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

The post LNCC participated in the 19th Brazilian Science and Technology National Week first appeared on RISC2 Project.

In the European and Latin American (EuroLatAm) HPC ecosystems, it tis possible to identify actors in different domains: industry, academy, research, society, and government. Each of them, at different levels, has a group of demands or interactions, depending on the interests. I.e., the industry demands capabilities to have HPC solutions for productivity and wants skills from the academy to perform development actors to build applications to use solutions. Another example could be the relationship between research and the government. In the HPC Ecosystem, collaborations allow synergies to face common interests. Still, it demands policies and coordinated roadmaps to support long-term projects and activities with a clear impact on society.

Of course, a historical relationship exists between Latin America and Europe from colonial history. In the case of advanced computing projects, it is possible to identify, from the first EuroLatAm Grid Computing projects more than twenty years ago until the real supercomputing projects such as RISC and RISC2. Still, now, more with shared interests and the different EuroLatAm HPC projects improve competitiveness and collaboration. Competitiveness for industrial and productive business, partnership (and competitiveness) in science and education goals, and human wellness. So paraphrasing Mateo Valero “who does not compute does not compete”, I would add “who does not collaborate does not survive”.

Taking collaboration and competitiveness, the RISC2 project allows identifying sustainability elements and sustainable workflows for different projects. The impressive interaction between the actors of the HPC EuroLatAm ecosystem has not only given scientific results but also policies, recommendations, best practices, and new questions. For these outcomes, in the past 2022 Supercomputing Conference, RISC2 was awarded the 2022 HPCWire Editors’ Choice Award as the Best HPC Collaboration.

Sustainable advanced computing ecosystems and their growth are evident with the knowledge of the results of projects such as RISC2. Collaboration, interaction, and competitiveness build human development and guarantee development, technological diversification, and peer-to-peer relationships to attack common interests and problems. So, RISC2 is a crucial step to advance to a RISC3 as it was at the time of the previous RISC.

By Universidad Industrial de Santander

The post Advanced Computing Collaboration to Growth Sustainable Ecosystems 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.

The post LNCC is making efforts to promote the best HPC practices first appeared on RISC2 Project.

However, to realize the full potential of this synergy, ML models (or models for short) must be built, combined and ensembled, which can be very complex as there can be many models to select from. Furthermore, they should be shared and reused, in particular, in different execution environments such as HPC or Spark clusters.

To address this problem, we proposed Gypscie [Porto 2022, Zorrilla 2022], a new framework that supports the entire ML lifecycle and enables model reuse and import from other frameworks. The approach behind Gypscie is to combine several rich capabilities for model and data management, and model execution, which are typically provided by different tools, in a unique framework. Overall, Gypscie provides: a platform for supporting the complete model life-cycle, from model building to deployment, monitoring and policies enforcement; an environment for casual users to find ready-to-use models that best fit a particular prediction problem, an environment to optimize ML task scheduling and execution; an easy way for developers to benchmark their models against other competitive models and improve them; a central point of access to assess models’ compliance to policies and ethics and obtain and curate observational and predictive data; provenance information and model explainability. Finally, Gypscie interfaces with multiple execution environments to run ML tasks, e.g., an HPC system such as the Santos Dumont supercomputer at LNCC or a Spark cluster. 

Gypscie comes with SAVIME [Silva 2020], a multidimensional array in-memory database system for importing, storing and querying model (tensor) data. The SAVIME open-source system has been developed to support analytical queries over scientific data. Its offers an extremely efficient ingestion procedure, which practically eliminates the waiting time to analyze incoming data. It also supports dense and sparse arrays and non-integer dimension indexing. It offers a functional query language processed by a query optimiser that generates efficient query execution plans.

References

[Porto 2022] Fabio Porto, Patrick Valduriez: Data and Machine Learning Model Management with Gypscie. CARLA 2022 – Workshop on HPC and Data Sciences meet Scientific Computing, SCALAC, Sep 2022, Porto Alegre, Brazil. pp.1-2. 

[Zorrilla 2022] Rocío Zorrilla, Eduardo Ogasawara, Patrick Valduriez, Fabio Porto: A Data-Driven Model Selection Approach to Spatio-Temporal Prediction. SBBD 2022 – Brazilian Symposium on Databases, SBBD, Sep 2022, Buzios, Brazil. pp.1-12. 

[Silva 2020] A.C. Silva, H. Lourenço, D. Ramos, F. Porto, P. Valduriez. Savime: An Array DBMS for Simulation Analysis and Prediction. Journal of Information Data Management 11(3), 2020. 

By LNCC and Inria 

The post Managing Data and Machine Learning Models in HPC Applications first appeared on RISC2 Project.

RISC2 was responsible for the organization of the “HPC and Data Sciences meet Scientific Computing” workshop, on September 26, which gathered 15 participants. This workshop discussed different topics, such as Scientific Machine Learning, High Performance Scientific Computing, and Data Science. Álvaro Coutinho, Marta Mattoso (from COPPE/Federal University of Rio de Janeiro), Frédéric Valentin (from the National Laboratory for Scientific Computing), Luc Giraud, Stéphane Lanteri, and Patrick Valduriez (from Inria) were the organizers of the workshop.

RISC2 also organized a tutorial about physics-informed neural networks. Our partners from Brazil, Álvaro Coutinho and Romulo Montalvão, from the Federal University of Rio de Janeiro, António Tadeu Gomes and Frédéric Valentin, from the National Laboratory for Scientific Computing, were the instructors of the session.

Our partners Carlos Barrios, from the Universidad Industrial de Santander, was one of the General Chairs of the Conference. “With 130 participants from all over the world, CARLA 2022 was a space of “rediscover” (to rediscover us) after two years in virtual mode. More than the scientific tracks and the panels, CARLA 2022 allowed us to discuss the challenges and the strengthening of collaboration between the partners (old and new)”, says Carlos Barrios.

Various RISC2 members also gave different presentations. Alba Cervera-Lierta, from the Barcelona Supercomputing Center, was one of the Keynote Speakers of the CARLA Conference, with a presentation about Quantum Computing. Esteban Meneses, from CeNAT, participated in a presentation about “Implementing a GPU-Portable Field-Line Tracing Application with OpenMP Offload”. Pablo Mininni, from the University of Buenos Aires, was responsible for one of the invited talks about “Multi-level parallelisation of computational fluid dynamics codes using CUDA, MPI and OpenMP.”

CARLA is an international conference that provides a forum to foste the growth and strength of the HPC community in Latin America through the exchange and dissemination of new ideas, techniques, and research in HPC and its application areas.

Also during the conference, the RISC2 members had a networking meeting with the SCALAC members, reinforcing the partnership with the SCALAC network.

About CARLA 2022:

“CARLA 2022 was a space of “rediscover” (to rediscover us) after two years in virtual mode. More than the scientific tracks and the panels, CARLA 2022 allowed us to discuss the challenges and the strengthening of collaboration between the partners (old and new)”.

Carlos Barrios Hernandez,  Universidad Industrial de Santander

“Having the RISC2 project supporting a networking dinner in CARLA was crucial in building up the next research collaboration we want to have in the region. I am thoroughly satisfied with the experience of connecting with European and Latin American peers”.

Esteban Meneses, CeNAT

“Among the most important elements, I can highlight the quality and variety of paper presented. This indicates to me that the Latin American HPC community is growing and getting stronger. In addition, I was able to notice efforts to generate relations between Europe and Latin America through the RISC2 project”.

Elvis Rojas Ramírez, CeNAT

The post RISC2 highly represented at CARLA 2022 first appeared on RISC2 Project.

Date: December 7, 2022 | 4 p.m. (UTC)

The post Webinar: HPC system and job monitoring with LLview first appeared on RISC2 Project.

Date: September 22, 2022 | 4 p.m. (UTC+1)

Speaker’s presentation is available here.

The post Webinar: Interactive High-Performance Computing with JupyterLab first appeared on RISC2 Project.

The post HPC and Data Sciences meet Scientific Computing Workshop first appeared on RISC2 Project.

The post CARLA 2022 first appeared on RISC2 Project.