PRACE

Partnership for Advanced Computing in Europe

PRACE https://tess.elixir-europe.org/content_providers/prace Partnership for Advanced Computing in Europe /system/content_providers/images/000/000/059/original/1c2d412b-c20c-43b8-926d-6febf042f341?1479828059
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  • Earth Sciences Simulation Environments @ BSC

    27 - 29 November 2018

    Earth Sciences Simulation Environments @ BSC https://tess.elixir-europe.org/events/earth-sciences-simulation-environments-bsc-bae8c213-51a1-4184-92c2-e3dc02f33b31 The registration to this course is now open. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course conveners: Maria Teresa Pay and Mario Acosta Course lecturers: Earth Sciences Department researchers involved in the group of Computational Earth Sciences, Atmospheric Composition, Climate Prediction and Earth System Services. Final lectures TBA. Objectives: The objective of this PATC course is to cover the basics of a high performance computing (HPC) environment oriented towards earth science applications, specifically chemical weather modelling and climate modelling. More precisely, the course will cover: Introduction to earth science fundamentals and modelling; Basic usage of an HPC environment: shell, compilers, libraries, file systems, queuing system and parallel computing; Build and configure targeted earth science applications with the NMMB/BSC-CTM chemical transport model and with the EC-EARTH climate model; Execute and monitor numerical experiments using a workflow manager; Analyse and visualise model outputs with a wide set of tools. Learning outcomes: Participants will learn and gain experience in accessing an HPC facility, installing earth science numerical models and related utilities and libraries, running numerical simulations, monitoring the execution of supercomputing jobs, analysing and visualising model results. Level: (All courses are designed for specialists with at least 1st cycle degree or similar background experience) For trainees with some theoretical and practical knowledge Prerequisites: At least University degree in progress on Earth Sciences, Computer Sciences or related area Basic knowledge of UNIX Knowledge of C, FORTRAN, MPI or openMP is recommended Knowledge of Earth Sciences data formats is recommended (grib, netcdf, hdf,…) Knowledge of R and Python Agenda: Day 1 (Nov. 27) Session 1 / 10:00am – 1:30pm (3 h lectures) 10:00-11:30 Introduction to earth science fundamentals and modelling.    11:30-11:50 Coffee break 11:50-13:30 Introduction to Linux and HPC, BSC facilities, PRACE and RES    13:30-14:30 Lunch break Session 2 / 2:30pm – 6:00 pm (1:30 h lectures, 2 h practical) 14:30-16:00 HPC hands-on tutorial. At the end of this tutorial, the students will be able to compile and execute jobs on Mare Nostrum 4.    16:00-16:20 Coffee break 16:20-18:00 Introduction to analysis and visualisation tools for model outputs (s2dverification, MapGenerator, CDO, NCO, panoply, ncview) 18:00  Adjourn    20:00 Social dinner (participants pay individually) Day 2 (Nov 28) Session 3 / 10:00am – 2:00pm (3 h lectures) 10:00-11:00 Lecture on the NMMB-MONARCH chemical transport model. 11:00-12:00 Lecture on setting up and running the model.    12:00-12:30 Coffee break 12:30-14:00 Model hands-on tutorial. Students will run a prepared case.    14:00-15:00 Lunch break Session 4 / 3:00pm – 5:00 pm (2 h practical) 15:00-17:00 Analysis hands-on tutorial. Students will apply tools for analysis and visualisation to the outputs created in the morning. Day 3 (Nov 29) Session 5 / 10:00am – 2:00pm (3 h lectures) 10:00-11:00 Lecture on the EC-EARTH climate model. 11:00-12:00 Lecture on setting up and running the model with Autosubmit.     12:00-12:30 Coffee break 12:30-14:00 Model hands-on tutorial. Students will run with a prepared case.    14:00-15:00 Lunch break Session 6/ 3:00pm – 5:30 pm (2 h practical) 15:00-17:00 Analysis hands-on tutorial. Students will apply tools for analysis and visualisation to the outputs created in the morning. 17:00-17:30 MareNostrum visit End of Course https://events.prace-ri.eu/event/757/ 2018-11-27 09:00:00 UTC 2018-11-29 16:30:00 UTC [] [] [] workshops_and_courses [] []
  • Debugging and Optimization of Scientific Applications@Cineca

    19 - 21 November 2018

    Debugging and Optimization of Scientific Applications@Cineca https://tess.elixir-europe.org/events/debugging-and-optimization-of-scientific-applications-cineca-07cb322f-f814-4bd1-b45f-e963b9e876fc The tipical approach to the art of programming from the point of view of a scientist only rarely permits to reach good results in terms of computational performances. The basic knowledge about how a computer machine really works permits even to a naif programmer to better write his own code and eventually to optimize properly any kind of scientific program. This knowledge is way more important in the field of High-Performance Computing where the correct exploitation of the modern architecures is crucial to the achievement of scientific results. This code is addressed to C and Fortran programmers that, even without notions of computer science, have necessities to learn tricks and techniques to quickly debug and optimize codes without restarting from scratch. Aim of this course is to guide the user to analyze and improve performances of his software, by introducing techniques and tools used in the HPC world. Software and hardware profilers will be presented and it will be showed how to find bottlenecks and how to fix them. Typical techniques of optimization (cache reuse, unrolling, inlining, vectorization) will be presented the use of mathematical libraries will be discussed. Furthermore, the use of compiler flags on different architectures and compilers will be introduced. Skills:  By the end of the course the student will be able to: manage efficiently the computer memory use tools to profile programs and measure their performance understand and use efficiently compilers and compiler options optimize programs understand and incorporate scientific libraries in their programs design a debugging strategy based on dedicated tools and other techniques Target audience:  Researchers and programmers interested to a quick and efficient debugging and to a knowledge of fundamental concepts of optimization. This course is particularly suitable for people approaching for the first time to issues of computer programming in the framework of scientific calculations. Pre-requisites:  Knowledge of Fortran or C/C++. Elementary notions of Linux/Unix. Grant The course is FREE of charge. The lunch for the three days will be offered to all the participants and some grants are available. The only requirement to be eligible is to be not funded by your institution to attend the course and to work and live in an institute outside the Bologna area. The grant  will be 300 euros for students working and living outside Italy and 150 euros for students working and living in Italy (outside Bologna area). Some documentation will be required and the grant will be paid only after a certified presence of minimum 80% of the lectures. Further information about how to request the grant, will be provided at the confirmation of the course: about 3 weeks before the starting date.   https://events.prace-ri.eu/event/789/ 2018-11-19 08:00:00 UTC 2018-11-21 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Performance Analysis and Tools @ BSC

    20 - 21 May 2019

    Performance Analysis and Tools @ BSC https://tess.elixir-europe.org/events/performance-analysis-and-tools-bsc-8d57b32e-7545-4c9f-8c7d-68fffe1ed7b7 The registration to this course will open in February. Please, bring your own laptop.  All the PATC courses at BSC are free of charge. Course convener: Judit Gimenez, Tools Group Manager, Computer Sciences - Performance Tools, BSC Objectives: The objective of this course is to learn how Paraver and Dimemas tools can be used to analyze the performance of parallel applications and to familiarize with the tools usage as well as instrumenting applications with Extrae. Learning Outcomes:The students who finish this course will have a basic knowledge on the usage of the BSC performance tools. They will be able to apply the same methodology to their applications, identifying potential bottlenecks and getting hints on how to improve the applications performance. Level:  INTERMEDIATE - for trainees with some theoretical and practical knowledge. (All courses are designed for specialists with at least finished 1st cycle degree) Prerequisites: Good knowledge of C/C++ Basic knowledge of CUDA/OpenCL Basic knowledge of MPI, OpenMP Course Outline: Day 1 (May, 20)   Session 1 / 9:30am - 1 pm (1:30 h lectures, 1:30 h practical) 1. Introduction to Paraver 2. Paraver demo Coffee Break (11:00h-11:30h) 3. Extrae and Paraver guided hands-on Lunch Break (13:00h-14:00h)   Session 2 / 2 pm- 5:30pm (3 h practical) Paraver Hands-on Coffee Break (16:00h-16:15h)   Day 2 (May, 21)   Session 3 / 9:30am- 1 pm 1. Performance Analytics (3 h lectures) Coffee Break (11:00h-11:30h) 2. Introduction to Dimemas Lunch Break (13:00h-14:00h)   Session 4 / 2 pm- 5:30 pm (3 h practical) 1. Tools Hands-on Coffee Break (16:00h-16:15h) 2. Students knowledge test END of COURSE https://events.prace-ri.eu/event/766/ 2019-05-20 07:30:00 UTC 2019-05-21 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Programming Distributed Computing Platforms with COMPSs @ BSC

    29 - 30 January 2019

    Programming Distributed Computing Platforms with COMPSs @ BSC https://tess.elixir-europe.org/events/programming-distributed-computing-platforms-with-compss-bsc-690d7bfe-6074-40ae-a706-b4a06ca5dfa8 The registration to this course will open in September. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course convener: Rosa Badia, Workflows and Distributed Computing Group Manager, Computer Sciences - Workflows and Distributed Computing Department Lecturers:  Rosa M Badia, Workflows and Distributed Computing Group Manager, Computer Sciences - Workflows and Distributed Computing Department, BSC Javier Conejero, Senior Researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Jorge Ejarque, Researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Daniele Lezzi, senior researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Objectives: The objective of this course is to give an overview of the COMPSs programming model, which is able to exploit the inherent concurrency of sequential applications and execute them in a transparent manner to the application developer in distributed computing platform. This is achieved by annotating part of the code as tasks, and building at execution a task-dependence graph based on the actual data used consumed/produced by the tasks. The COMPSs runtime is able to schedule the tasks in the computing nodes and take into account facts like data locality and the different nature of the computing nodes in case of heterogeneous platforms. Additionally, recently COMPSs has been enhanced with the possibility of coordinating Web Services as part of the applications. COMPSs supports Java, C/C++ and Python as programming languages. Learning Outcomes:  In the course, the COMPSs syntax, programming methodology and an overview of the runtime internals will be given. The attendees will get a first lesson about programming with COMPSs that will enable them to start programming with this framework. A hands-on with simple introductory exercises will be also performed. The students who finish this course will be able to develop simple COMPSs applications and to run them both in a local resource and in a distributed platform (initially in a private cloud) Level: for trainees with some theoretical and practical knowledge. INTERMEDIATE: for trainees with some theoretical and practical knowledge; those who finished the beginners course ADVANCED: for trainees able to work independently and requiring guidance for solving complex problems Prerequisites: Programming skills in Java and Python    Agenda:  Day 1 (January, 29) Session 1 / 9:30am – 1:00pm (1h lecture, 1:30h practical) 9: 30 am – 10:00 am Roundtable. Presentation and background of participants 10:00 am – 10:15 am Motivation and introduction to COMPSs 10:15 am – 11:00 am Programming mode: Python Syntax 11:00 am – 11:30 am Coffee Break 11:30 am – 13:00 pm Python Hands-on 13:00 pm – 14:30 pm Lunch Break   Session 2 / 2:30pm – 16:30pm (2h practical) 14:30 pm – 16:30 pm practical session on parallelizing with PyCOMPSs (bring your own code) 16:30pm - Adjourn     Day 2 (January, 30) Session 3 / 9:30am – 1:30pm (1:30h lecture, 2 h practical) 9:30 am – 10:00 am: Java Syntax 10:00 am – 11:00 pm Java Hands-on 11:00 am – 11:30 am Coffee Break 11:30 am – 12:00 pm COMPSs execution environment 12:00 pm – 12:30 pm Integration COMPSs+OmpSs 12:30 pm – 13:30 pm Cluster Hands-on (MareNostrum) 13.30 pm – 14.30 pm Lunch Break   Session 4 / 2:30pm – 16:30pm (2h practical) 14.30 pm – 16.00 pm practical session on parallelizing with COMPSs (bring your own code) 16:00 pm – 16:30 pm COMPSs Installation and Final Notes 16:30pm - Adjourn   END of COURSE     https://events.prace-ri.eu/event/760/ 2019-01-29 08:30:00 UTC 2019-01-30 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Parallel Design Patterns @ EPCC at University of Oxford

    6 - 8 November 2018

    Parallel Design Patterns @ EPCC at University of Oxford https://tess.elixir-europe.org/events/parallel-design-patterns-epcc-at-university-of-oxford If you were given a serial problem, conceptually, how would you go about splitting it up into many different parts that could run concurrently on the latest parallel computers? The good news is that you don't need to reinvent the wheel. Instead, there are many different approaches (called parallel patterns) that have been developed by the community and can be used in a variety of situations. These patterns apply equally well regardless of whether your problem is computational or data-driven. Understanding and being able to apply these patterns also helps in getting to grips with existing parallel codes and optimising poorly performing computation and data codes. Whilst the lectures take a top down approach, focusing on the patterns themselves, the practical exercises give the opportunity to explore the concepts by implementing pattern-based solutions to problems using common HPC technologies. The parallel patterns (known as a pattern language) that we cover are split into two categories. The closest to the problem area (and most abstract) are parallel algorithm strategy patterns and include: Task Parallelism Recursive Splitting Geometric Decomposition Pipeline Discrete Event Actors The other category of patterns is closer to the implementation and drives how the programmer should structure their code and data. These are implementation strategy patterns, and include: Master/Worker Loop Parallelism Fork/Join Shared Data and Queues Active Messaging Patterns are described on an abstract level and we will also discuss enhancements that can be made to improve performance/scalability but at the cost of code complexity. Practical implementations of these patterns are explored in depth in the hands-on exercises. Programming exercises use C and Fortran, with MPI and OpenMP. Trainer Nick Brown Nick is involved with the MSc in High Performance Computing, is the course organiser for the Parallel Design Patterns module and also supervises student dissertation projects. Course Pre-requisites Ability to program in C, C++ or Fortran. Familiarity with using MPI Some familiarity with OpenMP is beneficial but not essential Pre-course setup All course delegates will need to bring a wireless enabled laptop computer with them on the course. If you have an EduRoam account please ensure this is set up beforehand. Practical exercises will be done using a guest account on ARCHER. You will need to set up your laptop before the course with the required software. Setup information is available at http://www.archer.ac.uk/training/courses/software.php for Windows, Mac and Linux. Learning outcomes On completion of this course students should be able to: Recognise different strategies for structuring the parallelism of a specific problem in hand Understand the trade-offs between different approaches to, and specialisations of, parallelisation Identify the most appropriate ways to structure code and data with respect to the parallel strategy adopted https://events.prace-ri.eu/event/776/ 2018-11-06 09:00:00 UTC 2018-11-08 17:30:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction for Simulation Environments for Life Sciences @ BSC

    14 - 15 March 2019

    Introduction for Simulation Environments for Life Sciences @ BSC https://tess.elixir-europe.org/events/introduction-for-simulation-environments-for-life-sciences-bsc The registration to this course will open in January. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Objectives: The course will make the attendants familiar with simulation technologies used in Life Sciences and their specific adaptation to HPC environment Course convener: Josep Gelpi Detailed outline: Introduction to biomolecular simulation Coarse-grained and atomistic simulation strategies Automated setup for simulation HPC specifics: Large scale parallelization, use of GPU’s Storage and strategies for large scale trajectory analysis Learning Outcomes: Setup, execute, and analyze standard simulations in HPC environment Level: (All courses are designed for specialists with at least 1st cycle degree or similar background experience) INTERMEDIATE: for trainees with some theoretical and practical knowledge. Course Program Outline: TBA     https://events.prace-ri.eu/event/764/ 2019-03-14 08:00:00 UTC 2019-03-15 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Short course on HPC-based Computational Bio-Medicine @ BSC

    13 - 15 February 2019

    Short course on HPC-based Computational Bio-Medicine @ BSC https://tess.elixir-europe.org/events/short-course-on-hpc-based-computational-bio-medicine-bsc The registration to this course will open in November. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course convener: Mariano Vazquez and Ruth Aris Lecturers: Marco Verdicchio (SURFsara), Gábor Závodszky (UvA), Guillaume Houzeaux - Ricard Borrell (BSC), Dr Xinshan Li, Dr Alessandro Melis (USFD), Karl Podesta (MICROSOFT), Dr Alexander Heifetz (EVOTEC), Andrea Townsend-Nicholson, David Wright (UCL), Andrea Townsend-Nicholson, David Wright (UCL) Guillermo Marín (BSC), João Damas (ACELLERA), Adrià Perez (UPF), Alfonso Santiago (BSC), Jazmín Aguado-Sierra (BSC), Eva Casoni (BSC) Objectives:The objetive of this course is to give a panorama on the use of HPC-based computational mechanics in Engineering and Environment through the projects BSC are carrying on. This panorama includes the basics of what is behind the main tools: computational mechanics and parallelization. The training is delivered in collaboration with the center of excellence CompBioMed. Learning outcomes: The course gives a wide perspective and the latest trends of how HPC helps in industrial, clinical and research applications allowing to achieve more realistic multiphysics simulations.  In addition, the student has the opportunity of running Jobs in Marenostrum supercomputer. Level: INTERMEDIATE: For trainees with some theoretical and practical knowledge Agenda: Day 1 (Feb. 13) Session 1 / 9:00am – 1:00 pm  (4 h lectures) 9:00-11:00 Introduction to Computational Mechanics: Bioengineering Applications (Mariano Vázquez, BSC) 11:00-13:00 Introduction to HPC in Computational Modelling (Marco Verdicchio, SURFsara) 13:00-14:00 Lunch Break Session 2 / 2:00pm – 6:00 pm (4 h lectures) 14:00-16:00 Computational Hemodynamics on HPC (UvA) (Gábor Závodszky, UvA) 16:00-18:00 Parallel algorithms for Computational Mechanics (Guillaume Houzeaux - Ricard Borrell, BSC)     Day 2 (Feb. 14) Session 3 / 9:00am – 1:00 pm  (4 h lectures) 9:00-11:00 Predicting the risk of fall - A computational modelling approach using CT2S (Dr Xinshan Li, Dr Alessandro Melis, USFD) 11:00-13:00 Big Compute: HPC in the Cloud with Microsoft Azure (Karl Podesta, MICROSOFT) 13:00-14:00 Lunch Break Session 4 / 2:00pm – 6:00 pm (2 h lectures, 2 h practical) 14:00-15:00 Introduction to Computer-Aided Drug Design (CADD) and GPCR Modelling (Dr Alexander Heifetz, EVOTEC)   15:00-16:00 Innovations in HPC-training for medical, science and engineering students (Andrea Townsend-Nicholson, David Wright, UCL) 16:00-18:00 Molecular Medicine: Hands On (Andrea Townsend-Nicholson, David Wright, UCL)     Day 3 (Feb. 15) Session 5 / 9:00am – 1:00 pm  (4 h lectures) 9:00-11:00 Data Visulization for Researchers Crash Course (Guillermo Marín, BSC) 11:00-13:00 High Throughput Molecular Dynamics Simulations for Drug Discovery (João Damas, ACELLERA, Adrià Perez, UPF) 13:00-14:00 Lunch Break Session 6 / 2:00pm – 6:00 pm ((4 h lectures) 14:00-15:00 Fluid structure interaction applied to electromechanical models of the heart (Alfonso Santiago, BSC) 15:00-16:00 HPC Multi-scale computational modelling using Alya Red (Jazmín Aguado-Sierra, BSC) 16:00-18:00 Computational Biomechanics: trends in modelling and simulation (Eva Casoni, BSC)   END of COURSE https://events.prace-ri.eu/event/762/ 2019-02-13 08:00:00 UTC 2019-02-15 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Systems Workshop: Programming MareNostrum 4 @ BSC

    27 - 28 February 2019

    Systems Workshop: Programming MareNostrum 4 @ BSC https://tess.elixir-europe.org/events/systems-workshop-programming-marenostrum-4-bsc-93bcf81b-5b06-49e7-b43a-2905ce9ecab8 The registration to this course will open on November 2018. Please, bring your own laptop.  All the PATC courses at BSC are free of charge. Course convener: David Vicente Lecturers: David Vicente, Javier Bartolomé, Carlos Tripiana, Oscar Hernandez, Rubén Ramos, Félix Ramos, Pablo Ródenas, Jorge Rodríguez, Marta Renato, Cristian Morales Objectives: The objective of this course is to present to potential users the new configuration of MareNostrum and a introduction on how to use the new system (batch system, compilers, hardware, MPI, etc).Also It will provide an introduction about RES and PRACE infrastructures and how to get access to the supercomputing resources available. Learning Outcomes: The students who finish this course will know the internal architecture of the new MareNostrum, how it works, the ways to get access to this infrastructure and also some information about optimization techniques for its architecture. Level: INTERMEDIATE -for trainees with some theoretical and practical knowledge; those who finished the beginners course. Prerequisites:  Any potential user of a HPC infrastructure will be welcome Agenda: DAY 1 (Feb. 27) 9am - 5pm Session 1 / 9:00am – 1:00 pm  (2:45 h lectures, 45’ practical) 09:00h - 09:30h Introduction to BSC, PRACE PATC and this training (David Vicente) 09:30h - 10:30h MareNostrum 4 – the view from System administration group (Javier Bartolomé) 10:30h – 11:00h COFFEE BREAK 11:00h - 11:30h Deep Learning and Big data tools on MN4 (Carlos Tripiana) 11:30h - 12:15h How to use MN4 – Basics: Batch system, file systems, compilers, modules, DT, DL, BSC commands (Oscar Hernandez, Rubén Ramos, Félix Ramos) 12:15h - 13:00h Hands-on I (Oscar Hernandez, Rubén Ramos, Félix Ramos) 13:00h - 14:30h LUNCH (not hosted)   Session 2 / 2:30pm – 5:15 pm (3:30 h practical) 14:30h - 15:15h How to use MN4 – HPC architectures and parallelism (Jorge Rodriguez, Pablo Ródenas) 15:15h - 16:00h How to use MN4 – Parallel programming: MPI, MPI IO, MKL, GREASY (Pablo Ródenas, Jorge Rodríguez) 16:00h - 16:15h COFFEE BREAK 16:15h - 16:45h Hands-on II (Pablo Ródenas, Jorge Rodriguez) 16:45h - 17:15h Optional: MareNostrum 4 visit (In the chapel) 17:15h - Adjourn   DAY 2 (Feb. 28) 9:00am – 1:00 pm  Session 3 / 9:00am – 1:00 pm  (2 h lectures, 1:30 h practical) 09:00h - 09:30h Optional: Doubts + Continue previous hands-on + Tunning your app (David Vicente, Jorge Rodríguez) 09:30h - 10:00h How can I get resources from you? (RES Marta Renato) 10:00h - 10:30h How can I get Resources from you? – (PRACE Cristian Morales) 10:30h - 11:00h COFFEE BREAK 11:00h - 11:30h Debugging on MareNostrum, from GDB to DDT (Pablo Ródenas, Oscar Hernandez) 11:30h - 12:30h Hands-on III – Debugging your application (Pablo Ródenas, Oscar Hernandez) 12:30h - 13:00h Wrap-up : Can we help you in your porting ? How ? when ? (David Vicente) 13:00h - Adjourn   END of COURSE   END of COURSE https://events.prace-ri.eu/event/763/ 2019-02-27 08:00:00 UTC 2019-02-28 12:00:00 UTC [] [] [] workshops_and_courses [] []
  • Debugging & Optimization @ MdlS/CINES

    3 - 6 December 2018

    Debugging & Optimization @ MdlS/CINES https://tess.elixir-europe.org/events/debugging-optimization-mdls-cines-611eb697-eb92-4368-8166-e4e89c80bb1b This training will present basic elements first to enable developpers to understand when and how to use a debugger, and second to optimize the performance of their codes. Debugging : A short introduction to debugging with examples Optimization :  Basics (stripping, IOs, getting the calculations out of the loops, changing the algorithm, ...)  Compiler options   Vectorization - Data access (cache usage maximization)  OpenMP parallelization strategies  Theory to upper-bound the expected performance benefit (speedup, efficiency, peak, memory bandwidth, ...) Half of the course will be made of hands-on sessions. The hands-on will use the https://github.com/aff3ct/MIPP library Trainers Bertrand Cirou Mathieu Cloirec Cédric Jourdain Learning outcomes  Ability to understand the main issues for code optimization, knowledge of the main tools and techniques for basic debugging.Prerequisites  Basic knowledge of Unix, programming experience in C++, OpenMP https://events.prace-ri.eu/event/799/ 2018-12-03 08:00:00 UTC 2018-12-06 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Big Data Analytics @ BSC

    5 - 8 February 2019

    Big Data Analytics @ BSC https://tess.elixir-europe.org/events/big-data-analytics-bsc-259ac7f9-7780-44d6-82f8-fdf33e6037d8 Registration will open in November. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course Convener:  Maria-Ribera Sancho Objectives: The course brings together key information technologies used in manipulating, storing, and analysing data including: the basic tools for statistical analysis techniques for parallel processing tools for access to unstructured data storage solutions Learning outcomes: Students will be introduced to systems that can accept, store, and analyse large volumes of unstructured data. The learned skills can be used in data intensive application areas. Level: For trainees with some theoretical and practical knowledge AGENDA:  TBA       https://events.prace-ri.eu/event/761/ 2019-02-05 08:30:00 UTC 2019-02-08 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to OpenACC @ BSC

    4 - 5 April 2019

    Introduction to OpenACC @ BSC https://tess.elixir-europe.org/events/introduction-to-openacc-bsc-6b5fe755-572a-40b7-b62e-65213011ef43 The registration to this course will open in January. All PATC Courses at BSC do not charge fees. PLEASE BRING YOUR OWN LAPTOP. Local Web Page: This is an expansion of the topic "OpenACC and other approaches to GPU computing" covered on this year's and last year's editions of the Introduction to CUDA Programming. This course will provide very good introduction to the PUMPS Summer School run jointly with NVIDIA -  also  at Campus Nord, Barcelona. For further information visit the school website. Convener: Antonio Peña, Computer Sciences Senior Researcher, Accelerators and Communications for High Performance Computing, BSC Objectives:  As an NVIDIA GPU Center of Excellence, BSC and UPC are deeply involved in research and outreach activities around GPU Computing. OpenACC is a high-level, directive-based programming model for GPU computing. It is a very convenient language to leverage the GPU power with minimal code modifications, being the preferred option for non computer scientists. This course will cover the necessary topics to get started with GPU programming in OpenACC, as well as some advanced topics. The target audiences of the course are students who want to develop exciting applications for these processors, as well as those who want to develop programming tools and future implementations for these processors. Level:  BEGINNERS: for trainees from different background or very little knowledge. Agenda: DAY 1 Session 1 / 9:00am – 1:00 pm (2h lectures, 2 h practical) 9:00 - 10:00 Introduction to OpenACC on x86 CPU and GPU 10:00 - 11:00 Hands-on: Introduction 11:00 - 11:30 Break 11:30 - 12:30 Profiling and Parallelizing with the OpenACC Toolkit 12:30 - 13:30 Hands-on: Profiling and Parallelizing 13:30 - 15:00 Lunch break Session 2 / 2:00pm – 5:00 pm (2 h practical) 15:00 - 17:00 Hands-on: Open Labs   DAY 2 Session 3 / 9:00am – 1:00 pm (2h lectures, 2 h practical) 9:00 - 10:00 Expressing Data Locality and Optimizations with OpenACC 10:00 - 11:00 Hands-on: Data Locality and Optimizations 11:00 - 11:30 Break 11:30 - 12:30 Advanced OpenACC Techniques: Interoperability, MPI, and Pipelining 12:30 - 13:30 Hands-on: Advanced Techniques 13:30 - 15:00 Lunch break Session 4 / 2:00pm – 5:00 pm (2 h practical) 15:00 - 17:00 Hands-on: Open Labs End of Course   https://events.prace-ri.eu/event/769/ 2019-04-04 07:00:00 UTC 2019-04-05 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Fortran modernization workshop @ MdlS

    26 - 27 November 2018

    Fortran modernization workshop @ MdlS https://tess.elixir-europe.org/events/fortran-modernization-workshop-mdls This course is offered in cooperation with NAG This two day practical hands-on workshop is aimed at Fortran programmers who want to write modern code, or to modernize existing codes, to make it more readable and maintainable by encouraging good software engineering practices. This workshop will also present how to integrate tools and techniques for Fortran codes to help you develop sustainable software for your scientific and academic research particularly in a collaborative environment. Overall, the aim is to make you a better and more productive computational scientist by improving your applied computer science skills that are directly relevant to computational science. Program First day: 09:00 Registration  09:15 - 12:30 Lectures 14:00 - 18:00 Lectures and exercises Second day: 09:00 - 12:30 Lectures  14:00 - 18:00 Lectures and exercises Topics will include: Modern Fortran standards and how to write optimized and efficient Fortran; Overview of the new Fortran 2018 standard NetCDF and HDF5 scientific file formats for data sharing in Fortran; GNU Automake to automate the build process; pFUnit unit testing framework for testing Fortran codes; Fortran Documenter tool for Fortran code documentation; Git version control for collaborative code development; In-situ visualisation using PLplot in Fortran; IEEE Floating Point Exception Handling; Software verification and portability using the NAG Fortran Compiler; Fortran interoperability with C, Python and R; Introduction to parallelism for Fortran; Introduction to the NAG Fortran library. Prerequisites Basic knowledge of Fortran (any standard) Teacher Wadud Miah from NAG Supplementary material All Prace training events are run in English and are free of charge for all participants, and all material will be provided.  Participants are expected to bring their own laptop. A WiFi connection will be provided (Eduroam is available). All practical sessions will be carried out through an SSH connection For basic knowledge of Fortran, you may visit https://web.stanford.edu/class/me200c/tutorial_90/ or http://fortranwiki.org/fortran/show/Tutorials For more information see https://www.nag.com/content/fortran-modernization-workshop https://events.prace-ri.eu/event/781/ 2018-11-26 08:00:00 UTC 2018-11-27 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Data, lights, camera, action! Scientific visualization done beautifully @SURFsara

    28 November 2018

    Data, lights, camera, action! Scientific visualization done beautifully @SURFsara https://tess.elixir-europe.org/events/data-lights-camera-action-scientific-visualization-done-beautifully-surfsara-0b1000db-d081-45e0-ab55-46fcafc1d0fa Would you like to make 3D visualisations that are visually more attractive than what ParaView or VisIt can provide? Do you need an image for a grant application that needs to look spectacular? Would you like to create a cool animation of flying through your simulation data? Then this course may be for you! The goal of this course is to provide you with hands-on knowledge of producing great images and animations from 3D (scientific) data. We will be using the open-source package Blender (http://www.blender.org), which provides good basic functionality, while also being usable for advanced usage and general editing of 3D data. It is also a lot of fun to work with (once you get used to its graphical interface). Example types of relevant scientific data are 3D cell-based simulations, 3D models from photogrammetry, (isosurfaces of) 3D medical scans, molecular models and earth sciences data. Note that we don't focus on information visualization of abstract data, such as graphs (although you could convert those into a 3D model first and then use them in Blender). We like to encourage participants to bring along (a sample) of the data they normally work with and would like to apply the course knowledge to. https://events.prace-ri.eu/event/751/ 2018-11-28 08:00:00 UTC 2018-11-28 16:30:00 UTC [] [] [] workshops_and_courses [] []
  • Spring School in Computational Chemistry 2019 @ CSC

    19 - 22 March 2019

    Spring School in Computational Chemistry 2019 @ CSC https://tess.elixir-europe.org/events/spring-school-in-computational-chemistry-2019-csc Description The Spring School provides a comprehensive, tutorial-style, hands-on, introductory and intermediate-level treatment to the essential ingredients for molecular modeling and computational chemistry using modern supercomputers. The School program is being prepared, but the main content will be similar to last years and consists of: Classical molecular dynamics, intro + hands on (1 day) Electronic structure theory, intro  + hands on (1 day) Machine learning in chemistry, intro + hands on Special topics: e.g. on Visualization, Enchanced Sampling Techniques, etc. The school is a must for graduate students in the field, providing an overview on "what can be calculated and how should it be done", without forgetting the important aspect of network building. Note: the School has been overbooked in one week after registration was opened. We are investigating the possibility to accommodate more participants, but it is likely that new registrations will go to waiting list. Learning outcome The learning outcome is to gain an overview of the two main methods in computational chemistry — molecular dynamics and electronic structure calculations — in connection with related HPC software packages and other useful skills in the trade. The workshop is also suited for an intensive crash course (the first two days) in computational modelling and is expected to be useful for students and researchers also in physics, materials sciences and biosciences. The following "Special topics" then build on this foundation. Prerequisites Working knowledge and some work experience from some branch of computational chemistry will be useful. Basic linux skills for hands-on exercises and elementary Python for Machine Learning hands-on. More detailed description of pre-requisites and links for self study. Programme See tentative timetable on the left menu, browse 2018 materials or comments from participants in 2018. Lecturers:  Dr. Mikael Johansson, University of Helsinki, Finland Dr. Luca Monticelli, IBCP (CNRS), Lyon, France Dr. Michael Patzschke, Helmholtz-Zentrum Dresden-Rossendorf, Germany to be continued Dr. Martti Louhivuori, CSC - IT Center for Science, Finland Dr. Atte Sillanpää, CSC - IT Center for Science, Finland Dr. Nino Runeberg, CSC- IT Center for Science, Finland Language:  EnglishPrice:         Free of charge https://events.prace-ri.eu/event/786/ 2019-03-19 07:00:00 UTC 2019-03-22 13:00:00 UTC [] [] [] workshops_and_courses [] []
  • Heterogeneous Programming on GPUs with MPI + OmpSs @ BSC

    22 - 23 May 2019

    Heterogeneous Programming on GPUs with MPI + OmpSs @ BSC https://tess.elixir-europe.org/events/heterogeneous-programming-on-gpus-with-mpi-ompss-bsc-40ea3185-16fc-41df-bf8e-cceb481d9109 The registration to this course will open in February. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Objectives:  The tutorial will motivate the audience on the need for portable, efficient programming models that put less pressure on program developers while still getting good performance for clusters and clusters with GPUs. More specifically, the tutorial will: Introduce the hybrid MPI/OmpSs parallel programming model for future exascale systems Demonstrate how to use MPI/OmpSs to incrementally parallelize/optimize: MPI applications on clusters of SMPs, and Leverage CUDA kernels with OmpSs on clusters of GPUs Level: INTERMEDIATE: for trainees with some theoretical and practical knowledge; those who finished the beginners course ADVANCED: for trainees able to work independently and requiring guidance for solving complex problems Requirements:  Good knowledge of C/C++ Basic knowledge of CUDA/OpenCL Basic knowledge of Paraver/Extrae Learning Outcomes: The students who finish this course will be able to develop benchmarks and simple applications with the MPI/OmpSs programming model to be executed in clusters of GPUs. https://events.prace-ri.eu/event/650/ 2019-05-22 07:30:00 UTC 2019-05-23 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Heterogeneous Programming on FPGAs with OmpSs@FPGA

    24 May 2019

    Heterogeneous Programming on FPGAs with OmpSs@FPGA https://tess.elixir-europe.org/events/heterogeneous-programming-on-fpgas-with-ompss-fpga The registration of this course will open in February. Please, bring your own laptop.  All the PATC courses at BSC are free of charge. Course convener: Xavier Martorell Objectives:This tutorial will introduce the audience to the BSC tools for heterogenous programming on FPGA devices. It describes OmpSs@FPGA, as a productive programming environment for compute systems with FPGAs. More specifically, the tutorial will: Introduce the OmpSs@FPGA programming model, how to write, compile and execute applications on FPGAs Show the "implements" feature to explot parallelism across cores and IP cores Demonstrate how to analyze applications to determine which portions can be executed on FPGAs, and use OmpSs@FPGA to parallelize/optimize them. Learning Outcomes: The students who finish this course will be able to develop benchmarks and simple applications with the OmpSs@FPGA programming model to be executed in FPGA boards, like Zedboard or Xilinx ZCU102. Level: INTERMEDIATE: for trainees with some theoretical and practical knowledge; those who finished the beginners course ADVANCED: for trainees able to work independently and requiring guidance for solving complex problems Requirements:  Good knowledge of C/C++ Basic knowledge of acceleration architectures and offloading models Basic knowledge of Paraver/Extrae Agenda: Session 1 / 9:30am – 1:00 pm  (2 h lectures, 1:30 h practical) 09.30h – Global view of OmpSs@FPGA 10:30h - Instrumentation facilities and performance analysis 11.00h - Compilation and toolchain 11:30h - Hands-on: OmpSs@FPGA installation and setup 12:00h - Hands-on: Case study: vector multiplication 13.00h – Lunch Break Session 2 / 2:00pm – 5:30 pm (0:30 h lectures, 3 h practical) 14.00h – Hands-on: Case study: matrix multiply 15:00h - Hands-on: Heterogeneous programming using "implements" 16.30h – Hands-on: Bring your application. Study, initial analysis and recommendations 17:30h - Adjourn   END of COURSE https://events.prace-ri.eu/event/767/ 2019-05-24 07:30:00 UTC 2019-05-24 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Productivity tools for High Performance Computing @IT4I

    24 - 25 October 2018

    Productivity tools for High Performance Computing @IT4I https://tess.elixir-europe.org/events/productivity-tools-for-high-performance-computing-it4i-e46712b9-d023-439a-9ffc-de2a4392158f Annotation This HPC training continues to expand your skills and knowledge in using productivity tools and technologies, to be able to quickly build up an efficient HPC user environment, from scratch, without admin rights. We shall demonstrate tools and procedures tailored to the Salomon and Anselm clusters, however they are easily replicable on any HPC system. The topics include: GIT - a version control system for coordinating work among multiple developers GIT (the stupid content tracker) is the world's most used Version Control System. Originally designed for development of Linux kernel, it has evolved to universal tool for managing changes in code, configuration and documents, especially if those changes are not done by a single person. We will help you understand how GIT works internally and introduce you to basic GIT commands, that should cover 99% of daily GIT usage. KVM - a virtualization infrastructure for the Linux kernel that converts it into a hypervisor KVM (for Kernel-based Virtual Machine) is a full virtualization solution for Linux on x86 hardware containing virtualization extensions (Intel VT or AMD-V). It provides the ability to run complex software stacks, including MS Windows, on powerful, linux-based supercomputer nodes with very low overhead costs. Using KVM, one can run multiple virtual machines running unmodified Linux or Windows images. Each virtual machine has private virtualized hardware: a network card, disk, graphics adapter, etc. In this lesson we will introduce the QEMU machine emulator using KVM virtualization, learn how to set up the QEMU/KVM on the  Salomon supercomputer, create a QEMU system image, install the operating system into the image, set up the networking and data access  and execute the calculations via the QEMU/KVM. We will also discuss visualized Ethernet networks in the context of QEMU and VDE2. Docker & Singularity - technologies for paravirtualization Docker for HPC? Yes, Singularity! Docker provides the ability to package and run an application in a loosely isolated environment called a container. The application with all settings and libraries can be packed together and then run on any other computer. It is perfect for developers, hosting providers, server farms, you name it! But, is it so good for supercomputers too? Let's look at why there are some problems with using Docker in shared environment and why Singularity is different. Singularity is developed with HPC in mind and is directly intended for use on HPC clusters with the direct support of technology such as OpenMPI. We will show you how to use Singularity, convert Docker images, create new containers and everything else you need to know about running a Singularity container in an HPC environment. EasyBuild - install and build custom programs In the supercomputer environment, pre-configured modules of various programs can be used. But how do I get my own program when I am a developer, or I need a program that is not installed? What if I need a different version of the program than the available modules? There is the possibility of sending a request for installation to the support, but what if I need it immediately? There are more options to manually build a program, but not everyone can do it because the user cannot install on the system but only in his own storage, and you need to know the compiler switches and system settings. You can also build a program using the tools that compile for us and create environment setting modules for that. In the lecture, we shall demonstrate how to manually compile a program, how to modify the environment so that the program can be used. We shall show you the EasyBuild tool to build a program and introduce new releases, such as creating Docker or Singularity rules and installing programs using EasyBuild directly into the Singularity image. Purpose of the course The participants will broaden their range of techniques for efficient use of HPC by mastering modern technologies for code management and execution. About the tutors The tutors are core members of the Supercomputing Services division of IT4Innovations. Branislav Jansík obtained his PhD in computational chemistry at the Royal Institute of Technology, Sweden in 2004. He took a postdoctoral position at IPCF, Consiglio Niazionale delle Ricerche, Italy,  to carry on development and applications of high performance computational methods for molecular optical properties. From 2006 he worked on  the development of highly parallel optimization methods in the domain of electronic structure theory at Aarhus University, Denmark. In 2012 he joined IT4Innovations, the Czech national supercomputing center, as the head of Supercomputing Services. He has published over 35 papers and co-authored the DALTON electronic structure theory code. Josef Hrabal obtained his Master's Degree in Computer Science and Technology at VŠB - Technical University of Ostrava in 2014. Since then he has contributed to projects within the University, and in 2017 he joined IT4Innovations as an HPC application specialist. David Hrbáč obtained his Master's Degree in Measurement and Control Engineering at VŠB - Technical University of Ostrava in 1997. Since 1994 he has worked for many IT companies as a system architect and CIO. In 2013 he joined IT4Innovations. Lukáš Krupčík obtained his Master's Degree in Computer Science and Technology at VŠB - Technical University of Ostrava in 2017. In 2016 he joined IT4Innovations as an HPC application specialist. Lubomír Prda obtained his Master's Degree in Information and Communication Technologies at VŠB - Technical University of Ostrava in 2010. Before joining the IT4Innovations team as an HPC specialist in 2016, he worked at the Tieto Corporation as a network engineer, and later moved to identity and access management for the company's nordic and international customers. Lubomír's focus is to manage and maintain the centre's back-end IT infrastructure and services. Roman Slíva obtained his Master's Degree in Computer Science at VŠB - Technical University of Ostrava in 1998. He worked as an IT system specialist and project leader in the areas of servers, high performance computing, and storage and backup. From 2007-2009 he led the IT Server Infrastructure group at VŠB - Technical University of Ostrava. In 2011 he joined IT4Innovations as an HPC system specialist and architect. https://events.prace-ri.eu/event/780/ 2018-10-24 07:30:00 UTC 2018-10-25 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • Parallel and GPU Programming in Python @SURFsara

    10 - 11 December 2018

    Parallel and GPU Programming in Python @SURFsara https://tess.elixir-europe.org/events/parallel-and-gpu-programming-in-python-surfsara-41d46a5c-5b30-40ef-9685-54f10b175020 Scope of the course The Python programming language has become more and more popular among researchers for its simplicity and the availability of specific programming libraries, and at the same time the correct exploitation of heterogeneous architectures presents challenges for the development of parallel applications. In order to bring these two topics together, this course is focused on the use of Python on CPU and GPU platforms for scientific computing in general.   General description The basic concepts of good programming practices in Python and general parallel programming will be introduced, and then GPU computing will be explained combining the essential theory concepts with hands-on sessions. The proposed exercises will be tested in the supercomputing facilities provided by SURFsara using Python with different programming libraries: numba PyCUDA mpi4py https://events.prace-ri.eu/event/783/ 2018-12-10 08:00:00 UTC 2018-12-11 16:30:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to CUDA Programming @ BSC

    8 - 11 April 2019

    Introduction to CUDA Programming @ BSC https://tess.elixir-europe.org/events/introduction-to-cuda-programming-bsc-865fc5e1-a20d-4615-a4ea-a964fcd15bf5 The registration to this course will open in Jaunary. All PATC Courses at BSC do not charge fees. PLEASE BRING YOUR OWN LAPTOP. Local Web Page: This course will provide very good introduction to the PUMPS Summer School run jointly with NVIDIA -also  at Campus Nord, Barcelona. For further information visit the school website  as this school has attendee selection process. You may also be interested in our Introduction to OpenACC course. Convener:  Antonio Peña, Computer Sciences Senior Researcher, Accelerators and Communications for High Performance Computing, BSC Objectives:  The aim of this course is to provide students with knowledge and hands-on experience in developing applications software for processors with massively parallel computing resources. In general, we refer to a processor as massively parallel if it has the ability to complete more than 64 arithmetic operations per clock cycle. Many commercial offerings from NVIDIA, AMD, and Intel already offer such levels of concurrency. Effectively programming these processors will require in-depth knowledge about parallel programming principles, as well as the parallelism models, communication models, and resource limitations of these processors. Agenda: DAY 1 Session 1 / 9:00am – 1:00 pm (3:30 h lectures) L1 9:00-10:45 The GPU hardware: Many-core Nvidia developments 10:45-11:15 Coffee break L2 11:15-13:00 CUDA Programming: Threads, blocks, kernels, grids 13:00-14:00 Lunch break   Session 2 / 2:00pm – 6:00 pm (3:30 h lectures) L3 14:00-15:45 CUDA Tools: Compiling, debugging, profiling, occupancy calculator 15:45-16:15 Coffee break L4 16:15-18:00 CUDA Examples(1): VectorAdd, Stencil, ReverseArray   DAY 2 Session 3 / 9:00am – 1:00 pm (3:30 h lectures) L5   9:00-10:45 CUDA Examples (2): Matrices Multiply. Assorted optimizations 10:45-11:15 Coffee break L6 11:15-13:00 CUDA Examples (3): Dynamic parallelism, Hyper-Q, unified memory 13:00-14:00 Lunch break   Session 4 / 2:00pm – 6:00 pm (3:30 h practical) H1 14:00-15:45 Hands-on Lab 1 15:45-16:15 Coffee break H2 16:15-18:00 Hands-on Lab 2   DAY 3 Session 5 / 9:00am – 1:00 pm (3:30 h lectures) L7 9:00-10:45 Inside Pascal: Multiprocessors, stacked memory, NV-link 10:45-11:15 Coffee break L8 11:15-13:00 OpenACC and other approaches to GPU computing 13:00-14:00 Lunch break   Session 6 / 2:00pm – 6:00 pm (3:30 h practical) H3 14:00-15:45 Hands-on Lab 3 15:45-16:15 Coffee break H4 16:15-18:00 Hands-on Lab 4   DAY 4 Session 7 / 9:00am – 1:00 pm (3:30 h practical) H5 9:00-10:45 Hands-on Lab 5 10:45-11:15 Coffee break H6 11:15-13:00 Hands-on Lab 6 13:00-14:00 Lunch break   Session 8 / 2:00pm – 6:00 pm (3:30 h practical) H7 14:00-15:45 Hands-on Lab 7  15:45-16:15 Coffee break H8 16:15-18:00 Free Hands-on Lab End of Course The target audiences of the course are students who want to develop exciting applications for these processors, as well as those who want to develop programming tools and future implementations for these processors. Level: INTERMEDIATE: for trainees with some theoretical and practical knowledge; those who finished the beginners course ADVANCED: for trainees able to work independently and requiring guidance for solving complex problems Prerequisites: Basics of C programming and concepts of parallel processing will help, but are not critical to follow the lectures. https://events.prace-ri.eu/event/768/ 2019-04-08 07:00:00 UTC 2019-04-11 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to Heterogeneous Memory Usage @ BSC

    26 February 2019

    Introduction to Heterogeneous Memory Usage @ BSC https://tess.elixir-europe.org/events/introduction-to-heterogeneous-memory-usage The registration to this course will open in October. All PATC Courses at BSC do not charge fees. PLEASE BRING YOUR OWN LAPTOP. Convener:  Antonio Peña, Computer Sciences Senior Researcher, Accelerators and Communications for High Performance Computing, BSC Objectives:  The objective of this course is to learn how to use systems with more than one memory subsystem. We will see the different options on using Intel’s KNL memory subsystems and systems equipped with Intel’s Optane technology. Learning Outcomes: The students who finish this course will able to leverage applications using multiple memory subsystems Agenda: To be announced Level: INTERMEDIATE: for trainees with some theoretical and practical knowledge; those who finished the beginners course Prerequisites: Basic skills in C programming. https://events.prace-ri.eu/event/770/ 2019-02-26 08:00:00 UTC 2019-02-26 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Analysing large datasets with Apache Spark @ CSC

    19 - 20 November 2018

    Analysing large datasets with Apache Spark @ CSC https://tess.elixir-europe.org/events/analysing-large-datasets-with-apache-spark-csc-2f054efd-ac02-4dc2-b05c-69dbce55cde7 Description With the rapid growth in data volume that is being used in data analysis tasks, it gets more and more challenging for the user to process it using standard methods. One typically runs into into several problems - low memory/cpu, waiting forever for a job to complete or starting all over again if a job fails. Enter Spark, a high-performance distributed computing framework, which allows us to tackle big-data problems by distributing the workload across a cluster of machines. The two day course addresses the technical architecture and use cases of Spark, writing Spark code using Python, using Spark's machine learning library to perform ML based tasks. Then, we would be looking at the methods for running a spark cluster on a cloud based infrastructure, along with ways to manage and fine tune your cluster. The course will also demonstrate how to work with real-time data streams. The first day includes the overview, architectural concepts, programming with Spark's fundamental data structure (RDD) and Spark's Machine Learning library. The second day focuses on the analysis of data by running SQL queries in Spark, working with real-time data streams and how to setup and manage a spark cluster. Learning outcome After the course the participants should be able to write simple to intermediate programmes in Spark using RDD and dataframes. Intended Audience and Prerequisites The course is intended for researchers, students, and professionals with programming skills, preferably in Python, as the exercises are in Python. Some knowledge of SQL is also recommended.   Please NOTE: This is not a regular programming course, participants would be expected to learn emerging concepts in the field of big data / distributed processing, which might be completely different from the concepts of a general programming language. Agenda Day 1, Monday 19.11    09.00 – 09.45    Overview and architechture of Spark    09:45 – 10.30    Basics of RDDs and Demo    10.30 – 10.45    Coffee break    10.45 – 11.30    RDD: Transformations and Actions    11.30 – 12.00    Exercises    12.00 – 13.00    Lunch    13.00 – 13.30    Word Count Example    13.30 – 14.00    Exercises    14.00 – 14.30    Short overviewof Machine learning library of Spark    14.30 – 14.45    Coffee break    14.45 – 15.30    Exercises    15.30 – 15.45    Wrap-up and further topics    15.45 – 16.00    Summary of the first day & exercises walk-through Day 2, Tuesday, 20.11    09.00 – 09.30    Spark Dataframes and SQL Overview    09:30 – 10.15    Exercises    10.15 – 10.30    Coffee break    10.30 – 10.45    Dataframes and SQL (contd.)    10.45 – 12.00    Exercises    12.00 – 13.00    Lunch    13.00 – 14.00    Setting up a Spark cluster    14.00 – 14.30    Exercises    14.00 – 14.30    Best practices and other useful stuff    14.30 – 14.45    Coffee break    14.45 – 15.00    Brief overview of Spark Streaming    15.00 – 15.15    Demo: Processing live twitter stream data    15.15 – 16.00    Summary of the course & exercises walk-through Lecturers:  Apurva Nandan (CSC) Language:   EnglishPrice:          Free of charge https://events.prace-ri.eu/event/785/ 2018-11-19 07:00:00 UTC 2018-11-20 14:00:00 UTC [] [] [] workshops_and_courses [] []
  • High Performance Bioinformatics@CINECA

    10 - 12 December 2018

    High Performance Bioinformatics@CINECA https://tess.elixir-europe.org/events/high-performance-bioinformatics-cineca-c301d319-cd9b-4214-81c5-8228f31df18e Description: This course focuses on the development and execution of bioinformatics pipelines and on their optimization with regards to computing time and disk space. In an era where the data produced per-analysis is in the order of terabytes, simple serial bioinformatic pipelines are no longer feasible. Hence the need for scalable, high-performance parallelization and analysis tools which can easily cope with large-scale datasets. To this end we will study the common performance bottlenecks emerging from everyday bioinformatic pipelines and see how to strike down the execution times for effective data analysis on current and future supercomputers. As a case study, two different bioinformatics pipelines (whole-exome and transcriptome analysis) will be presented and re-implemented on the supercomputers of Cineca thanks to ad-hoc hands-on sessions aimed at applying the concepts explained in the course. Skills: By the end of the course each student should be able to: Manage the transfer of big data files and/or large number of files from the local computer to the Cineca platforms and vice versa Prepare the environment to analyse big amount of biological data on a supercomputer Run single parallel bioinformatic programs on a supercomputer Combine bioinformatics applications into pipelines on a supercomputer Target audience: Biologists, bioinformaticians and computer scientists interested in approaching large-scale NGS-data analysis for the first time. Pre-requisites: Basic knowledge of python and shell command line. A very basic knowledge of biology is recommended but not required. Grant The course is FREE of charge. The lunch for the three days will be offered to all the participants and some grants are available. The only requirement to be eligible is to be not funded by your institution to attend the course and to work or live in an institute outside the Roma area. The grant  will be 300 euros for students working and living outside Italy and 150 euros for students working and living in Italy (except Rome area). Some documentation will be required and the grant will be paid only after a certified presence of minimum 80% of the lectures. Further information about how to request the grant, will be provided at the confirmation of the course: about 3 weeks before the starting date. https://events.prace-ri.eu/event/791/ 2018-12-10 08:00:00 UTC 2018-12-12 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to Parallel Programming @GRNET

    20 - 22 November 2018

    Introduction to Parallel Programming @GRNET https://tess.elixir-europe.org/events/introduction-to-parallel-programming-grnet-b727f687-5799-4df8-9445-0887d8424c97 Introduction to Parallel Programming 20 - 22 November 2018 Purpose of the course The focus is to understand the basics of parallel programming with the message-passing interface (MPI) and OpenMP parallel programming paradigms. MPI is the dominant parallelization paradigm in high performance computing and enables one to write programs that run on distributed memory machines, such as the ARIS Greek supercomputer and other systems of the PRACE infrastructure. OpenMP is a threading based approach which enables one to parallelize a program over a single shared memory machine, such as a single node in ARIS. The course also contains performance and best practice considerations, e.g., hybrid MPI+OpenMP parallelisation. The course ends with a section presenting profiling and code optimisations to understand the behavior and performance of parallelized codes. The 3 day course consists of lectures and hands-on exercises on parallel programming. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the taught constructs of the Message Passing  Interface (MPI) and the shared memory directives of OpenMP. The course ends with a section presenting profiling and code optimizations to understand the behavior and performance of parallelized codes. After the course the participants should be able to write simple parallel programs and parallelize existing programs with the basic features of MPI and/or OpenMP. Users should also be able to perform basic profiling and debugging of parallel applications. . Prerequisites The course addresses participants who are familiar with the C/C++ or Fortran programming languages and have working experience with the Linux operating system and the use of the command line. Experience with parallel programming (MPI and OpenMP) is not required. Bring your own laptop in order to be able to participate in the training hands on. Hands on work will be done in pairs so if you don’t have a laptop you might work with a colleague. Course language is English. Registration The maximum number of participants is 25. Registrations will be evaluated on a first-come, first-served basis. GRNET is responsible for the selection of the participants on the basis of the training requirements and the technical skills of the candidates. GRNET will also seek to guarantee the maximum possible geographical coverage with the participation of candidates from many countries. Venue GRNET headquarters Address: 2nd  Floor, 7, Kifisias Av. GR 115 23 Athens Information on how to reach GRNET headquarters ia available on GRNET website: https://grnet.gr/en/contact-us/   Accommodation options near GRNET can be found at: https://grnet.gr/wp-content/uploads/sites/13/2015/11/Hotels-near-GRNET-en.pdf ARIS - System Information ARIS is the name of the Greek supercomputer, deployed and operated by GRNET (Greek Research and Technology Network) in Athens. ARIS consists of 532 computational nodes seperated in four “islands” as listed here: 426 thin nodes: Regular compute nodes without accelerator. 44 gpu nodes: “2 x NVIDIA Tesla k40m” accelerated nodes. 18 phi nodes: “2 x INTEL Xeon Phi 7120p” accelerated nodes. 44 fat nodes: Fat compute nodes have larger number of cores and memory per core than a thin node. All the nodes are connected via Infiniband network and share 2PB GPFS storage.The infrastructure also has an IBM TS3500 library of maximum storage capacity of about 6 PB. Access to the system is provided by two login nodes. About Tutors Dr. Dellis (Male) holds a B.Sc. in Chemistry (1990) and PhD in Computational Chemistry (1995) from the National and Kapodistrian University of Athens, Greece. He has extensive HPC and grid computing experience. He was using HPC systems in computational chemistry research projects on fz-juelich machines (2003-2005). He received an HPC-Europa grant on BSC (2009). In EGEE/EGI projects he acted as application support and VO software manager for SEE VO, grid sites administrator (HG-02, GR-06), NGI_GRNET support staff (2008-2014). In PRACE 1IP/2IP/3IP/4IP/5IP he was involved in benchmarking tasks either as group member or as BCO (2010-2017). Currently he holds the position of “Senior HPC Applications Support Engineer” at GRNET S.A. where he is responsible for activities related to user consultations, porting, optimization and running HPC applications at national and international resources. Dr. Ioannis E. Venetis received his PhD in 2006 from the Computer Engineering and Informatics Department at the University of Patras, Greece. Currently he teaches "Parallel Processing" and "Software and Programming for High Performance Systems" at the same Department. He has participated in numerous research projects in the area of Parallel Computing. His main research interests include parallel programming models, run-time systems for supporting such models, co-processor programming (especially using GPUs and the Intel Xeon Phi) and parallelization of computationally demanding applications. Mr. Nikolaos Nikoloutsakos holds a diploma of Engineering in Computer Engineering and Informatics (2014) from the University of Patras, Greece. From 2015 he works as software engineer at GRNET S.A. where he is part of the user application support team for the ARIS HPC system. He has been involved in major national and European projects, such as PRACE and EUDAT. His main research interests include parallel programming models, co-processor programming using GPUs and Intel Xeon Phis. Dr. Aristeidis Sotiropoulos received his BSc in Computer Science in 1998 from the University of Crete, Greece and his PhD in Parallel Processing and Cluster Computing in 2004 from the National Technical University of Athens, Greece. His interests mainly focus on the fields of Large Scale Computing & Storage Systems, System Software for Scalable High Speed Interconnects for Computer Clusters and Advanced Microprocessor Architectures. He has published several scientific papers in international journals and conference proceedings. He has received the IEEE IPDPS 2001 best paper award for the paper "Minimizing Completion Time for Loop Tiling with Computation and Communication Overlapping". He has worked in several European and National R&D programs in the field of High Performance Computing, Grid Computing, Cloud Computing and Storage. In 2013, he was appointed as the Head of Operations and Financial Management Services, in charge of 15 people. Currently, he is managing EC projects at GRNET SA, the Greek NREN responsible for the provision of advanced e-infrastructure services to the Greek Academic and Research Community. About GRNET GRNET provides Internet connectivity, high-quality e-Infrastructures and advanced services to the Greek Educational, Academic and Research community. Through its high-speed, high-capacity infrastructure that spans across the entire country, GRNET interconnects more than 150 institutions, including all universities and technological institutions, as well as many research institutes and the public Greek School Network. GRNET operates the National High Performance Computing system (a Tier-1 in the European HPC ecosystem) and offers user and application support services, that provide Greek scientists with the computing infrastructure and expertise they need for their research enabling them to perform large scale simulations. GRNET offers innovative IaaS cloud computing services to the Greek and global research & education communities: “ ~okeanos” and “okeanos global” allow users to create multi-layer virtual infrastructure and instantiate virtual computing machines, local networks to interconnect them, and a reliable storage space within seconds, with few, simple mouse clicks. GRNET aims at contributing towards Greece’s Digital Convergence with the EU, by supporting the development and encouraging the use of e-Infrastructures and services. The right and timely planning strategies, together with the long experience and know-how of its people, guarantee the continuation and enhancement of GRNET’s successful course. Greek Research and Technology Network – Networking Reserach and Education: www.grnet.gr, hpc.grnet.gr https://events.prace-ri.eu/event/792/ 2018-11-20 08:30:00 UTC 2018-11-22 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • GPU Programming with CUDA @ EPCC at Imperial College London

    26 - 27 November 2018

    GPU Programming with CUDA @ EPCC at Imperial College London https://tess.elixir-europe.org/events/gpu-programming-with-cuda-epcc-at-imperial-college-london Graphics Processing Units (GPUs) were originally developed for computer gaming and other graphical tasks, but for many years have been exploited for general purpose computing in a number of areas. They offer advantages over traditional CPUs because they have greater computational capability, and use high-bandwidth memory systems (memory bandwidth is the main bottleneck for many scientific applications).   This introductory course will describe GPUs, and the advantages they offer. It will teach participants how to start to program GPUs, which cannot be used in isolation, but are usually used in conjunction with CPUs. Important issues affecting performance will be covered. The course focuses on NVIDIA GPUs, and the CUDA programming language (an extension to C/C++ or Fortran). Please note the course is aimed at application programmers; it does not consider machine learning or any of the packages available in the machine learning arena. Hands-on practical sessions are included. You will require your laptop, and your institutional credentials to connect to eduroam.  The training will be run on a web-based system so all you will need is a relatively recent web browser (Firefox, Chrome and Safari are known to work). Timetable Day 1 10:00 Introduction 10:20 GPU Concepts/Architectures 11:00 Break 11:20 CUDA Programming 12:00 First CUDA Programming Exercise 13:00 Lunch 14:00 Optimisation 14:30 CUDA Optimisation Practical Exercise 15:00 Break 15:20 CUDA Constant and Shared memory 16:00 Practical exercise 17:00 Close Day 2 10:00 Recap 10:10 OpenCL and OpenCL exercise 11:00 Break 11:30 NVIDIA Volta (Alan Gray NVIDIA) 13:00 Lunch 14:00 OpenACC directives and exercise 15:00 Break 15:20 The future? Performance portability and Kokkos 16:00 Close https://events.prace-ri.eu/event/784/ 2018-11-26 09:00:00 UTC 2018-11-27 17:30:00 UTC [] [] [] workshops_and_courses [] []
  • HPC methods for Computational Fluid Dynamics and Astrophysics@CINECA

    3 - 5 December 2018

    HPC methods for Computational Fluid Dynamics and Astrophysics@CINECA https://tess.elixir-europe.org/events/hpc-methods-for-computational-fluid-dynamics-and-astrophysics-cineca-1d9d3dbc-13ab-4d0f-883a-f9a0f4fd5505 The aim of this workshop is to present the HPC numerical methods used in the fields of Computational Fluid Dynamics (CFD) and Numerical Astrophysics. The workshop aims to share the methodologies, numerical methods and their implementation used by the state-of-the-art codes in the HPC environment.  Key-note lectures will present the challenges of numerically solving Partial Differential Equations (PDE) in problems related to fluid/hydrodynamics, using massively parallel clusters. The workshop will focus on state-of the art of the different HPC architectures and the related numerical methods. Lecture topics will highlight major areas of Numerical Astrophysics and CFD including N-body dynamics, hydrodynamics/magnetohydrodynamics, relativistic hydrodynamics and magnetohydrodynamics, compressible and incompressible flows, turbulence, multi-phase flows and computational tools (visualization and parallel computing), etc... For each thematic area, state-of-the-art codes used by the community/research group will be described. The key-note lectures will be based on the forefront numerical techniques within the aforementioned areas, and a follow-up will be partially devoted to hands-on experiences, where the participants will be invited to share their knowledge, by opened discussion. Further information will be available later for participants upon confirmations of the speakers. Skills: At the end of the course, the student will possess and know how to use the following skills: Numerical analysis Algorithms for PDE Solution Parallel computing (MPI, OpenMP, GPGPUs)  HPC architecture Strategies for massively parallelization of numerical methods Numerical Libraries for HPC Target audience: Academic and industrial researchers, software developer  which use / are planning to use / develop a code for CFD or plasma physics. Pre-requisites: Basic knowledge on parallel computing, numerical analysis and algorithms for p.d.e. solution. The course is FREE of charge   https://events.prace-ri.eu/event/790/ 2018-12-03 07:00:00 UTC 2018-12-05 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Petaflop System Administration; Marenostrum 4 @ BSC

    20 - 21 March 2019

    Petaflop System Administration; Marenostrum 4 @ BSC https://tess.elixir-europe.org/events/petaflop-system-administration-marenostrum-4-bsc-6ce6f94e-a95e-432c-9e44-f7ceec5653c8 The registration to this course will open in January. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course Convener: Javier Bartolome, Systems Group Manager, Operations - System Administration, BSC Objectives: Explain the different components that MareNostrum 4 is composed, which were the design decisions taken and why. Explain how the system administration is taken in this Petaflop system. Learning Outcomes: The students will learn how MareNostrum 4 is organized and how it works. This can have some insights and ideas about how to manage clusters of thousands of nodes in a HPC or no-HPC environment. Level: INTERMEDIATE, for trainees with some theoretical and practical knowledge; those who finished the beginners course. Prerequisites: Experience on Linux system administration is required. Lecturer: Javier Bartolome, Systems Group Manager, Operations - System Administration, BSC Agenda: Day 1 (March, 20) Session 1 / 9:00am – 1:00 pm  (3:30 h lectures) 9h-9:20h Introduction & outline of the course 9:20h-9:40h MareNostrum4 Overview 9:40h-10:40h Storage in MareNostrum4 10:40h-11h COFFE BREAK 11h-11:30h Networks on MareNostrum4 11:30h -13h Clustering Software 13h-14h LUNCH BREAK   Session 2 / 2:00pm – 6:00 pm (3:30 h practical) 14h-15:30h Practice on clustering software 15:30h-15:45h COFFE BREAK 15:45-16:30h Monitoring MareNostrum4 16:30h-17h MareNostrum4 Facility 17h-18h Visit to MareNostrum4 18h Adjourn   Day 2 (March, 21) 9am – 12:30pm Session 3 / 9:00am – 12:30 pm  (3 h lectures) 9h-10h MareNostrum4 Schedule system 10h-11h PRACE Project and Services 11h-11:15h COFFEE BREAK 11:15h-12h MareNostrum4 software stack 12h-12:30h Questions/Wrap-up   End Of Course https://events.prace-ri.eu/event/765/ 2019-03-20 08:00:00 UTC 2019-03-21 12:00:00 UTC [] [] [] workshops_and_courses [] []
  • Data science with R @ Cineca

    28 - 30 November 2018

    Data science with R @ Cineca https://tess.elixir-europe.org/events/data-science-with-r-cineca The purpose of this course is to present researchers and scientists with R implementation of Machine Learning methods. The first part of the course will consist of introductory lectures on popular Machine Learning algorithms including unsupervised methods (Clustering, Association Rules) and supervised ones (Decision Trees, Naive Bayes, Random Forests and Deep Neural Network). Basic Machine Learning concepts such as training set, test set, validation set, overfitting, bagging, boosting will be introduced as well as performance evaluation for supervised and unsupervised methods. The second part will consist of practical exercises such as reading data, using packages and building machine learning applications. Different options for parallel programming will be shown using specific R packages (parallel, h2o,…). For Deep Learning applications the Keras package will be presented. The examples will cover the analysis of large datasets and images datasets. Participants will use R on Cineca HPC facilities for practical assignments. Skills: At the end of the course, the student will be expected to have acquired:     • the ability to perform basic operations on matrices and dataframes      • the ability to manage packages     • the ability to navigate in the RStudio interface     • a general knowledge of Machine and Deep Learning methods     • a general knowledge of the most popular packages for Machine and Deep Learning     • a basic knowledge of different parallel programming techniques     • the ability to build machine learning applications with large datasets and images datasets Target audience: Students and researchers with different backgrounds, looking for technologies and methods to analyze a large amount of data. Pre-requisites: Participants must have a basic statistics knowledge. Participants must also be familiar with basic Linux. Grant: The course is FREE of charge. The lunch for the three days will be offered to all the participants and some grants are available. The only requirement to be eligible is to be not funded by your institution to attend the course and to work or live in an institute outside the MILANO area. The grant  will be 300 euros for students working and living outside Italy and 150 euros for students working and living in Italy (outside MILANO). Some documentation will be required and the grant will be paid only after a certified presence of minimum 80% of the lectures. Further information about how to request the grant, will be provided at the confirmation of the course: about 3 weeks before the starting date. https://events.prace-ri.eu/event/788/ 2018-11-28 08:00:00 UTC 2018-11-30 16:00:00 UTC [] [] [] workshops_and_courses [] []