The session began with a welcome and introduction by Mateo Valero (BSC), one of the main drivers of this cooperation and a leading name in the field of HPC. This intervention was later complemented by Fabrizio Gagliardi (BSC). Afterward, Elsa Carvalho (INESC TEC) presented the work done in terms of communication by the RISC2 team, an important segment for all the news and achievements to reach all the partners and countries involved.

Carlos J. Barrios Hernandez then presented the work done within the HPC Observatory, a relevant source of information that European and Latin American research organizations can address with HPC and/or AI issues.

The session closed with an important and pertinent debate on how to strengthen cooperation in HPC between the European Union and Latin America, in which all participants contributed and gave their opinion, committing to efforts so that the work developed within the framework of RISC2 is continued.

What our partners had to say about the meeting?

Rafael Mayo Garcia, CIEMAT:

“The policy event organized by RISC2 in Brussels was of utmost importance for the development of HPC and digital capabilities for a shared infrastructure between EU and LAC. Even more, it has had crucial contributions to international entities such as CYTED, the Ibero-American Programme for the Development of Science and Technology. On the CIEMAT side, it has been a new step beyond for building and participating in a HPC shared ecosystem.”

Esteban Meneses, CeNAT:

“In Costa Rica, CeNAT plays a critical role in fostering technological change. To achieve that goal, it is fundamental to synchronize our efforts with other key players, particularly government institutions. The event policy in Brussels was a great opportunity to get closer to our science and technology ministry and start a dialogue on the importance of HPC, data science, and artificial intelligence for bringing about the societal changes we aim for.”

Esteban Mocskos, UBA:

“The Policy Event recently held in Brussels and organized by the RISC2 project had several remarkable points. The gathering of experts in HPC research and management in Latin America and Europe served to plan the next steps in the joint endeavor to deepen the collaboration in this field. The advance in management policies, application optimization, and user engagement are fundamental topics treated during the main sessions and also during the point-to-point talks in every corner of the meeting room.
I can say that this meeting will also spawn different paths in these collaboration efforts that we’ll surely see their results during the following years with a positive impact on both sides of this fruitful relationship: Latin America and Europe.”

Sergio Nesmachnow, Universidad de la República:

“The National Supercomputing Center (Uruguay) and Universidad de la República have led the development of HPC strategies and technologies and their application to relevant problems in Uruguay. Specific meetings such as the policy event organized by RISC2 in Brussels are key to present and disseminate the current developments and achievements to relevant political and technological leaders in our country, so that they gain knowledge about the usefulness of HPC technologies and infrastructure to foster the development of national scientific research in capital areas such as sustainability, energy, and social development. It was very important to present the network of collaborators in Latin America and Europe and to show the involvement of institutional and government agencies.

Within the contacts and talks during the organization of the meeting, we introduced the projecto to national authorities, including the National Director of Science and Technology, Ministry of Education and Culture, and the President of the National Agency for Research and Innovation, as well as the Uruguayan Agency for International Cooperation and academic authorities from all institutions involved in the National Supercomputing Center initiative. We hope the established contacts can result in productive joint efforts to foster the development of HPC and related scientific areas in our country and the region.”

Carla Osthoff, LNCC:

“In Brazil, LNCC is critical in providing High Performance Computing Resources for the Research Community and training Human Resources and fostering new technologies. The policy event organized by RISC2 in Brussels was fundamental to synchronizing LNCC efforts with other government institutions and international  entities. On the LNCC side, it has been a new step beyond building and participating in an HPC-shared ecosystem.

Specific meetings such as the policy event organized by RISC2 in Brussels  were very important to present the network of collaborators in Latin America and Europe and to show the involvement of institutional and government agencies.

As a result of joint activities in research and development in the areas of information and communication technologies (ICT), artificial intelligence, applied mathematics, and computational modelling, with emphasis on the areas of scientific computing and data science, a Memorandum of Understanding (MoU) have been signed between LNCC and Inria/France. As a  result of new joint activities, LNCC and INESC TEC/Portugal are starting  collaboration through INESC TEC International Visiting Researcher Programme 2023.”

The post RISC2’s partners gather in Brussels to reflect on three years of collaboration between EU and Latin America first appeared on RISC2 Project.

Last month, students from the field of Computer Sciences, Engineering and others related to HPC (Physics & Material Sciences, Biology/Bioinformatics, Finance, etc), gathered for six days in Cartagena de Indias, Colombia, for the SC-Camp, where they had the chance to learn more about Super Computing and Distributed Systems. The week was filled with courses with focus on practical sessions, keynotes and a collaborative project.

As such, the aim of the SC-Camp was to give undergraduate and master students state-of-the-art lectures and programming practical sessions about High Performance and Distributed Computing topics.

SC-Camp is an itinerant school, which means that every year t will take HPC knowledge to a different place. This was the first time, since the Covid-19 pandemic, the SC-Camp took place in person.

The post SC-Camp 2023 gathers students from HPC related fields in Cartagena de Indias first appeared on RISC2 Project.

The ENERXICO Project focused on developing advanced simulation software solutions for oil & gas, wind energy and transportation powertrain industries.  The institutions that collaborated in the project are for México: ININ (Institution responsible for México), Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Universidad Nacional Autónoma de México (UNAM IINGEN, FCUNAM), Universidad Autónoma Metropolitana-Azcapotzalco, Instituto Mexicano del Petróleo, Instituto Politécnico Nacional (IPN) and Pemex, and for the European Union: Centro de Supercómputo de Barcelona (Institution responsible for the EU), Technische Universitäts München, Alemania (TUM), Universidad de Grenoble Alpes, Francia (UGA), CIEMAT, España, Repsol, Iberdrola, Bull, Francia e Universidad Politécnica de Valencia, España.  

The Project contemplated four working packages (WP): 

WP1 Exascale Enabling: This was a cross-cutting work package that focused on assessing performance bottlenecks and improving the efficiency of the HPC codes proposed in vertical WP (UE Coordinator: BULL, MEX Coordinator: CINVESTAV-COMPUTACIÓN); 

WP2 Renewable energies:  This WP deployed new applications required to design, optimize and forecast the production of wind farms (UE Coordinator: IBR, MEX Coordinator: ININ); 

WP3 Oil and gas energies: This WP addressed the impact of HPC on the entire oil industry chain (UE Coordinator: REPSOL, MEX Coordinator: ININ); 

WP4 Biofuels for transport: This WP displayed advanced numerical simulations of biofuels under conditions similar to those of an engine (UE Coordinator: UPV-CMT, MEX Coordinator: UNAM); 

For WP1 the following codes were optimized for exascale computers: Alya, Bsit, DualSPHysics, ExaHyPE, Seossol, SEM46 and WRF.   

As an example, we present some of the results for the DualPHYysics code. We evaluated two architectures: The first set of hardware used were identical nodes, each equipped with 2 ”Intel Xeon Gold 6248 Processors”, clocking at 2.5 GHz with about 192 GB of system memory. Each node contained 4 Nvidia V100 Tesla GPUs with 32 GB of main memory each. The second set of hardware used were identical nodes, each equipped with 2 ”AMD Milan 7763 Processors”, clocking at 2.45 GHz with about 512 GB of system memory. Each node contained 4 Nvidia V100 Ampere GPUs with 40 GB of main memory each. The code was compiled and linked with CUDA 10.2 and OpenMPI 4. The application was executed using one GPU per MPI rank. 

In Figures 1 and 2 we show the scalability of the code for the strong and weak scaling tests that indicate that the scaling is very good. Motivated by these excellent results, we are in the process of performing in the LUMI supercomputer new SPH simulations with up to 26,834 million particles that will be run with up to 500 GPUs, which is 53.7 million particles per GPU. These simulations will be done initially for a Wave Energy Converter (WEC) Farm (see Figure 3), and later for turbulent models. 

Figure 1. Strong scaling test with a fix number of particles but increasing number of GPUs.

Figure 2. Weak scaling test with increasing number of particles and GPUs.

Figure 3. Wave Energy Converter (WEC) Farm (taken from https://corpowerocean.com/)

As part of WP3, ENERXICO developed a first version of a computer code called Black Hole (or BH code) for the numerical simulation of oil reservoirs, based on the numerical technique known as Smoothed Particle Hydrodynamics or SPH. This new code is an extension of the DualSPHysics code (https://dual.sphysics.org/) and is the first SPH based code that has been developed for the numerical simulation of oil reservoirs and has important benefits versus commercial codes based on other numerical techniques.  

The BH code is a large-scale massively parallel reservoir simulator capable of performing simulations with billions of “particles” or fluid elements that represent the system under study. It contains improved multi-physics modules that automatically combine the effects of interrelated physical and chemical phenomena to accurately simulate in-situ recovery processes. This has led to the development of a graphical user interface, considered as a multiple-platform application for code execution and visualization, and for carrying out simulations with data provided by industrial partners and performing comparisons with available commercial packages.  

Furthermore, a considerable effort is presently being made to simplify the process of setting up the input for reservoir simulations from exploration data by means of a workflow fully integrated in our industrial partners’ software environment.  A crucial part of the numerical simulations is the equation of state.  We have developed an equation of state based on crude oil data (the so-called PVT) in two forms, the first as a subroutine that is integrated into the code, and the second as an interpolation subroutine of properties’ tables that are generated from the equation of state subroutine.  

An oil reservoir is composed of a porous medium with a multiphase fluid made of oil, gas, rock and other solids. The aim of the code is to simulate fluid flow in a porous medium, as well as the behaviour of the system at different pressures and temperatures.  The tool should allow the reduction of uncertainties in the predictions that are carried out. For example, it may answer questions about the benefits of injecting a solvent, which could be CO2, nitrogen, combustion gases, methane, etc. into a reservoir, and the times of eruption of the gases in the production wells. With these estimates, it can take the necessary measures to mitigate their presence, calculate the expense, the pressure to be injected, the injection volumes and most importantly, where and for how long. The same happens with more complex processes such as those where fluids, air or steam are injected, which interact with the rock, oil, water and gas present in the reservoir. The simulator should be capable of monitoring and preparing measurement plans. 

In order to be able to perform a simulation of a reservoir oil field, an initial model needs to be created.  Using geophysical forward and inverse numerical techniques, the ENERXICO project evaluated novel, high-performance simulation packages for challenging seismic exploration cases that are characterized by extreme geometric complexity. Now, we are undergoing an exploration of high-order methods based upon fully unstructured tetrahedral meshes and also tree-structured Cartesian meshes with adaptive mesh refinement (AMR) for better spatial resolution. Using this methodology, our packages (and some commercial packages) together with seismic and geophysical data of naturally fractured reservoir oil fields, are able to create the geometry (see Figure 4), and exhibit basic properties of the oil reservoir field we want to study.  A number of numerical simulations are performed and from these oil fields exploitation scenarios are generated.

Figure 4. A detail of the initial model for a SPH simulation of a porous medium.

More information about the ENERXICO Project can be found in: https://enerxico-project.eu/

By: Jaime Klapp (ININ, México) and Isidoro Gitler (Cinvestav, México)

The post Subsequent Progress And Challenges Concerning The México-UE Project ENERXICO: Supercomputing And Energy For México first appeared on RISC2 Project.

The goal of the investigation is to provide users with simplified access to computing structures through scientific solutions that represent significant developments in their fields. In the case of this project, it is intended to develop intelligent green scientific solutions for BioinfoPortal (a multiuser Brazilian infrastructure)supported by High-Performance Computing environments.

Technologically, it includes areas such as scientific workflows, data mining, machine learning, and deep learning. The outlook, in case of success, is the analysis and interpretation of Big Data allowing new paths in molecular biology, genetics, biomedicine, and health— so it becomes necessary tools capable of digesting the amount of information, efficiently, which can come.

The team performed several large-scale bioinformatics experiments that are considered to be computationally intensive. Currently, artificial intelligence is being used to generate models to analyze computational and bioinformatics metadata to understand how automatic learning can predict computational resources efficiently. The workshop was held from April 10th to 11th, and took place in the University of Sao Paulo.

RISC2 Project, which aims to explore the HPC impact in the economies of Latin America and Europe, relies on the interaction between researchers and policymakers in both regions. It also includes 16 academic partners such as the University of Buenos Aires, National Laboratory for High Performance Computing of Chile, Julich Supercomputing Centre, Barcelona Supercomputing Center (the leader of the consortium), among others.

The post Latin American researchers present greener gateways for Big Data in INRIA Brazil Workshop first appeared on RISC2 Project.

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 post 14th International SuperComputing Camp 2023 first appeared on RISC2 Project.

A country that does not have the computational capacity to solve its own problems will have no alternative but to try to acquire solutions provided by others. One of the most important aspects of sovereignty in the 21st century is the ability to produce mathematical models and to have the capacity to solve them. Today, the availability of computing power commensurate with one’s wealth exponentially increases a country’s capacity to produce knowledge. in the developed world, it is estimated that for every dollar invested in supercomputing, the return to society is of the order of US$ 44(1) and to the academic world US$ 30(2). For these reasons, HPC occupies an important place on the political and diplomatic agendas of developed countries. 

In Latin America, investment in HPC is very low compared to what’s the US, Asia and Europe are doing. In order to quantify this difference, we present the tables below, which show the accumulated computing capacity in the ranking of the 500 most powerful supercomputers in the world – the TOP500(3) – (Table 1), and the local reality (Table 2). Other data are also included, such as the population (in millions), the number of researchers per 1,000 inhabitants (Res/1000), the computing capacity per researcher (Gflops/Res) and the computing capacity per US$ million of GPD. In Table 1, we have grouped the countries by geographical area. America appears as the area with the highest computing capacity, essentially due to the USA, which has almost 45% of the world’s computing capacity in the TOP500. It if followed by Asia and then Europe. Tis TOP500 list includes mainly academic research centres, but also industry ones, typically those used in applied research (many private ones do not wish to publish such information for obvious reasons). For example, in Brazil – which shows good computing capacity with 88,175 TFlops – the vast majority is in the hands of the oil industry and only about 3,000 TFlops are used for basic research. Countries listed in the TOP500 invest in HPC from a few TFlops per million GDP (Belgium 5, Spain 7, Bulgaria 8), through countries investing in the order of hundreds (Italy 176, Japan 151, USA 138), to even thousands, as is the case in Finland with 1,478. For those countries where we were able to find data on the number of researchers, these range from a few Gflops per researcher (Belgium 19, Spain 24, Hungary 52) to close to 1,000 GFlops, i.e. 1 TFlop (USA 970, Italy 966), with Finland surpassing this barrier with 4,647. Note that, unlike what happens locally, countries with a certain degree of development invest every 3-4 years in supercomputing, so the data we are showing will soon be updated and there will be variations in the list. For example, this year a new supercomputer will come into operation in Spain(4), which, with an investment of some 150 million euros, will give Spain one of the most powerful supercomputers in Europe – and the world.

Table 1. HPC availability per researcher and relative to GDP in the TOP500 countries (includes HPC in industry).

The local reality is far from this data. Table 2 shows data from Argentina, Brazil, Chile and Mexico. In Chile, the availability of computing power is 2-3 times less per researcher than in countries with less computing power in the OECD and up to 100 times less than a researcher in the US. In Chile, our investment measured in TFlops per million US$ of GDP is 166 times less than in the US; with respect to European countries that invest less in HPC it is 9 times less, and with respect to the European average (including Finland) it is 80 times less, i.e. the difference is considerable. It is clear that we need to close this gap. An investment go about 5 million dollars in HPC infrastructure in the next 5 years would close this gap by a factor of almost 20 times our computational capacity. However, returning to the example of Spain, the supercomputer it will have this year will offer 23 times more computing power than at present and, therefore, we will only maintain our relative distance. If we do not invest, the dap will increase by at least 23 times and will end up being huge. Therefore, we do not only need a one-time investment, but we need to ensure a regular investment. Some neighbouring countries are already investing significantly in supercomputing. This is the case in Argentina, where they are investing 7 million dollars (2 million for the datacenter and 5 million to buy a new supercomputer), which will increase their current capacities by almost 40 times(5).

Table 2. HPC availability per researcher and relative to GDP in the region (*only HPC capacity in academia is considered in this table).

For the above reasons, we are working to convince the Chilean authorities that we must have greater funding and, more crucially, permanent state funding in HPC. In relation to this, on July 6 we signed a collaboration agreement between 44 institutions with the support of the Ministry of Science to work on the creation of the National Supercomputing Laboratory(6). The agreement recognised that supercomputers are a critical infrastructure for Chile’s development, that it is necessary to centralise the requirements/resources at the national level, obtain permanent funding from the State and create a new institutional framework to provide governance. In an unprecedented inter-institutional collaboration in Chile, the competition for HPC resources at the national level is eliminated ad the possibility of direct funding from the State is opened up without generating controversy.

Undoubtedly, supercomputing is a fundamental pillar for the development of any country, where increasing investment provides a strategic advantage, and in Latin America we should not be left behind.

By NLHPC

References

(1) Hyperion Research HPC Investments Bring High Returns

(2) EESI-2 Special Study To Measure And Model How Investments In HPC Can Create Financial ROI And Scientific Innovation In Europe 

(3) https://top500.org/ 

(4) https://www.lavanguardia.com/ciencia/20230129/8713515/llega-superordenador-marenostrum-5-bsc-barcelona.html

(5) https://www.hpcwire.com/2022/12/15/argentina-announces-new-supercomputer-for-national-science/

(6) https://uchile.cl/noticias/187955/44-instituciones-crearan-el-laboratorio-nacional-de-supercomputacion

The post Towards a greater HPC capacity in Latin America first appeared on RISC2 Project.

Building on the success of previous editions, the seventh installment of the Costa Rica High Performance Computing School (CRHPCS) aims at preparing students and researchers to introduce HPC tools in their workflows. A selected team of international experts taught sessions on shared-memory programming, distributed-memory programming, accelerator programming, and high performance computing.  This edition had instructors Alessandro Marani and Nitin Shukla from CINECA, which greatly helped in bringing a vibrant environment to the sessions.

Bernd Mohr, from Jülich Supercomputing Centre, was the Keynote Speaker of this year’s edition of the event.  A well-known figure in the HPC community at large, Bernd presented the talk Parallel Performance Analysis at Scale: From Single Node to one Million HPC Cores. In an amazing voyage through different architecture setups, Bernd highlighted the importance and challenges of performance analysis.

For Esteban Meneses, Costa Rica HPC School General Chair, the School is a key element in building a stronger and more connected HPC community in the region. This year, thanks to the RISC2 project, we were able to gather participants from Guatemala, El Salvador, and Colombia. Creating these ties is fundamental for later developing more complex initiatives. We aim at preparing future scientists that will develop groundbreaking computer applications that tackle the most pressing problems of our region.

More information here. 

The post Costa Rica HPC School 2023 aimed at teaching the fundamental tools and methodologies in parallel programming first appeared on RISC2 Project.

Date: April 26, 2023 | 3 p.m. (UTC+1)

The post Webinar: Improving energy-efficiency of High-Performance Computing clusters first appeared on RISC2 Project.

Date: May 31, 2023 | 4 p.m. (UTC+1)

The post Webinar: Addressing the challenges of scientific visualization in the exascale age first appeared on RISC2 Project.