Search

Applying malleability to HPC systems can increase their productivity without degrading or even improving the performance of running applications. This paper presents Proteo, a configurable framework that allows to design benchmarks to study the effect of malleability on a system, and also incorporates malleability into a real application. Proteo consists of two modules: SAM allows to emulate the computational behavior of iterative scientific MPI applications, and MaM is able to reconfigure a job during execution, adjusting the number of processes, redistributing data, and resuming execution. An in-depth study of all the possibilities shows that Proteo is able to behave like a real malleable or non-malleable application in the range [0.85, 1.15]. Furthermore, the different methods defined in MaM for process management and data redistribution are analyzed, concluding that asynchronous malleability, where reconfiguration and application execution overlap, results in a 1.15 speedup., Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work has been funded by project PID2020-113656RB-C21 supported by MCIN/AEI/10.13039/501100011033. Researcher I. Martín-Álvarez was supported by the predoctoral fellowship ACIF/2021/260 from Valencian Region Government and European Social Funds. The European DEEP-SEA project has received funding from the European Commission’s EuroHPC-JU program under grant agreement No. 955606; the JU receives support from the European Union’s Horizon 2020 research and innovation programme and by the Spanish Ministry under Grant PCI2021-121958 funded by MCIN / AEI / 10.13039 / 501100011033 and by the “European Union NextGenerationEU/PRTR.”, Peer Reviewed, Postprint (published version)

Nowadays, the throughput improvement in large clusters of computers recommends the development of malleable applications. Thus, during the execution of these applications in a job, the resource management system (RMS) can modify its resource allocation, in order to increase the global throughput. There are different alternatives to complete the different steps in which the reallocation of resources is decomposed. To find the best alternatives, this paper introduces a configurable synthetic iterative MPI malleable application capable of modifying, in execution time, the number of MPI processes according to several parameters. The application includes a performance module to measure stages time within steps, from processes management to data redistribution. In this way, the analysis of different scenarios will allow to conclude how the reconfiguration of application has to be made in different circumstances. At the same time, this tool can be used to create workloads that will allow to analyse the impact of malleability on a system and the work in progress., This work has been funded by the following projects: Project PID2020-113656RB-C21 supported by MCIN/AEI/10.13039/501100011033 and project UJI-B2021-58. Researcher S. Iserte was supported by the postdoctoral fellowship APOSTD/2020/026, and researcher I. Mart´ın was supported by the predoctoral fellowship ACIF/2021/260, both from Valencian Region Government and European Social Funds. The authors would like to thank the HPC Advisory Council for providing access to their high-performance computing clusters Jupiter and Thor which correspond, respectively, to System 2 and System 3 in the paper., Peer Reviewed, Postprint (author's final draft)

Malleability allows computing facilities to adapt their workloads through resource management systems to maximize the throughput of the facility and the efficiency of the executed jobs. This technique is based on reconfiguring a job to a different resource amount during execution and then continuing with it. One of the stages of malleability is the dynamic spawning of processes in execution time, where different decisions in this stage will affect how the next stage of data redistribution is performed, which is the most time-consuming stage. This paper describes different methods and strategies, defining eight different alternatives to spawn processes dynamically and indicates which one should be used depending on whether a strong or weak scaling application is being used. In addition, it is described for both types of applications which strategies benefit most the application performance or the system productivity. The results show that reducing the number of spawning processes by reusing the older ones can reduce reconfiguration time compared to the classical method by up to 2.6 times for expanding and up to 36 times for shrinking. Furthermore, the asynchronous strategy requires analysing the impact of oversubscription on application performance., This work has been funded by the following projects: project PID2020-113656RB-C21 supported by MCIN/AEI/10.13039/501100011033 and project UJI-B2019-36 supported by UniversitatJaume I. Researcher S. Iserte was supported by the postdoctoralfellowship APOSTD/2020/026, and researcher I. Martín- Álvarez was supported by the predoctoral fellowship ACIF/2021/260, both from Valencian Region Government and European Social Funds., Peer Reviewed, Postprint (author's final draft)

Our findings confirm the existence of educational quality agglomeration in Cali (Moran’s Index = 0.311). High educational quality is concentrated in schools in the south of the city (commune 22), while low educational quality is found in schools located in the east (communes 13, 14 and 15). Our study also confirms the importance of the determinants for school performance identified in the previous literature. The main contribution of this study is the finding that crime negatively affects educational quality. When the number of homicides in the neighbourhood in which a school is located increases by one percentage point, the quality of education decreases, on average, by 0.63 points., Este artículo confirma la existencia de aglomeración en la calidad educativa en Cali (índice de Moran = 0,311): la alta calidad se concentra en los colegios del sur de Cali (comuna 22), mientras la baja está ubicada al oriente de la ciudad (comunas 13, 14 y 15). Como factores determinantes, se establece lo que la literatura en general concluye, además, y como aporte principal, se determinó que la criminalidad afecta de forma negativa la calidad educativa en Cali, esto es, cuando aumenta en un punto porcentual la cantidad de homicidios alrededor del colegio, la calidad educativa disminuye, en promedio, en 0,63 puntos.

[EN] The advances in genomic sequencing during the past few years have motivated the development of fast and reliable software for DNA/RNA sequencing on current high performance architectures. Most of these efforts target multicore processors, only a few can also exploit graphics processing units, and a much smaller set will run in clusters equipped with any of these multi-threaded architecture technologies. Furthermore, the examples that can be used on clusters today are all strongly coupled with a particular aligner. In this paper we introduce an alignment framework that can be leveraged to coordinately run any single-node aligner, taking advantage of the resources of a cluster without having to modify any portion of the original software. The key to our transparent migration lies in hiding the complexity associated with the multi-node execution (such as coordinating the processes running in the cluster nodes) inside the generic-aligner framework. Moreover, following the design and operation in our Message Passing Interface (MPI) version of HPG Aligner RNA BWT, we organize the framework into two stages in order to be able to execute different aligners in each one of them. With this configuration, for example, the first stage can ideally apply a fast aligner to accelerate the process, while the second one can be tuned to act as a refinement stage that further improves the global alignment process with little cost.

[EN] We introduce a version of the epistasis test in FaST-LMM for clusters of multithreaded processors. This new software maintains the sensitivity of the original FaST-LMM while delivering acceleration that is close to linear on 12-16 nodes of two recent platforms, with respect to improved implementation of FaST-LMM presented in an earlier work. This efficiency is attained through several enhancements on the original single-node version of FaST-LMM, together with the development of a message passing interface (MPI)-based version that ensures a balanced distribution of the workload as well as a multigraphics processing unit (GPU) module that can exploit the presence of multiple GPUs per node.

This article presents new estimations for Valle del Cauca’s matching function using information from the SENA’s Public Service record between the first quarter of 2008 and the fourth quarter of 2014. The results show that efficiency in the matching processes in Valle del Cauca cannot only be attained through improvements in the search processes. This is because it also depends on the presence of a strong and traditional-employment component that is stable over time, and evidence is provided of a structural mismatch (technical change biased towards professional occupations)., Este artículo presenta nuevas estimaciones de la función de emparejamiento para el departamento del Valle del Cauca con base en información del Servicio Público del SENA para el período entre el primer trimestre de 2008 y el cuarto trimestre de 2014. Los resultados muestran que la eficiencia en los procesos de emparejamiento del Valle del Cauca no se puede lograr solamente a través de mejoras en los procesos de búsqueda, sino que depende también de la existencia de un componente de ocupaciones fuerte y tradicional que se mantiene en el tiempo, pero que evidencia un desajuste estructural (cambio técnico sesgado hacia ocupaciones profesionales)., Este artigo apresenta novas estimativas da função de emparelhamento para o departamento de Valle del Cauca com base em informações do Serviço Público do SENA para o período entre o primeiro trimestre de 2008 e o quarto trimestre de 2014. Os resultados mostram que a eficiência nos Processos de Emparelhamento do Valle del Cauca não podem ser alcançados apenas através de melhorias nos processos de busca, mas também depende da existência de um componente profissional forte e tradicional que seja mantido ao longo do tempo, mas que evidencia um desequilíbrio estrutural (mudança tendenciosa na direção de ocupações profissionais).