallel and Distributed Systems, 4(12), 1320-1331. doi:10.1109/71.250114José Duato Sudhakar Yalamanchili and Lionel Ni. 2003. Interconnection Networks. An Engineering Approach. Morgan Kaufmann Publishers Inc. San Francisco CA. José Duato Sudhakar Yalamanchili and Lionel Ni. 2003. Interconnection Networks. An Engineering Approach. Morgan Kaufmann Publishers Inc. San Francisco CA.GALGO 2017. GALGO—Albacete Research Institute of Informatics Supercomputer Center homepage. Retrieved from http://www.i3a.uclm.es/galgo. GALGO 2017. GALGO—Albacete Research Institute of Informatics Supercomputer Center homepage. Retrieved from http://www.i3a.uclm.es/galgo.Greenberg, A., Hamilton, J., Maltz, D. A., & Patel, P. (2008). The cost of a cloud. ACM SIGCOMM Computer Communication Review, 39(1), 68-73. doi:10.1145/1496091.1496103HPCC {n.d.}. HPC Challenge Benchmark. Retrieved from http://icl.cs.utk.edu/hpcc/index.html. HPCC {n.d.}. HPC Challenge Benchmark. Retrieved from http://icl.cs.utk.edu/hpcc/index.html.Hluchyj, M. G., & Karol, M. J. (1988). Queueing in high-performance packet switching. IEEE Journal on Selected Areas in Communications, 6(9), 1587-1597. doi:10.1109/49.12886Koibuchi, M., Otsuka, T., Hiroki Matsutani, & Amano, H. (2009). An on/off link activation method for low-power ethernet in PC clusters. 2009 IEEE International Symposium on Parallel & Distributed Processing. doi:10.1109/ipdps.2009.5161069Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., … Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781-1802. doi:10.1002/jcc.20289Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Lindahl, E. (2013). GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845-854. doi:10.1093/bioinformatics/btt055Reviriego, P., Hernandez, J., Larrabeiti, D., & Maestro, J. (2009). Performance evaluation of energy efficient ethernet. IEEE Communications Letters, 13(9), 697-699. doi:10.1109/lcomm.2009.090880K. P. Saravanan and P. Carpenter. 2018. PerfBound: Conserving energy with bounded overheads in on/off-based HPC interconnects. IEEE Trans. Comput. (2018) 1--1. 10.1109/TC.2018.2790394 K. P. Saravanan and P. Carpenter. 2018. PerfBound: Conserving energy with bounded overheads in on/off-based HPC interconnects. IEEE Trans. Comput. (2018) 1--1. 10.1109/TC.2018.2790394Saravanan, K. P., Carpenter, P. M., & Ramirez, A. (2013). Power/performance evaluation of energy efficient Ethernet (EEE) for High Performance Computing. 2013 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS). doi:10.1109/ispass.2013.6557171Soteriou, V., & Li-Shiuan Peh. (s. f.). Dynamic power management for power optimization of interconnection networks using on/off links. 11th Symposium on High Performance Interconnects, 2003. Proceedings. doi:10.1109/conect.2003.1231472Totoni, E., Jain, N., & Kale, L. V. (2013). Toward Runtime Power Management of Exascale Networks by on/off Control of Links. 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum. doi:10.1109/ipdpsw.2013.191VEF 2017. VEF traces homepage. Retrieved from http://www.i3a.info/VEFtraces. VEF 2017. VEF traces homepage. Retrieved from http://www.i3a.info/VEFtraces

Anàlisi de les accions defensives del porter en el futbol 7

L’anàlisi de la competició serà un mitjà per millorar el coneixement del joc del porter des d’una perspectiva física i tecnicotàctica. A més a més, suposarà una font d’informació per a l’organització i el disseny de les tasques específiques per a l’entrenament del porter, que han d’assegurar un treball en què es realitzin situacions semblants a la mateixa competició. Per tal de desenvolupar el joc defensiu, el porter ha de coordinar les seves accions amb la defensa del seu equip i, alhora, el joc defensiu de l’equip estarà condicionat per l’atac de l’equip contrari. Per això, per analitzar l’aportació del porter en el joc defensiu de l’equip, es va valorar l’atac contrari, l’acció tècnica defensiva, l’acció física i la zona d’intervenció on realitza l’acció el porter. La mostra de l’estudi la formaven 34 porters de les seleccions nacionals participants en 56 partits del Mundial de Corea i el Japó 2002. L’instrument d’observació que es va utilitzar va ser el sistema de categories. Abans de la recollida de les dades es va realitzar l’entrenament dels observadors, per a la qual cosa es va fer servir la metodologia exposada per Behar (1993). Es van utilitzar 5 observadors i es va establir un índex de confiança (Coeficient de Correlació Intraclasse o Índex de Kappa) del 0,95. Es va realitzar una anàlisi estadística de caràcter descriptiu, dintre de la qual es van calcular les mitjanes, desviacions típiques, mínims i màxims dels comportaments efectuats pels diferents porters; es va utilitzar el programa estadístic SPSS.11.5

Systemic effects of hypophosphatasia characterization of two novel variants in the ALPL gene

IntroductionHypophosphatasia (HPP) is an inborn metabolic error caused by mutations in the ALPL gene encoding tissue non-specific alkaline phosphatase (TNSALP) and leading to decreased alkaline phosphatase (ALP) activity. Although the main characteristic of this disease is bone involvement, it presents a great genetic and clinical variability, which makes it a systemic disease.MethodsPatients were recruited based on biochemical assessments. Diagnosis was made by measuring serum ALP and pyridoxal 5-phosphate levels and finally by Sanger sequencing of the ALPL gene from peripheral blood mononuclear cells. Characterization of the new variants was performed by transfection of the variants into HEK293T cells, where ALP activity and cellular localization were measured by flow cytometry. The dominant negative effect was analyzed by co-transfection of each variant with the wild-type gene, measuring ALP activity and analyzing cellular localization by flow cytometry.ResultsTwo previously undescribed variants were found in the ALPL gene: leucine 6 to serine missense mutation (c.17T>C, L6S) affecting the signal peptide and threonine 167 deletion (c.498_500delCAC, T167del) affecting the vicinity of the active site. These mutations lead mainly to non-pathognomonic symptoms of HPP. Structural prediction and modeling tools indicated the affected residues as critical residues with important roles in protein structure and function. In vitro results demonstrated low TNSALP activity and a dominant negative effect in both mutations. The results of the characterization of these variants suggest that the pleiotropic role of TNSALP could be involved in the systemic effects observed in these patients highlighting digestive and autoimmune disorders associated with TNSALP dysfunction.ConclusionsThe two new mutations have been classified as pathogenic. At the clinical level, this study suggests that both mutations not only lead to pathognomonic symptoms of the disease, but may also play a role at the systemic level

Diversity and relationships in key traits for functional and apparent quality in a collection of eggplant: fruit phenolics content, antioxidant activity, polyphenol oxidase activity, and browning

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Agricultural and Food Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work seehttp://dx.doi.org/10.1021/jf402429kEggplant (Solanum melongena) varieties with increased levels of phenolics in the fruit present enhanced functional quality, but may display greater fruit flesh browning. We evaluated 18 eggplant accessions for fruit total phenolics content, chlorogenic acid content, DPPH scavenging activity, polyphenol oxidase (PPO) activity, liquid extract browning, and fruit flesh browning. For all the traits we found a high diversity, with differences among accessions of up to 3.36-fold for fruit flesh browning. Variation in total content in phenolics and in chlorogenic acid content accounted only for 18.9% and 6.0% in the variation in fruit flesh browning, and PPO activity was not significantly correlated with fruit flesh browning. Liquid extract browning was highly correlated with chlorogenic acid content (r = 0.852). Principal components analysis (PCA) identified four groups of accessions with different profiles for the traits studied. Results suggest that it is possible to develop new eggplant varieties with improved functional and apparent quality.This project has been funded by Universitat Politecnica de Valencia through the grants SP20120681 and PAID-06-11 Nr. 2082, and by Ministerio de Economia y Competitividad Grant AGL2012-34213 (jointly funded by FEDER).Plazas Ávila, MDLO.; López Gresa, MP.; Vilanova Navarro, S.; Torres Vidal, C.; Hurtado Ricart, M.; Gramazio, P.; Andújar Pérez, I.... (2013). Diversity and relationships in key traits for functional and apparent quality in a collection of eggplant: fruit phenolics content, antioxidant activity, polyphenol oxidase activity, and browning. Journal of Agricultural and Food Chemistry. 61(37):8871-8879. https://doi.org/10.1021/jf402429kS88718879613

Investigación joven con perspectiva de género III

Actas del III Congreso Internacional de Estudios de Género, Perspectivas y Retos de Futuro: Jóvenes Investigadores (Getafe, 13 - 15 de junio de 2018) organizado por el Instituto Universitario de Estudios de Género de la Universidad Carlos III de Madrid