By:

Carneiro, B. Fagundes, C. Osthoff, G. Freire, K. Ocaña, L. Cruz, L. Gadelha, M. Coelho, M. Galheigo, and R. Terra are with the National Laboratory of Scientific Computing, Rio de Janeiro, Brazil.

Carvalho is with the Federal Center for Technological Education Celso Suckow da Fonseca, Rio de Janeiro, Brazil.

Douglas Cardoso is with the Polytechnic Institute of Tomar, Portugal.

Boito and L, Teylo is with the University of Bordeaux, CNRS, Bordeaux INP, INRIA, LaBRI, Talence, France.

Navaux is with the Informatics Institute, the Federal University of Rio Grande do Sul, and Rio Grande do Sul, Brazil.

References:

Ocaña, K. A. C. S.; Galheigo, M.; Osthoff, C.; Gadelha, L. M. R.; Porto, F.; Gomes, A. T. A.; Oliveira, D.; Vasconcelos, A. T. BioinfoPortal: A scientific gateway for integrating bioinformatics applications on the Brazilian national high-performance computing network. Future Generation Computer Systems, v. 107, p. 192-214, 2020.

Mondelli, M. L.; Magalhães, T.; Loss, G.; Wilde, M.; Foster, I.; Mattoso, M. L. Q.; Katz, D. S.; Barbosa, H. J. C.; Vasconcelos, A. T. R.; Ocaña, K. A. C. S; Gadelha, L. BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments. PeerJ, v. 1, p. 1, 2018.

Coelho, M.; Freire, G.; Ocaña, K.; Osthoff, C.; Galheigo, M.; Carneiro, A. R.; Boito, F.; Navaux, P.; Cardoso, D. O. Desenvolvimento de um Framework de Aprendizado de Máquina no Apoio a Gateways Científicos Verdes, Inteligentes e Eficientes: BioinfoPortal como Caso de Estudo Brasileiro In: XXIII Simpósio em Sistemas Computacionais de Alto Desempenho – WSCAD 2022 (https://wscad.ufsc.br/), 2022.

Terra, R.; Ocaña, K.; Osthoff, C.; Cruz, L.; Boito, F.; Navaux, P.; Carvalho, D. Framework para a Construção de Redes Filogenéticas em Ambiente de Computação de Alto Desempenho. In: XXIII Simpósio em Sistemas Computacionais de Alto Desempenho – WSCAD 2022 (https://wscad.ufsc.br/), 2022.

Ocaña, K.; Cruz, L.; Coelho, M.; Terra, R.; Galheigo, M.; Carneiro, A.; Carvalho, D.; Gadelha, L.; Boito, F.; Navaux, P.; Osthoff, C. ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression. In: Latin America High-Performance Computing Conference (CARLA), 2022, Rio Grande do Sul, Brazil. Proceedings of the Latin American High-Performance Computing Conference – CARLA 2022 (http://www.carla22.org/), 2022.

^[1] https://bioinfo.lncc.br/

^[2] https://git.tecgraf.puc-rio.br/csbase-dev/csgrid/-/tree/CSGRID-2.3-LNCC

^[3] https://https://sdumont.lncc.br

The post Developing Efficient Scientific Gateways for Bioinformatics in Supercomputer Environments Supported by Artificial Intelligence first appeared on RISC2 Project.

The School aimed to provide mini-courses and talks related to programming on high-performance computers, such as parallel programming models, profiling tools, and libraries for developing optimized parallel algorithms for the SDumont user community and the high-performance computing programming community.

Due to the extensive territory of Brazil and the number of research projects, it is mandatory to provide regular HPC schools for the research community. According to Carla Osthoff, one of the organizers of this school, “SDumont is the only Brazilian supercomputer dedicated to the research community that is part of the TOP 500 list. The Brazilian Ministry of Science and Technology offers free access to all Brazilian research projects in the country and foreign collaborators. Currently, we have 238 research projects from 18 research areas.  This edition of the School received 350 registrations, but we also provided online YouTube access to the community.”

The event happened remotely, and all the sessions are available on Youtube.

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The talk “The Santos Dumont Supercomputer in the scenario of National and International Scientific Research” was presented on December 3, 2022, and is available here. 

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The school aims to provide the SDumont user community and the high performance computing programming community in general with mini-courses related to programming on high performance computers such as parallel programming models, profiling tools and libraries for the development of optimized parallel algorithms.

Know more. 

The post HPC Summer School “Escola Supercomputador Santos Dumont 2023” first appeared on RISC2 Project.

On November 7, 2022, LNCC researchers, Carla Osthoff and Kary Ocaña, participated in a seminar in collaboration with our partner Inria, with a presentation entitle “Developing Efficient Scientific Gateways for Bioinformatics in Supercomputer Environments Supported by Artificial Intelligence”. The seminar aimed at promoting the interaction between LNCC’s and Inria’s high-performance computing researchers.

On November 18, Carla Osthoff participated in a seminar organized by the University of Campinas, where she presented the Santos Dumont Supercomputer. The event aimed to promote the exchange of the best HPC practices, promoting the interaction between computer science researchers towards the definition of a coordinated policy and a concrete roadmap for the future.

On November 23, Carla Osthoff also presented the Santos Dumont Supercomputer, on an online lecture, organized by the Research Centre in Digitalization and Intelligent Robotics of the Polytechnic Institute of Bragança, promoting the knowledge exchange between both regions.

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The posters “Developing Efficient Scientific Gateways for Bioinformatics in Supercomputing Environments Supported by Artificial Intelligence” and “Scalable Numerical Method for Biphasic Flows in Heterogeneous Porous Media in High-Performance Computational Environments” are part of the activities of the LNCC RISC2 projects.

According to Carla Osthoff (LNCC) , former poster presents a collaboration project that aims to develop green and intelligent scientific gateways for bioinformatics supported by high-performance computing environments (HPC) and specialized technologies such as scientific workflows, data mining, machine learning, and deep learning.  The efficient analysis and interpretation of Big Data open new challenges to explore molecular biology, genetics, biomedical, and healthcare to improve personalized diagnostics and therapeutics; then, it becomes necessary to availability of new avenues to deal with this massive amount of information. New paradigms in Bioinformatics and Computational Biology drive the storing, managing, and accessing of data. HPC and Big Data advances in this domain represent a vast new field of opportunities for bioinformatics researchers and a significant challenge. The Bioinfo-Portal science gateway is a multiuser Brazilian infrastructure for bioinformatics applications, benefiting from the HPC infrastructure. We present several challenges for efficiently executing applications and discussing the findings on how to improve the use of computational resources. We performed several large-scale bioinformatics experiments that are considered computationally intensive and time-consuming. We are currently coupling artificial intelligence to generate models to analyze computational and bioinformatics metadata to understand how automatic learning can predict computational resources’ efficient use. The computational executions are carried out at Santos Dumont Supercomputer. This is a multi-disciplinary project requiring expertise from several knowledge areas from four research institutes (LNCC, UFRGS, INRIA Bordeaux, and CENAT in Costa Rica). Finally, Brazilian funding agencies (CNPQ, CAPES) and the RISC-2 project from the European Economic and Social Committee (EESC) support the project.

Latter poster presents a project that aims to develop a scalable numerical approach for biphasic flows in heterogeneous porous media in high-performance computing environments based on the high-performance numerical methodology. In this system, an elliptical subsystem determines the velocity field, and a non-linear hyperbolic equation represents the transport of the flowing phases (saturation equation). The model applies a locally conservative finite element method for the mixing speed. Furthermore, the model employs a high-order non-oscillatory finite volume method, based on central schemes, for the non-linear hyperbolic equation that governs phase saturation. Specifically, the project aims to build scalable codes for a high-performance environment. Identified the bottlenecks in the code, the project is now working in four different research areas. Parallel I/O routines and high-performance visualization to decrease the I/O transfers bottleneck, Parallel programming to reduce code bottlenecks for multicore and manycore architectures. and Adaptive MPI  to decrease the message communication bottleneck. The poster presents the first performance evaluation results used to guide the project research areas. This endeavor is a multi-disciplinary project requiring expertise from several knowledge areas from four research institutes (LNCC, UFRGS, UFLA in Brazil, and CENAT in Costa Rica). Finally, Brazilian funding agencies (CNPQ, CAPES) and the RISC-2 project.

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