A Review of Lightweight Thread Approaches for High Performance Computing

High-level, directive-based solutions are becoming the programming models (PMs) of the multi/many-core architectures. Several solutions relying on operating system (OS) threads perfectly work with a moderate number of cores. However, exascale systems will spawn hundreds of thousands of threads in order to exploit their massive parallel architectures and thus conventional OS threads are too heavy for that purpose. Several lightweight thread (LWT) libraries have recently appeared offering lighter mechanisms to tackle massive concurrency. In order to examine the suitability of LWTs in high-level runtimes, we develop a set of microbenchmarks consisting of commonly-found patterns in current parallel codes. Moreover, we study the semantics offered by some LWT libraries in order to expose the similarities between different LWT application programming interfaces. This study reveals that a reduced set of LWT functions can be sufficient to cover the common parallel code patterns andthat those LWT libraries perform better than OS threads-based solutions in cases where task and nested parallelism are becoming more popular with new architectures.The researchers from the Universitat Jaume I de Castelló were supported by project TIN2014-53495-R of the MINECO, the Generalitat Valenciana fellowship programme Vali+d 2015, and FEDER. This work was partially supported by the U.S. Dept. of Energy, Office of Science, Office of Advanced Scientific Computing Research (SC-21), under contract DEAC02-06CH11357. We gratefully acknowledge the computing resources provided and operated by the Joint Laboratory for System Evaluation (JLSE) at Argonne National Laboratory.Peer ReviewedPostprint (author's final draft

Consumer Attitudes and Concerns about Beef Consumption in Argentina and Other South American Countries

In South America, modifications in beef consumption habits, mainly related to economic reasons, new lifestyles, and new eating behaviors, are being observed. If this trend continues, beef consumption could continue to fall or there would be a greater share of cheaper types of meat. In general, consumer concerns related to health, animal welfare, and environmental impact are increasing. Most of the population in South America follows an omnivorous diet, with a minority of vegetarians/vegans. In Argentina, around 30% consider themselves as flexitarians and around 5% as vegetarians/vegans, with centennials and millennials being the ones that mostly follow these types of behaviors. For flexitarians, the main reason that leads them to adopt this diet is the search for healthier eating. In general, consumers consider livestock production to be a sustainable activity; although, ethical concerns are growing among the younger generations. Finally, around 30% of the total population is willing to partially replace the consumption of beef to avoid animal slaughter and 8% would abandon it for this reason. The current trend would indicate that, if the conditions defined by the present scenarios continue, the motivations to consume less beef could be strengthened.EEA BalcarceFil: Bifaretti, Adrián. Instituto de Promoción de la Carne Vacuna Argentina. Departamento de Promoción Interna; ArgentinaFil: Pavan, Enrique. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina.Fil: Pavan, Enrique. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina.Fil: Grigioni, Gabriela María. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Tecnología de Alimentos; Argentina.Fil: Grigioni, Gabriela María. Instituto de Ciencia y Tecnología de Sistemas Alimentarios Sustentables (ICyTeSAS). UEDD INTA CONICET; Argentina

What is meat in Argentina?

Due to its strong cultural significance, the term “meat” in Argentina has been historically associated with beef, despite its wider definition in the Argentine Food Code. Only by the end of the last century did other meats (poultry and pork) start gaining participation in the Argentinean diet as a result of economic and health-related issues. Meat, in general, is recognized as an important source of high-value proteins by consumers and professionals but not as an important source of minerals and vitamins.EEA BalcarceFil: Pavan, Enrique. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina. Clemson University. Department of Animal and Veterinary Science; Estados UnidosFil: Grigioni, Gabriela Maria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Tecnología de Alimentos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; ArgentinaFil: Aguirre, Patricia. Universidad Nacional de Lanús. Instituto de Salud Colectiva; Argentina. FLACSO Facultad Latinoamericana de Ciencias Sociales. Maestría de Estudios Sociales Agrarios; Argentina. Universidad Nacional de San Martín. Antropología Alimentaria- Doctorado en Antropología Social; ArgentinaFil: Leal, Marcela. Universidad Maimónides. Facultad de Ciencias Médicas. Licenciatura en Nutrición; Argentin

GLTO: On the Adequacy of Lightweight Thread Approaches for OpenMP Implementations

OpenMP is the de facto standard application programming interface (API) for on-node parallelism. The most popular OpenMP runtimes rely on POSIX threads (pthreads) implementations that offer an excellent performance for coarse-grained parallelism and match perfectly with the current hardware. However, a recent trend in runtimes/applications points in the direction of leveraging massive on-node parallelism in conjunction with fine-grained and dynamic scheduling paradigms. It has been demonstrated that lightweight thread (LWT) solutions are more appropriate for these new parallel paradigms. We have developed GLTO, an OpenMP implementation over the recently-emerged Generic Lightweight Threads (GLT) API. GLT exports a common API for LWT libraries that offers the possibility of running the same application over different native LWT solutions. In this paper we use GLTO to analyze different scenarios where OpenMP implementations may benefit from the use of either LWT or pthreads. Our study reveals that none of the threading approaches obtains the best performance in all the scenarios, but that there are important gaps among them.The Researchers from the Universitat Jaume I de Castelló were supported by project TIN2014-53495-R of the MINECO and FEDER, the Generalitat Valenciana fellowship programme Vali+d 2015. Antonio J. Peña is cofinancied by the Spanish Ministry of Economy and Competitiveness under Juan de la Cierva fellowship number IJCI-2015-23266. This work was partially supported by the U.S. Dept. of Energy, Office of Science, Office of Advanced Scientific Computing Research (SC-21), under contract DE-AC02-06CH11357. We gratefully acknowledge the computing resources provided and operated by the Joint Laboratory for System Evaluation (JLSE) at Argonne National Laboratory.Peer ReviewedPostprint (author's final draft

Living in an extremely polluted environment: Clues from the genome of melanin-producing Aeromonas salmonicida subsp. pectinolytica 34melT

Aeromonas salmonicida subsp. pectinolytica 34mel(T) can be considered an extremophile due to the characteristics of the heavily polluted river from which it was isolated. While four subspecies of A. salmonicida are known fish pathogens, 34mel(T) belongs to the only subspecies isolated solely from the environment. Genome analysis revealed a high metabolic versatility, the capability to cope with diverse stress agents, and the lack of several virulence factors found in pathogenic Aeromonas. The most relevant phenotypic characteristics of 34mel(T) are pectin degradation, a distinctive trait of A. salmonicida subsp. pectinolytica, and melanin production. Genes coding for three pectate lyases were detected in a cluster, unique to this microorganism, that contains all genes needed for pectin degradation. Melanin synthesis in 34mel(T) is hypothesized to occur through the homogentisate pathway, as no tyrosinases or laccases were detected and the homogentisate 1,2-dioxygenase gene is inactivated by a transposon insertion, leading to the accumulation of the melanin precursor homogentisate. Comparative genome analysis of other melanogenic Aeromonas strains revealed that this gene was inactivated by transposon insertions or point mutations, indicating that melanin biosynthesis in Aeromonas occurs through the homogentisate pathway. Horizontal gene transfer could have contributed to the adaptation of 34mel(T) to a highly polluted environment, as 13 genomic islands were identified in its genome, some of them containing genes coding for fitness-related traits. Heavy metal resistance genes were also found, along with others associated with oxidative and nitrosative stresses. These characteristics, together with melanin production and the ability to use different substrates, may explain the ability of this microorganism to live in an extremely polluted environment

Analysis of threading libraries for high performance computing

© 2020 IEEE. Personal use of this material is permitted. Permissíon from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertisíng or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.[EN] With the appearance of multi-/many core machines, applications and runtime systems have evolved in order to exploit the new on-node concurrency brought by new software paradigms. POSIX threads (Pthreads) was widely-adopted for that purpose and it remains as the most used threading solution in current hardware. Lightweight thread (LWT) libraries emerged as an alternative offering lighter mechanisms to tackle the massive concurrency of current hardware. In this article, we analyze in detail the most representative threading libraries including Pthread- and LWT-based solutions. In addition, to examine the suitability of LWTs for different use cases, we develop a set of microbenchmarks consisting of OpenMP patterns commonly found in current parallel codes, and we compare the results using threading libraries and OpenMP implementations. Moreover, we study the semantics offered by threading libraries in order to expose the similarities among different LWT application programming interfaces and their advantages over Pthreads. This article exposes that LWT libraries outperform solutions based on operating system threads when tasks and nested parallelism are required.The researchers from the Universitat Jaume I and Universitat Politecnica de Valencia were supported by project TIN2014-53495-R of the MINECO and FEDER, and the Generalitat Valenciana fellowship programme Vali+d 2015. Antonio J. Pena is financed by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant No. 749516. This work was partially supported by the U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research (SC-21), under contract DE-AC02-06CH11357.Castelló, A.; Mayo Gual, R.; Seo, S.; Balaji, P.; Quintana Ortí, ES.; Peña, AJ. (2020). Analysis of threading libraries for high performance computing. IEEE Transactions on Computers. 69(9):1279-1292. https://doi.org/10.1109/TC.2020.2970706S1279129269

Effect of Diet Supplementation on the Expression of Bovine Genes Associated with Fatty Acid Synthesis and Metabolism

Conjugated linoleic acids (CLA) are of important nutritional and health benefit to human. Food products of animal origin are their major dietary source and their concentration increases with high concentrate diets fed to animals. To examine the effects of diet supplementation on the expression of genes related to lipid metabolism, 28 Angus steers were fed either pasture only, pasture with soybean hulls and corn oil, pasture with corn grain, or high concentrate diet. At slaughter, samples of subcutaneous adipose tissue were collected, from which RNA was extracted. Relative abundance of gene expression was measured using Affymetrix GeneChip Bovine Genome array. An ANOVA model nested within gene was used to analyze the background adjusted, normalized average difference of probe-level intensities. To control experiment wise error, a false discovery rate of 0.01 was imposed on all contrasts. Expression of several genes involved in the synthesis of enzymes related to fatty acid metabolism and lipogenesis such as stearoyl-CoA desaturase (SCD), fatty acid synthetase (FASN), lipoprotein lipase (LPL), fatty-acyl elongase (LCE) along with several trancription factors and co-activators involved in lipogenesis were found to be differentially expressed. Confirmatory RT-qPCR was done to validate the microarray results, which showed satisfactory correspondence between the two platforms. Results show that changes in diet by increasing dietary energy intake by supplementing high concentrate diet have effects on the transcription of genes encoding enzymes involved in fat metabolism which in turn has effects on fatty acid content in the carcass tissue as well as carcass quality. Corn supplementation either as oil or grain appeared to significantly alter the expression of genes directly associated with fatty acid synthesis

Cross-Cultural Differences in the Perception of Lamb between New Zealand and Chinese Consumers in New Zealand

This study investigated differences between general New Zealand consumers and ethnic Chinese consumers living in New Zealand regarding the importance of lamb attributes at the point of purchase and opinions of New Zealand lamb. A central location test survey was undertaken with 156 New Zealand consumers living in Dunedin, New Zealand, and 159 Chinese consumers living in Auckland, New Zealand. In terms of importance at the point of purchase, Chinese consumers rated a number of attributes as more important than New Zealand consumers by a difference of >1.0 on a 9-point Likert scale for importance: animal origin, feeding, age, presence of hormones/residues, traceability, food safety, place of purchase, brand/quality label, and label information (p 1.0 on a 7-point Likert scale for agreement. New Zealand consumers considered New Zealand lamb more traditional and boring (p < 0.05); however, the differences in scores were <1.0.info:eu-repo/semantics/publishedVersio

Exploring the interoperability of remote GPGPU virtualization using rCUDA and directive-based programming models

[EN] Directive-based programming models, such as OpenMP, OpenACC, and OmpSs, enable users to accelerate applications by using coprocessors with little effort. These devices offer significant computing power, but their use can introduce two problems: an increase in the total cost of ownership and their underutilization because not all codes match their architecture. Remote accelerator virtualization frameworks address those problems. In particular, rCUDA provides transparent access to any graphic processor unit installed in a cluster, reducing the number of accelerators and increasing their utilization ratio. Joining these two technologies, directive-based programming models and rCUDA, is thus highly appealing. In this work, we study the integration of OmpSs and OpenACC with rCUDA, describing and analyzing several applications over three different hardware configurations that include two InfiniBand interconnections and three NVIDIA accelerators. Our evaluation reveals favorable performance results, showing low overhead and similar scaling factors when using remote accelerators instead of local devices.The researchers from the Universitat Jaume I de Castello were supported by Universitat Jaume I research project (P11B2013-21), project TIN2014-53495-R, a Generalitat Valenciana grant and FEDER. The researcher from the Barcelona Supercomputing Center (BSC-CNS) Lausanne was supported by the European Commission (HiPEAC-3 Network of Excellence, FP7-ICT 287759), Intel-BSC Exascale Lab collaboration, IBM/BSC Exascale Initiative collaboration agreement, Computacion de Altas Prestaciones VI (TIN2012-34557) and the Generalitat de Catalunya (2014-SGR-1051). This work was partially supported by the U.S. Dept. of Energy, Office of Science, Office of Advanced Scientific Computing Research (SC-21), under contract DE-AC02-06CH11357. The initial version of rCUDA was jointly developed by Universitat Politecnica de Valencia (UPV) and Universitat Jaume I de Castellon (UJI) until year 2010. This initial development was later split into two branches. Part of the UPV version was used in this paper. The development of the UPV branch was supported by Generalitat Valenciana under Grants PROMETEO 2008/060 and Prometeo II 2013/009. We gratefully acknowledge the computing resources provided and operated by the Joint Laboratory for System Evaluation (JLSE) at Argonne National Laboratory.Castelló-Gimeno, A.; Peña Monferrer, AJ.; Mayo Gual, R.; Planas, J.; Quintana Ortí, ES.; Balaji, P. (2018). Exploring the interoperability of remote GPGPU virtualization using rCUDA and directive-based programming models. The Journal of Supercomputing. 74(11):5628-5642. https://doi.org/10.1007/s11227-016-1791-yS562856427411Strohmaier E, Dongarra J, Simon H, Meuer M (2015) TOP500 supercomputing sites. http://www.top500.org/lists/2015/11 . Accessed Nov 2015NVIDIA (2015) CUDA API reference, version 7.5Shreiner D, Sellers G, Kessenich JM, Licea-Kane BM (2013) OpenGL programming guide: the official guide to learning OpenGL. Addison-Wesley Professional, BostonMark WR, Glanville RS, Akeley K, Kilgard MJ (2003) Cg: a system for programming graphics hardware in a C-like language. ACM Trans Graph (TOG) 22(3):896–907Munshi A (2014)The OpenCL specification 2.0. 0.5em minus 0.4em Khronos OpenCL working groupOpenACC directives for accelerators (2015). http://www.openacc-standard.org . Accessed Dec 2015OmpSs project home page. http://pm.bsc.es/ompss . Accessed Dec 2015OpenMP application program interface 4.0 (2013). OpenMP Architecture BoardPeña AJ (2013) Virtualization of accelerators in high performance clusters. Ph.D. dissertation, Universitat Jaume I, CastellónKawai A, Yasuoka K, Yoshikawa K, Narumi T (2012) Distributed-shared CUDA: virtualization of large-scale GPU systems for programmability and reliability. In: International conference on future computational technologies and applicationsShi L, Chen H, Sun J, Li K (2012) vCUDA: GPU-accelerated high-performance computing in virtual machines. IEEE Trans Comput 61(6):804–816Xiao S, Balaji P, Zhu Q, Thakur R, Coghlan S, Lin H, Wen G, Hong J, Feng W (2012) VOCL: an optimized environment for transparent virtualization of graphics processing units. In: Innovative parallel computing. IEEE, New YorkKim J, Seo S, Lee J, Nah J, Jo G, Lee J (2012) SnuCL: an OpenCL framework for heterogeneous CPU/GPU clusters. In: International conference on supercomputingDuran A, Ayguadé E, Badia RM, Labarta J, Martinell L, Martorell X, Planas J (2011) OmpSs: a proposal for programming heterogeneous multi-core architectures. Parallel Process Lett 21(02):173–193Castelló A, Duato J, Mayo R, Peña AJ, Quintana-Ortí ES, Roca V, Silla F (2014) On the use of remote GPUs and low-power processors for the acceleration of scientific applications. In: The fourth international conference on smart grids, green communications and IT energy-aware technologies, pp 57–62Iserte S, Castelló A, Mayo R, Quintana-Ortí ES, Reaño C, Prades J, Silla F, Duato J (2014) SLURM support for remote GPU virtualization: implementation and performance study. In: International symposium on computer architecture and high performance computing (SBAC-PAD)Peña AJ, Reaño C, Silla F, Mayo R, Quintana-Ortí ES, Duato J (2014) A complete and efficient CUDA-sharing solution for HPC clusters. Parallel Comput 40(10):574–588Kegel P, Steuwer M, Gorlatch S (2012) dOpenCL: towards a uniform programming approach for distributed heterogeneous multi-/many-core systems. In: International parallel and distributed processing symposium workshops (IPDPSW)Castelló A, Peña AJ, Mayo R, Balaji P, Quintana-Ortí ES (2015) Exploring the suitability of remote GPGPU virtualization for the OpenACC programming model using rCUDA. In: IEEE international conference on cluster computingCastelló A, Mayo R, Planas J, Quintana-Ortí ES (2015) Exploiting task-parallelism on GPU clusters via OmpSs and rCUDA virtualization. In: IEEE international workshop on reengineering for parallelism in heterogeneous parallel platformsHP Corp., Intel Corp., Microsoft Corp., Phoenix Tech. Ltd., Toshiba Corp. (2011) Advanced configuration and power interface specification, revision 5.0Reaño C, Silla F, Castelló A, Peña AJ, Mayo R, Quintana-Ortí ES, Duato J (2014) Improving the user experience of the rCUDA remote GPU virtualization framework. Concurr Comput 27(14):3746–3770PGI compilers and tools (2015) http://www.pgroup.com/ . Accessed Dec 2015Johnson N (2013) EPCC OpenACC benchmark suite. https://www.epcc.ed.ac.uk/ . Accessed Dec 2015Herdman J, Gaudin W, McIntosh-Smith S, Boulton M, Beckingsale D, Mallinson A, Jarvis SA (2012) Accelerating hydrocodes with OpenACC, OpenCL and CUDA. 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Según los Consumidores Argentinos: ¿el Color y el Nivel de Marmoreo son indicadores de la Calidad de la Carne?

Socializamos el resultado de una encuesta que analiza las preferencias de los consumidores argentinos en base al color y contenido de grasa de la carne bovina.Publishe