dedicated applications - RISC2 Project https://www.risc2-project.eu Thu, 28 Sep 2023 10:22:04 +0000 en-US hourly 1 https://wordpress.org/?v=6.6.2 60 students participated in the ACM Europe Summer School dedicated to HPC Computer Architectures https://www.risc2-project.eu/2023/08/22/60-students-participated-in-the-acm-europe-summer-school/ Tue, 22 Aug 2023 09:41:19 +0000 https://www.risc2-project.eu/?p=3017 At the beginning of July, the Barcelona Super Computing Center hosted the 4th edition of the ACM Europe Summer School on HPC Computer Architectures for AI and Dedicated Applications. The initiative, which featured several renowned personalities from the field, consisted of lectures and tutorials, as well as invited talks. The RISC2 project was also represented, […]

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At the beginning of July, the Barcelona Super Computing Center hosted the 4th edition of the ACM Europe Summer School on HPC Computer Architectures for AI and Dedicated Applications. The initiative, which featured several renowned personalities from the field, consisted of lectures and tutorials, as well as invited talks.

The RISC2 project was also represented, having made it possible, through monetary support, for some students from Latin America to take part – thus continuing its work in the social field. In total, 60 students from 25 different nationalities took part in the initiative.

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Developing Efficient Scientific Gateways for Bioinformatics in Supercomputer Environments Supported by Artificial Intelligence https://www.risc2-project.eu/2023/03/20/developing-efficient-scientific-gateways-for-bioinformatics-in-supercomputer-environments-supported-by-artificial-intelligence/ Mon, 20 Mar 2023 09:37:46 +0000 https://www.risc2-project.eu/?p=2781 Scientific gateways bring enormous benefits to end users by simplifying access and hiding the complexity of the underlying distributed computing infrastructure. Gateways require significant development and maintenance efforts. BioinfoPortal[1], through its CSGrid[2]  middleware, takes advantage of Santos Dumont [3] heterogeneous resources. However, task submission still requires a substantial step regarding deciding the best configuration that […]

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Scientific gateways bring enormous benefits to end users by simplifying access and hiding the complexity of the underlying distributed computing infrastructure. Gateways require significant development and maintenance efforts. BioinfoPortal[1], through its CSGrid[2]  middleware, takes advantage of Santos Dumont [3] heterogeneous resources. However, task submission still requires a substantial step regarding deciding the best configuration that leads to efficient execution. This project aims to develop green and intelligent scientific gateways for BioinfoPortal supported by high-performance computing environments (HPC) and specialised technologies such as scientific workflows, data mining, machine learning, and deep learning. The efficient analysis and interpretation of Big Data opens new challenges to explore molecular biology, genetics, biomedical, and healthcare to improve personalised diagnostics and therapeutics; finding new avenues to deal with this massive amount of information becomes necessary. New Bioinformatics and Computational Biology paradigms drive storage, management, and data access. HPC and Big Data advanced in this domain represent a vast new field of opportunities for bioinformatics researchers and a significant challenge. the BioinfoPortal science gateway is a multiuser Brazilian infrastructure. We present several challenges for efficiently executing applications and discuss the findings on improving 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 conducted at Santos Dumont, the largest supercomputer in Latin America, dedicated to the research community with 5.1 Petaflops and 36,472 computational cores distributed in 1,134 computational nodes.

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

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ACM Europe Summer School on HPC Computer Architectures for AI and Dedicated Applications https://www.risc2-project.eu/events/acm-europe-summer-school-on-hpc-computer-architectures-for-ai-and-dedicated-applications-2/ Wed, 08 Mar 2023 09:14:13 +0000 https://www.risc2-project.eu/?post_type=mec-events&p=2776

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RISC2 supported ACM Europe Summer School 2022 https://www.risc2-project.eu/2022/09/20/risc2-supported-acm-europe-summer-school-2022/ Tue, 20 Sep 2022 15:49:19 +0000 https://www.risc2-project.eu/?p=2356 The 2022 ACM Europe Summer School on “HPC Computer Architectures for AI and Dedicated Applications” was hosted by the Barcelona Supercomputing Center, RISC2’s coordinator, and the Universitat Politècnica de Catalunya. The event took place between August 29 and September 2. The RISC2 project supported the participation of five Latin American students, boosting the exchange of […]

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The 2022 ACM Europe Summer School on “HPC Computer Architectures for AI and Dedicated Applications” was hosted by the Barcelona Supercomputing Center, RISC2’s coordinator, and the Universitat Politècnica de Catalunya. The event took place between August 29 and September 2.

The RISC2 project supported the participation of five Latin American students, boosting the exchange of experience and knowledge between Europe and Latin America on the HPC fields. After the Summer School, the students whose participation supported by RISC2 wrote on a blog post: “We have brought home a new vision of the world of computing, new contacts, and many new perspectives that we can apply in our studies and share with our colleagues in the research groups and, perhaps, start a new foci of study”.

Distinguished scientists in the HPC field gave lectures and tutorials addressing architecture, software stack and applications for HPC and AI, invited talks, a panel on The Future of HPC and a final keynote by Prof Mateo Valero. On the last day of the week, the ACM School merged with MATEO2022 (“Multicore Architectures and Their Effective Operation 2022”), attended by world-class experts in computer architecture in the HPC field.

The ACM Europe Summer School joined 50 participants, from 28 different countries, from young computer science researchers and engineers, outstanding MSC students, and senior undergraduate students.

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ACM Europe Summer School on HPC Computer Architectures for AI and Dedicated Applications https://www.risc2-project.eu/events/acm-europe-summer-school-on-hpc-computer-architectures-for-ai-and-dedicated-applications/ Thu, 02 Jun 2022 07:33:51 +0000 https://www.risc2-project.eu/?post_type=mec-events&p=2143

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RISC2 with a strong presence at CARLA 2021 https://www.risc2-project.eu/2021/10/05/https-www-risc2-project-eu-2021-10-05-risc2-with-a-strong-presence-at-carla-2021/ Tue, 05 Oct 2021 08:20:04 +0000 http://192.168.10.124/risc/?p=1016 The RISC2 project participated at the Latin America High-Performance Computing Conference (CARLA 2021), which took place between September 27 and October 15, 2021, with 888 registered attendees from 25 different countries. The consortium of the RISC2 project participated in the organization of several activities during this international conference, within the scope of the collaboration between […]

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The RISC2 project participated at the Latin America High-Performance Computing Conference (CARLA 2021), which took place between September 27 and October 15, 2021, with 888 registered attendees from 25 different countries. The consortium of the RISC2 project participated in the organization of several activities during this international conference, within the scope of the collaboration between Europe and Latin America communities, working on HPC-related topics.

CARLA is an international conference aimed at providing a forum to foster the growth and strength of the High-Performance Computing (HPC) community in Latin America through the exchange and dissemination of new ideas, techniques, and research in HPC and its applications areas. The general chair of the 2021 edition is Isidoro Gitler, from Cinvestav, who coordinates and participates in all the event’s activities.

Workshops

Different partners of the RISC2 were involved in the organization of the scientific workshops as part of the CARLA 2021 conference. Between seven workshops organized to this conference, two of them are from the RISC2 consortium. The workshop on HPC Collaboration between Europe and Latin America took place online, on October 5, 2021. The goal was to provide a space dedicated to exchange experiences, towards the promotion and support of new collaborations across different countries of Europe and Latin America, within the framework of the recently launched ‘A network for supporting the coordination of High-Performance Computing research between Europe and Latin America’ (RISC2). This workshop achieved a maximum number of 55 participants, with Pedro Vieira Alberto, from the University of Coimbra, as one of the Invited Speakers. Ulisses Cortés, from Barcelona Supercomputing Center, presented the RISC2 project, as an example of HPC collaboration between Europe and Latin America. The chairs of this event were Ulisses Cortés and Rafael Mayo-García, from CIEMAT.

Another workshop organized by the RISC2 team was the workshop on HPC an Energy, which was held online on October 4, with Álvaro Coutinho, from COPPE, as Chair. This workshop focused on HPC techniques applied to the energy sector, in order to improve and reform many industrial sectors. HPC can provide several solutions to the energy sector, e.g., oil and gas solutions in upstream, midstream, and downstream problems; improve wind energy performance; solve issues of combustion efficiency for transportation systems; making nuclear systems more efficient and safer; improving solar energy systems; optimizing wind energy systems; improving the quality and efficiency of seismic and geophysical simulations, etc.

It is important to mention that Ginés Guerrero, from NLHPC, was one of the chairs of workshops organized by CARLA 2021.

Tutorials

Carla Osthoff, from Laboratório Nacional de Computação Científica, was Tutorial Chair Member of the 11 tutorials that were accepted at the CARLA 2021. CARLA 2021 provided tutorials and hands-on workshops for both introductory and advanced levels, specifically designed to undergraduate and master students all over Latin- American countries. There were two different periods: Fundamental Tutorials, which included six different tutorials the week before CARLA 2021, and Advanced Tutorials, with five different tutorials held a week after CARLA 2021. CARLA 2021 Tutorials were supported by Latin American, Caribbean, and European institutions.
Esteban Mosckos, from the Universidad de Buenos Aires, was involved in the organization of two different tutorials: “OpenMP: Introduction to shared memory models” and “Introduction to Distributed Memory Models using MPI”. Both activities consisted of theory and hands-on exercises, lasting four hours, with close to 40 assistants each.

The NLHPC partner was also responsible for a tutorial focused on Working with a resource manager on an HPC infrastructure, for the use of SLURM. Two more tutorials were organized by NLHPC, including, the tutorial on Performance Analysis Tools, with the participation of one of the members of the NLHPC Scientific Committee, and the other on Quantum Computing, with the participation of IBM.

The CARLA 2021 conference had more than 30 institutions on the board committee and more than 115 in attendance, connected simultaneously.

All the videos are available here.

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