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  • CAS Personalized Molecular Oncology

    1 October 2018 - 31 July 2019

    Basel, Switzerland

    Elixir node event
    CAS Personalized Molecular Oncology https://tess.elixir-europe.org/events/cas-personalized-molecular-oncology The CAS in Personalized Molecular Oncology aims at providing a comprehensive and integrative view of the field, by covering all the aspects involved along the pipeline: (i) tumor biology and genetics, (ii) molecular pathology, (iii) clinical bioinformatics, and (iv) clinical oncology. First of its kind in Switzerland, it will focus on the methodologies used to generate, analyze and interpret patients’ molecular profiles, also touching upon the associated technical, regulatory and ethical challenges. As an important outcome, it will establish a common language between the wide range of professionals involved in the personalized oncology process, from biologists, bioinformaticians, pathologists to clinicians, enabling an efficient and better informed use of e.g. genomic data for both routine clinical practice and clinical research. Moreover, it should empower professionals to develop a vision for their own institution, by critically evaluating the potential benefits and limitations of current and future developments in personalized oncology. The CAS is organized jointly by the University Hospital of Basel, the University Hospital of Lausanne, and the SIB Swiss Institute of Bioinformatics. 2018-10-01 09:00:00 UTC 2019-07-31 17:00:00 UTC SIB Swiss Institute of Bioinformatics Pathologie Universitätsspital Basel, 40, Schönbeinstrasse, Basel, Switzerland Pathologie Universitätsspital Basel, 40, Schönbeinstrasse Basel Switzerland University Hospital of BaselSIB Swiss Institute of BioinformaticsUniversity Hospital of Lausanne Dr. Aitana Lebrand Clinical Bioinformatics SIB | Swiss Institute of Bioinformatics Ch. des Mines 9 CH-1202 Genève Tel. +41 (0)22 379 02 67 aitana.lebrand@sib.swiss [] Professionals involved in personalized molecular oncology, including laboratory managers, biologists, bioinformaticians, pathologists, geneticists, clinicians and pharmaceutical company employees. workshops_and_courses registration_of_interest Tumor biology and geneticsMolecular pathologyClinical BioinformaticsClinical oncology
  • Data science with R and Python @ IT4Innovations

    24 - 25 April 2019

    Data science with R and Python @ IT4Innovations https://tess.elixir-europe.org/events/data-science-with-r-and-python-it4innovations Annotation The R part of course (first day) will be focused on presenting the basics of data analysis in R and visualization of data. The course will cover the introduction to the R statistical language introducing the basic data types and workflow. Afterwards, packages from the “tidyverse” collection will be presented. These includes packages for the loading of data, preprocessing data, basic data exploration, and visualization. The Python oriented part (second day) will introduce essential data-scientific packages and will be complemented with hands-on exercises that will demonstrate their usage with real world data analytic problems, and showing how to tackle such problems. The course will be up to 50% hands-on exercises covering all topics to practice the techniques, and patterns gained. Purpose of the course (benefits for the attendees) Target audience: Users that want to use Python and/or R for data analysis and prototyping. The participants will learn basic and intermediate skills for exploratory data analysis and visualization in the programming languages of R and Python. About the tutor(s) Tomáš Martinovič obtained his PhD in computational sciences at IT4Innovations, VSB - Technical University of Ostrava in 2018. From 2015 to 2018 he worked in a team focused on analysis of complex dynamical systems, where he worked on scalable implementations of algorithms from the field of nonlinear time series analysis. Since the start of 2019 he has been working in a team focused on high performance data analysis with the defined objective of research and transfer of knowledge in cooperation with industry. Stanislav Böhm has a PhD in computer science, and is a researcher at IT4Innovations. He is interested in distributed systems, verification, and scheduling. https://events.prace-ri.eu/event/869/ 2019-04-24 07:30:00 UTC 2019-04-25 13:30:00 UTC [] [] [] workshops_and_courses [] []
  • Performance Analysis Workshop @ EPCC at Bristol

    24 - 26 April 2019

    Performance Analysis Workshop @ EPCC at Bristol https://tess.elixir-europe.org/events/performance-analysis-workshop-epcc-at-bristol 32nd VI-HPS Tuning Workshop (Bristol, England) - PATC course Date Wednesday 24th - Friday 26th April 2019 Location The workshop will take place at the University of Bristol, England. Co-organizing Institutions Goals This workshop is organised by VI-HPS for the UK PRACE Advanced Training Centre to: give an overview of the VI-HPS programming tools suite explain the functionality of individual tools, and how to use them effectively offer hands-on experience and expert assistance using the tools On completion participants should be familiar with common performance analysis and diagnosis techniques and how they can be employed in practice (on a range of HPC systems). Those who prepared their own application test cases will have been coached in the tuning of their measurement and analysis, and provided optimization suggestions. Programme Overview Presentations and hands-on sessions are on the following topics: BSC tools for trace analysis and performance prediction Score-P instrumentation and measurement Scalasca automated trace analysis TAU performance system A brief overview of the capabilities of these and associated tools is provided in the VI-HPS Tools Guide. The workshop will be held in English and run from 09:00 to not later than 17:00 each day, with breaks for lunch and refreshments. There is no fee for participation, however, participants are responsible for their own travel and accommodation. Classroom capacity is limited, therefore priority will be given to applicants with MPI, OpenMP and hybrid OpenMP+MPI parallel codes already running on the workshop computer systems, and those bringing codes from similar systems to work on. Attendees will need to bring their own notebook computers (with SSH and X11 configured) and use (eduroam) wifi to connect to the workshop computer systems. Outline The workshop introduces tools that provide a practical basis for portable performance analysis of parallel application execution, covering both profiling and tracing. It will be delivered as a series of presentations with associated hands-on practical exercises using the ARM-based Isambard Cray XC50 computer. While analysis of provided example codes will be used to guide the class through the relevant steps and familiarise with usage of the tools, coaching will also be available to assist participants to analyse their own parallel application codes and may suggest opportunities for improving their execution performance and scalability. Programme (preliminary) Day 1: Wednesday 24th April 09:30 Welcome messages ARCHER Training Courses 09:45 Introduction Introduction to VI-HPS & overview of tools Introduction to parallel performance engineering Computer systems and software environment 11:00 (break) 11:30 Cray tools 13:00 (lunch) 14:00 BSC performance tools 15:00 (break) 15:30 Hands-on coaching to apply tools to analyze participants' own code(s). 17:15 Review of day and schedule for remainder of workshop 17:30 (adjourn)   Day 2: Thursday 25th April 09:30 Instrumentation & measurement with Score-P Execution profile analysis report exploration with CUBE 11:00 (break) 11:30 TAU performance system 13:00 (lunch) 14:00 Hands-on coaching to apply tools to analyze participants' own code(s). 17:30 (adjourn)   Day 3: Friday 26th April 09:30 Automated trace analysis with Scalasca 11:00 (break) 11:30 TAU PerfExplorer 13:00 (lunch) 14:00 Hands-on coaching to apply tools to analyze participants' own code(s). 16:45 Review of workshop 17:00 (adjourn) Hardware and Software Platforms Isambard: Cray XC50 with 164 dual Marvell ThunderX2 32-core 2.1 GHz nodes (64-bit ARMv8-A cores) with 256GB DRAM and Aries dragonfly interconnect, Cray MPI, Cray, GCC & ARM toolchains. Training accounts will be provided! ARCHER: Cray XC30 with 3008 compute nodes consisting of two 12-core Intel E5-2697 (IvyBridge) processors sharing 64GB (or 128GB) of NUMA memory, Aries dragonfly interconnect, Cray MPI, Cray, GCC & Intel compilers, PBS Pro job management system. Training accounts will be provided! Other systems where up-to-date versions of the tools are installed can also be used when preferred, though support may be limited. Participants are expected to already possess user accounts on non-local systems they intend to use, and should be familiar with the procedures for compiling and running parallel applications. Registration Please register via the Registration tab on this page. Local organisers information page. https://events.prace-ri.eu/event/867/ 2019-04-24 08:00:00 UTC 2019-04-26 16:30:00 UTC [] [] [] workshops_and_courses [] []
  • NGS - Genome variant analysis

    29 - 30 April 2019

    Bern, Switzerland

    Elixir node event
    NGS - Genome variant analysis https://tess.elixir-europe.org/events/ngs-genome-variant-analysis-61e3f31b-dcd2-48bf-b446-9a115382b002 This course is over subscribed. You can still add your name to the waiting list by applying using the button at the bottom of this page. You will only be contacted if a place becomes available. 2019-04-29 09:00:00 UTC 2019-04-30 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Scalable Parallel Computations with PETSc @ CSC

    2 - 3 May 2019

    Scalable Parallel Computations with PETSc @ CSC https://tess.elixir-europe.org/events/scalable-parallel-computations-with-petsc-csc Description The Portable Extensible Toolkit for Scientific computing (PETSc) is a software framework for scalable numerical solution of complex problems in science and engineering. It is designed primarily for typical computations connected with Partial Differential Equations (PDE) solution, but is already successfully used also e.g., in data science. PETSc provides implementations of distributed sparse/dense/unassembled matrices, linear algebra, linear/non-linear system solvers, time integrators, mathematical optimization, discretization and more. It can as well be selectively extended with user's own implementations at any level. Codes using PETSc can be compiled on a wide range of computer architectures from iPhone to a large cluster with no code changes. PETSc is written in C but can be employed e.g., in C++, Fortran and Python programs as well. The course will interleave theory and practice — presentations and hands-on exercises with individual consultations. Learning outcome After the course participants are able to:  make use of the vast functionality available in PETSc to write their own programs, from mini-apps to bigger projects;  write their PETSc-based programs in a way allowing experiments with command-line options with no need for recompiling — for example, to apply different preconditioners to the same problem and compare their performance;  add their own functionality if needed by extending prefabricated building blocks available in PETSc; take advantage of the debugging and profiling tools within PETSc; use PETSc as a "package manager" to fetch, compile and link various external libraries such as ParMETIS easily;  do something more with PETSc, also based on their individual preferences. Prerequisites Participants need some experience in C programming, but expertise is not required. One should be familiar with:  C syntax; Control flow (if/else, loops, writing/calling functions);  Writing and calling functions; Compiling a C program on their target platform.  One also needs some conceptual knowledge of MPI:  What is message passing about; What are MPI communicators. Agenda (will be later) Day 1: Thursday, May 2 Day 2: Friday, May 3 Lecturers:  Vaclav Hapla  (ETH) Language:  English Price:          Free of charge https://events.prace-ri.eu/event/871/ 2019-05-02 06:00:00 UTC 2019-05-03 13:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to R Shiny

    2 May 2019

    Lausanne, Switzerland

    Elixir node event
    Introduction to R Shiny https://tess.elixir-europe.org/events/shiny This course is over subscribed. You can still add your name to the waiting list by applying using the button at the bottom of this page. You will only be contacted if a place becomes available. 2019-05-02 09:00:00 UTC 2019-05-02 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Using MOFA for integration of omics data

    3 May 2019

    Leuven, Belgium

    Elixir node event
    Using MOFA for integration of omics data https://tess.elixir-europe.org/events/using-mofa-for-integration-of-omics-data 2019-05-03 09:30:00 UTC 2019-05-03 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Fortran for Scientific Computing @ HLRS

    6 - 10 May 2019

    Fortran for Scientific Computing @ HLRS https://tess.elixir-europe.org/events/fortran-for-scientific-computing-hlrs-1eea0cf9-97bc-4560-aff3-896bc194648b Overview This course is dedicated to scientists and students to learn (sequential) programming with Fortran of scientific applications. The course teaches newest Fortran standards. Hands-on sessions will allow users to immediately test and understand the language constructs. This workshop provides scientific training in Computational Science, and in addition, the scientific exchange of the participants among themselves. Only the last three days of this course are sponsored by the PATC project. For further information and registration please visit the HLRS course page. https://events.prace-ri.eu/event/808/ 2019-05-06 06:30:00 UTC 2019-05-10 13:30:00 UTC [] [] [] workshops_and_courses [] []
  • DAVIDE OpenPower GPU cluster@Cineca

    6 - 7 May 2019

    DAVIDE OpenPower GPU cluster@Cineca https://tess.elixir-europe.org/events/davide-openpower-gpu-cluster-cineca Description: D.A.V.I.D.E. (Development of an Added Value Infrastructure Designed in Europe) is an energy-aware Petaflops Class High Performance Cluster based on IBM Power Architecture and coupled with NVIDIA Tesla Pascal GPUs with NVLink. The innovative design of DAVIDE has  the aim of providing a leading edge HPC cluster showing higher performance, reduced power consumption and ease of use.  A key technology of the architecture, developed in collaboration with the University of Bologna, is an innovative infrastructure for measuring, monitoring and capping the power consumption of the node and of the whole system, as well as the presence of last release GPUs. In this course we describe in more details the DAVIDE architecture and its production environment, with the help of uses cases in fields such as materials science and energy production , illustrate the new opportunities available to users thanks to the introduction of this system into the Cineca HPC infrastructure. Skills: By the end of the course, participants will be expected to: have a good understanding of the technologies employed in the DAVIDE HPC supercomputer recognize the types of problem and application particularly suited to the cluster understand how the energy monitoring system can be used to improve the energy efficiency of applications Target Audience: Researchers who may wish to use the cluster in the future for their research or simply those interested in the evolving field of new architectures for HPC and energy monitoring in HPC. 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 200 euros for students working and living outside Italy and 100 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/835/ 2019-05-06 07:00:00 UTC 2019-05-07 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to R Shiny

    6 May 2019

    Zurich, Switzerland

    Elixir node event
    Introduction to R Shiny https://tess.elixir-europe.org/events/introduction-to-r-shiny This course is over subscribed. You can still add your name to the waiting list by applying using the button at the bottom of this page. You will only be contacted if a place becomes available. 2019-05-06 09:00:00 UTC 2019-05-06 00:00:00 UTC SIB, Zurich, Switzerland SIB Zurich Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Introduction to openBIS

    7 May 2019

    Lausanne, Switzerland

    Elixir node event
    Introduction to openBIS https://tess.elixir-europe.org/events/introduction-to-openbis Overview openBIS is a combined data management platform, Electronic Laboratory Notebook, and Inventory Management System. 2019-05-07 09:00:00 UTC 2019-05-07 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First Steps in Parallelization with OpenMP

    8 May 2019

    Basel, Switzerland

    Elixir node event
    First Steps in Parallelization with OpenMP https://tess.elixir-europe.org/events/first-steps-in-parallelization-with-openmp-1bbfd630-8e6e-424b-93c3-692f1df61027 Overview We currently live in the era of multicore computers, where almost every computing machine has many CPUs. In order to benefit from this computational power we need to devise programs explicitly written for parallel machines. 2019-05-08 09:00:00 UTC 2019-05-08 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • ELIXIR-EXCELERATE Train the trainer

    8 - 10 May 2019

    Basel, Switzerland

    Elixir node event
    ELIXIR-EXCELERATE Train the trainer https://tess.elixir-europe.org/events/elixir-excelerate-train-the-trainer-7b9d0389-490f-46f6-89af-697c998d655e This course is over subscribed. You can still add your name to the waiting list by applying using the button at the bottom of this page. You will only be contacted if a place becomes available. 2019-05-08 09:00:00 UTC 2019-05-10 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Docker for reproducible computational research

    13 May 2019

    Bern, Switzerland

    Elixir node event
    Docker for reproducible computational research https://tess.elixir-europe.org/events/docker-for-reproducible-computational-research-4fbe7a5a-06bb-4c5f-8ae1-4fed251567d8 Overview Bioinformatics analysis usually involves a large number of software tools, reference data and pipelines used to elaborate the results. 2019-05-13 09:00:00 UTC 2019-05-13 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Live Long-Read sequencing and data analysis

    15 - 17 May 2019

    Fribourg, Switzerland

    Elixir node event
    Live Long-Read sequencing and data analysis https://tess.elixir-europe.org/events/live-long-read-sequencing-and-analysis More information here 2019-05-15 09:00:00 UTC 2019-05-17 00:00:00 UTC SIB, Fribourg, Switzerland SIB Fribourg Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • HPC code optimisation workshop @ LRZ

    20 - 22 May 2019

    HPC code optimisation workshop @ LRZ https://tess.elixir-europe.org/events/hpc-code-optimisation-workshop-lrz-c5f2f459-a0b0-431c-9d17-7a08e3cdeae6          Contents In the ever-growing complexity of computer architectures, code optimization has become the main route to keep pace with hardware advancements and effectively make use of current and upcoming High Performance Computing systems. Have you ever asked yourself: Where does the performance of my application lay? What is the maximum speed-up achievable on the architecture I am using? Is my implementation matching the HPC objectives? In this workshop, we will answer these questions and provide a unique opportunity to learn techniques, methods and solutions on how to improve code, how to enable the new hardware features and how to use the roofline model to visualize the potential benefits of an optimization process. We will begin with a description of the latest micro-processor architectures and how the developers can efficiently use modern HPC hardware, in particular the vector units via SIMD programming and AVX-512 optimization and the memory hierarchy. The attendees are then conducted along the optimization process by means of hands-on exercises and learn how to enable vectorization using simple pragmas and more effective techniques, like changing data layout and alignment. The work is guided by the hints from the Intel® compiler reports, and using Intel® Advisor. NEW: this year the workshop will consist of three days. We will dedicate most of the third day to the Intel Math Kernel Library (MKL), in order to show how to gain performance through the use of libraries. We provide also an N-body code, to support the described optimization solutions with practical hands-on. The course is a PRACE training event. Learning Goals Through a sequence of simple, guided examples of code modernization, the attendees will develop awareness on features of multi and many-core architecture which are crucial for writing modern, portable and efficient applications. A special focus will be dedicated to scalar and vector optimizations for the latest Intel® Xeon® Scalable processor, code-named Skylake, utilized in the SuperMUC-NG machine at LRZ. The tutorial will have presentations and demo session. The workshop interleaves frontal and practical sessions. Further details will be provided later. About the Lecturers Fabio Baruffa is a software technical consulting engineer in the Developer Products Division (DPD) of the Software and Services Group (SSG) at Intel. He is working in the compiler team and provides customer support in the high performance computing (HPC) area. Prior at Intel, he has been working as HPC application specialist and developer in the largest supercomputing centers in Europe, mainly the Leibniz Supercomputing Center and the Max-Plank Computing and Data Facility in Munich, as well as Cineca in Italy. He has been involved in software development, analysis of scientific code and optimization for HPC systems. He holds a PhD in Physics from University of Regensburg for his research in the area of spintronics device and quantum computing. Luigi Iapichino holds a position of scientific computing expert at LRZ and he is member of the Intel Parallel Computing Center (IPCC). His main tasks are code modernization for many-core systems, and HPC support. He got in 2005 a PhD in physics from TU München, working at the Max Planck Institute for Astrophysics. Before moving to LRZ in 2014, he worked at the Universities of Würzburg and Heidelberg, involved in research projects related to computational astrophysics. Gerald Mathias works in the application support for the HPC systems at LRZ since 2015 and leads the Biolab@lrz. After his PhD in Computational Biopyhsics at the LMU Munich he joined the chair of Theoretical Chemistry at the RUB in Bochum afterwards as a postdoc. He is experienced in the development and optimization of highly parallel ab initio and force field based molecular dynamics codes, both in Fortran and C. https://events.prace-ri.eu/event/872/ 2019-05-20 07:00:00 UTC 2019-05-22 15:00:00 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 is now open. 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 [] []
  • Data, lights, camera, action! Scientific visualization done beautifully using Blender @SURFsara

    21 May 2019

    Data, lights, camera, action! Scientific visualization done beautifully using Blender @SURFsara https://tess.elixir-europe.org/events/data-lights-camera-action-scientific-visualization-done-beautifully-surfsara-66cf8248-fbcd-4fe4-8d54-4b3ce75f0e12 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/866/ 2019-05-21 07:00:00 UTC 2019-05-21 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • HPC for Industry 4.0@Cineca

    21 - 23 May 2019

    HPC for Industry 4.0@Cineca https://tess.elixir-europe.org/events/hpc-for-industry-4-0-cineca Description: The aim of the workshop is to present the state-of-the-art of Industry 4.0 technologies in particular, presenting methods and techniques that might be used to transform a manufacturing plant into a plant 4.0.  The programme will include the relation among High Performance Computing (HPC), Artificial Intelligence (AI), Big Data and visualization: the basic ingredients to create a digital twin of your 4.0 factory.  Taking into consideration a remote manufacturing plant, a digital twin is a cyber replica of the plant that allows operation technology to be digitalized allowing a large amount of data from the plant’s sensors to be collected. In addition, since the data can be analyzed with HPC, so to simulate and forecast the plant behaviour.   Furthermore, with AI automatic decisions can be taken to optimize the production and the Industry management can visualize with a convenient dashboard or with virtual reality what is happening in real time in the remote plant.   The workshop is organised around five sections, each covering one of the themes mentioned, and associated to a question to which the presenters will try to answer. The last day, organised in collaboration with the HPC-Europa3 project (www.hpc-europa.eu), is dedicated to SMEs and to present them the advantages in the use of HPC and related technologies     May 21st AI (morning) : What can we do with the Al?  What can we do with artificial intelligence? What are our limits? Which problems can be tackled with such a technology? This session shows current applications and gives an insight into the future of this rapidly developing field.  ANSWERS FROM: Axyon, Bioretics, NVIDIA, Dr. Andrea Borghesi (UniBo), Prof. Fabrizio Riguzzi (UniFE)... BigData and Analytics (afternoon) : How can I manage and analyze data in a scalable and smart way?  How can I turn my DB into a scalable DB ready for the new challenges of the I4.0? Are there any methods and best practices to do this? But if I collect a lot of data then I can analyze it? In this section we will highlight new techniques to make DBs scalable and we will illustrate methodologies on how, which and how much data to collect in order to have analyses that produce knowledge in time to make decisions.   ANSWERS FROM: Datalogic, Engineering, Porini1968, Leithà (Unipol Group), DataRiver, Dr. Alessandro Spelta (UniPV)....     May 22nd HPC & Simulation (morning) :  How can I accelerate design and optimize production processes?  This session will show the latest optimization and parallelization techniques to make applications scalable, both to optimize the software for production and to accelerate the design of new products.   ANSWERS FROM: Ansys, Chiesi, Dompè, eXactLab, Intel, M3... Digital twins (afternoon) : How do I create my company's digital twin?  What does it mean and how do you digitize an industrial process? What are the benefits of investing in these technologies? In this section we will show what are the new possibilities that the digital transformation opens up to the company but also what are the necessary requirements to do so. We will give space to direct testimonies of companies that have already taken this path.  ANSWERS FROM: Ansys, ESI, Optimad, RBF Morph, Saipem, Dr. Andrea Borghesi (UniBO)....     May 23rd HPC 4 SME (all day) : Can HPC help my SME grow?   What are the opportunities for my SME in using HPC? Is it too big an investment for me? This section will show success stories and opportunities provided by EU programmes for SMEs. Speakers will present how important it is to grow the business to innovate and adopt high technology solutions.  ANSWERS FROM: BI-REX, E4, MADE, Moxoff, RED Fluid Dynamics, Dr Federico Perini (HPC-EU3), Prof. Lucia Ramundo... The initiative aims to involve industrial and academic participants to create a collaborative environment where will be possible to share industrial needs and find possible solutions.  Skills : By the end of the workshop each participants should be able to know technologies involved in Industry 4.0 and  possible applications. Target Audience : Academic and Industrial researcher and technical management Pre-requisites : For participation on all three days is not required any technical knowledge.  PLEASE WRITE IN THE "REASON FOR PARTICIPATION" FIELD IN THE REGISTRATION FORM WHICH DAYS YOU WILL ATTEND. EMPTY FIELD MEANS THAT YOU WILL TAKE PART ALL OF THE THREE DAYS.  https://events.prace-ri.eu/event/834/ 2019-05-21 07:00:00 UTC 2019-05-23 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • Node-level performance optimization @ CSC

    22 - 24 May 2019

    Node-level performance optimization @ CSC https://tess.elixir-europe.org/events/node-level-performance-optimization-csc Description This course includes topics on code optimization for x86 platforms and efficient code parallelization on node-level using OpenMP threading. Advanced aspects of threading and optimization, such as selected topics of new features in OpenMP 5.0 standard, will be covered during the course. Learning outcome Awareness of modern features in x86 CPUs Ability to vectorize computations Ability to use advanced features of OpenMP  Ability to increase code performance using threading and x86 optimization Prerequisites Good knowledge of C/C++ or Fortran Good knowledge of threading using OpenMP Basic knowledge of modern CPU architectures Agenda (preliminary) Day 1: Wednesday, May 22 Course introduction and intro to CSC's new systems  Introduction to the latest Intel(r) Xeon(r) Scalable Processor  Performance analysis methods and tools  Vectorization using SIMD Day 2: Thursday, May 23 OpenMP SIMD vectorization Optimizing memory accesses Day 3: Friday, May 24 Advanced OpenMP features OpenMP performance considerations Future outlook Lecturers:  Sebastian von Alfthan (CSC), Mikko Byckling (Intel), Fredrick Robertsén (CSC) Language:  English Price:          Free of charge https://events.prace-ri.eu/event/874/ 2019-05-22 06:00:00 UTC 2019-05-24 13:00:00 UTC [] [] [] workshops_and_courses [] []
  • OpenMP GPU Directives for Parallel Accelerated Supercomputers - an alternative to CUDA from Cray perspective @ HLRS

    22 - 23 May 2019

    OpenMP GPU Directives for Parallel Accelerated Supercomputers - an alternative to CUDA from Cray perspective @ HLRS https://tess.elixir-europe.org/events/openmp-gpu-directives-for-parallel-accelerated-supercomputers-an-alternative-to-cuda-from-cray-perspective-hlrs-f423be53-abbd-4597-922f-d472b88dd6d2 Overview This workshop will cover the directive-based programming model based on OpenMP v4 whose multi-vendor support allows users to portably develop applications for parallel accelerated supercomputers. It also includes comparison to the predecessor interface OpenACC v2. The workshop will also demonstrate how to use the Cray Programming Environment tools to identify application bottlenecks, facilitate the porting, provide accelerated performance feedback and to tune the ported applications. The Cray scientific libraries for accelerators will be presented, and interoperability of the directives approach with these and with CUDA will be demonstrated. Through application case studies and tutorials, users will gain direct experience of using both OpenMP and OpenACC directives in realistic applications. Users may also bring their own codes to discuss with Cray specialists or begin porting. This course provides scientific training in Computational Science, and in addition, the scientific exchange of the participants among themselves. For further information and registration please visit the HLRS course page. https://events.prace-ri.eu/event/809/ 2019-05-22 07:00:00 UTC 2019-05-23 14:30:00 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 is now open. 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 @BSC

    24 May 2019

    Heterogeneous Programming on FPGAs with OmpSs@FPGA @BSC https://tess.elixir-europe.org/events/heterogeneous-programming-on-fpgas-with-ompss-fpga The registration of this course is now open. 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 [] []
  • High-performance scientific computing in C++ @ JSC

    27 - 29 May 2019

    High-performance scientific computing in C++ @ JSC https://tess.elixir-europe.org/events/high-performance-scientific-computing-in-c-jsc-ee5bae79-ed57-4de5-bfad-0ca030797e59 Modern C++, with its support for procedural, objected oriented, generic and functional programming styles, offers many powerful abstraction mechanisms to express complexity at a high level while remaining very efficient. It is therefore the language of choice for many scientific projects. However, achieving high performance on contemporary computer hardware, with many levels of parallelism, requires understanding C++ code from a more performance centric viewpoint. In this course, the participants will learn how to write C++ programs which better utilize typical HPC hardware resources of the present day. The course is geared towards scientists and engineers, who are already familiar with C++14, and wish to develop maintainable and fast applications. They will learn to identify and avoid performance degrading characteristics, such as unnecessary memory operations, branch mispredictions, and unintentionally strong ordering assumptions. Two powerful open source libraries to help write structured parallel applications will also be introduced: Intel (R) Threading Building Blocks NVIDIA Thrust Prerequisites: Good working knowledge of C++, especially the C++14 standard. Please check with these questions whether your C++ knowlegde fulfills the requirements. Application Registrations are only considered until 1May 2019 due to available space, the maximal number of participants is limited. Applicants will be notified, whether they are accepted for participitation. Instructor: Dr. Sandipan Mohanty, JSC Contact For any questions concerning the course please send an e-mail to s.mohanty@fz-juelich.de https://events.prace-ri.eu/event/824/ 2019-05-27 07:00:00 UTC 2019-05-29 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • Uncertainty quantification @MdlS

    27 - 29 May 2019

    Uncertainty quantification @MdlS https://tess.elixir-europe.org/events/uncertainty-quantification-mdls-8ab27eae-4c4e-457e-bc99-0ccf6ee93b78 Uncertainty in computer simulations, deterministic and probabilistic methods for quantifying uncertainty, OpenTurns software, Uranie software Content Uncertainty quantification takes into account the fact that most inputs to a simulation code are only known imperfectly. It seeks to translate this uncertainty of the data to improve the results of the simulation. This training will introduce the main methods and techniques by which this uncertainty propagation can be handled without resorting to an exhaustive exploration of the data space. HPC plays an important role in the subject, as it provides the computing power made necessary by the large number of simulations needed. The course will present the most important theoretical tools for probability and statistical analysis, and will illustrate the concepts using the OpenTurns software. Course Outline Day 1 - General methodology for handling uncertainty, presentation of a case study - Fundamental notions from probability and statistics - General introduction to the software tools: OpenTurns and Uranie   Day 2 - Statistical estimation: parametric and non-parametric, testing - Modeling with non-numerical data: expert judgement, entropy - Central trend: local and gloal sensitivity indices (design of experiments, sampling, Sobol indices) - computing the probability of rare events, simulation methods, FORM/SORM   Day 3 - Distributed computing: parallel solvers, batch jobs submission on a parallel computer, implementation within OpenTurns / Salome and Uranie - Introduction to meta-model building, least-squares, other response surface, Kriging, neural networks - Introduction to polynomial chaos Learning outcomes Learn to recognize when uncertainty quantification can bring new insight to simulations. Know the main tools and techniques to investigate uncertainty propagation. Gain familiarity with modern tools for actually carrying out the computations in a HPC context. Prerequisites Basic knowledge of probability will be useful, as will a basic familiarity with Linux. https://events.prace-ri.eu/event/815/ 2019-05-27 07:30:00 UTC 2019-05-29 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • First Steps with UNIX in Life Sciences

    28 May 2019

    Lausanne, Switzerland

    Elixir node event
    First Steps with UNIX in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-unix-in-life-sciences-36cb482a-4e6a-4f85-a4f9-2f53b42cdea7 Overview With a constant evolution of technologies, life scientists (such as laboratory biologists) are faced with an increasing need for bioinformatics skills to deal with high-throughput data storage, retrieval and analysis. 2019-05-28 09:00:00 UTC 2019-05-28 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Deep Learning and GPU programming workshop @ LRZ

    3 - 6 June 2019

    Deep Learning and GPU programming workshop @ LRZ https://tess.elixir-europe.org/events/deep-learning-and-gpu-programming-workshop-lrz Overview Learn how to train and deploy a neural network to solve real-world problems, how to generate effective descriptions of content within images and video clips, how to effectively parallelize training of deep neural networks on Multi-GPUs and how to accelerate your applications with CUDA C/C++ and OpenACC. This new 4-days workshop offered for the first time at LRZ combines lectures about fundamentals of Deep Learning for Multiple Data Types and Multi-GPUs with lectures about Accelerated Computing with CUDA C/C++ and OpenACC. The lectures are interleaved with many hands-on sessions using Jupyter Notebooks. The exercises will be done on a fully configured GPU-accelerated workstation in the cloud. The workshop is co-organized by LRZ and NVIDIA Deep Learning Institute (DLI) for the Partnership for Advanced Computing in Europe (PRACE). Since 2012 LRZ as part of GCS is one of currently 10 PRACE Training Centres which serve as European hubs and key drivers of advanced high-quality training for researchers working in the computational sciences. NVIDIA DLI offers hands-on training for developers, data scientists, and researchers looking to solve challenging problems with deep learning.  All instructors are NVIDIA certified University Ambassadors. Agenda 1st day: Fundamentals of Deep Learning for Multiple Data Types This day explores how convolutional and recurrent neural networks can be combined to generate effective descriptions of content within images and video clips. Learn how to train a network using TensorFlow and the Microsoft Common Objects in Context (COCO) dataset to generate captions from images and video by: Implementing deep learning workflows like image segmentation and text generation Comparing and contrasting data types, workflows, and frameworks Combining computer vision and natural language processing Upon completion, you’ll be able to solve deep learning problems that require multiple types of data inputs. 2nd day: Fundamentals of Deep Learning for Multi-GPUs The computational requirements of deep neural networks used to enable AI applications like self-driving cars are enormous. A single training cycle can take weeks on a single GPU or even years for larger datasets like those used in self-driving car research. Using multiple GPUs for deep learning can significantly shorten the time required to train lots of data, making solving complex problems with deep learning feasible. On the 2nd day we will teach you how to use multiple GPUs to train neural networks. You'll learn: Approaches to multi-GPUs training Algorithmic and engineering challenges to large-scale training Key techniques used to overcome the challenges mentioned above Upon completion, you'll be able to effectively parallelize training of deep neural networks using TensorFlow. 3rd day: Fundamentals of Accelerated Computing with CUDA C/C++ The CUDA computing platform enables the acceleration of CPU-only applications to run on the world’s fastest massively parallel GPUs. On the 3rd day you experience C/C++ application acceleration by: Accelerating CPU-only applications to run their latent parallelism on GPUs Utilizing essential CUDA memory management techniques to optimize accelerated applications Exposing accelerated application potential for concurrency and exploiting it with CUDA streams Leveraging command line and visual profiling to guide and check your work Upon completion, you’ll be able to accelerate and optimize existing C/C++ CPU-only applications using the most essential CUDA tools and techniques. You’ll understand an iterative style of CUDA development that will allow you to ship accelerated applications fast. 4th day: Fundamentals of Accelerated Computing with OpenACC On the last day you learn the basics of OpenACC, a high-level programming language for programming on GPUs. Discover how to accelerate the performance of your applications beyond the limits of CPU-only programming with simple pragmas. You’ll learn: How to profile and optimize your CPU-only applications to identify hot spots for acceleration How to use OpenACC directives to GPU accelerate your codebase How to optimize data movement between the CPU and GPU accelerator Upon completion, you'll be ready to use OpenACC to GPU accelerate CPU-only applications. Important information After you are accepted, please create an account under courses.nvidia.com/join using the same email address as for event registration, since lab access is given based on the event registration list. Please be aware that for adminstrative reasons, after you register, Nvidia will use your email address to contact you for the final feedback of the workshop. PRACE Training and Education The mission of PRACE (Partnership for Advanced Computing in Europe) is to enable high-impact scientific discovery and engineering research and development across all disciplines to enhance European competitiveness for the benefit of society.  PRACE has an extensive education and training effort through seasonal schools, workshops and scientific and industrial seminars throughout Europe. Seasonal Schools target broad HPC audiences, whereas workshops are focused on particular technologies, tools or disciplines or research areas. NVIDIA Deep Learning Institute The NVIDIA Deep Learning Institute delivers hands-on training for developers, data scientists, and engineers. The program is designed to help you get started with training, optimizing, and deploying neural networks to solve real-world problems across diverse industries such as self-driving cars, healthcare, online services, and robotics. https://events.prace-ri.eu/event/860/ 2019-06-03 07:00:00 UTC 2019-06-06 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • Statistical methods for big data in life sciences and health with R

    3 - 6 June 2019

    Lausanne, Switzerland

    Elixir node event
    Statistical methods for big data in life sciences and health with R https://tess.elixir-europe.org/events/statistical-methods-for-big-data-in-life-sciences-and-health-with-r Overview In this course, biologists, computational biologists and bioinformatics scientists will acquire the key competencies that they need when dealing with big data from the health and life sciences fields. 2019-06-03 09:00:00 UTC 2019-06-06 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • School on Scientific Data Analytics and Deep Learning @ Cineca

    10 - 14 June 2019

    School on Scientific Data Analytics and Deep Learning @ Cineca https://tess.elixir-europe.org/events/school-on-scientific-data-analytics-and-deep-learning-cineca Description: The increasing amount of scientific data collected through sensors or computational simulations can take advantage of new techniques for being processed in order to extract new insights out of raw data. The purpose of this one-week school is to present researchers and scientists with methods, tools and techniques for exploring and mining, large data sets using Cineca high performance resources. The school is an introductory set of lectures aimed at training beginner participants in the application of relevant statistical, machine and deep learning algorithms to create classification and predictive models using Cineca resources to execute efficient processing jobs. The school will consist of introductory lectures held by data scientists, and hands-on sessions. Skills: At the end of the course, the student will possess and know how to use the following skills: • Use of Cineca HPC resources • Machine Learning algorithms and libraries  • Deep Learning frameworks Target Audience: Young students, PhD, and researchers in computational sciences and scientific areas with different backgrounds, looking for new technologies and methods to process and analyse large amount of data. Prerequisites: Participants must have basic knowledge in statistics, on the fundamentals of computer programming with python and R and in using GNU/Linux-based systems. Grant The lunch for the five 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. 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. The number of participants is limited to 20 students. Applicants will be selected according to their experience, qualification and scientific interest BASED ON WHAT WRITTEN IN THE "Reason for participation" FIELD OF THE REGISTRATION FORM.    APPLICATION DEADLINE May 3rd, 2019.  STUDENTS WILL BE NOTIFIED ON THEIR ADMISSION OR NOT WITH AN EMAIL ON MONDAY MAY,13TH.  Attendance is FREE.    https://events.prace-ri.eu/event/832/ 2019-06-10 08:00:00 UTC 2019-06-14 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to High-Performance Machine Learning @SURFsara

    11 - 12 June 2019

    Introduction to High-Performance Machine Learning @SURFsara https://tess.elixir-europe.org/events/introduction-to-high-performance-machine-learning-surfsara-202d1ebb-8b23-4dc2-93c9-008a19a832eb In recent years machine learning and deep learning techniques in particular have developed tremendously. Neural networks are being used in more and more application domains going from computer vision to speech recognition, and even replacing parts of the compute pipeline for scientific HPC applications.   In this course you will start from the essential concepts up to the efficient use of HPC infrastructures to get the best performance out of different machine learning tools. Several hands-on sessions are set up to present general algorithms and some scalability challenges involved in when using both large-scale data and large-scale models. https://events.prace-ri.eu/event/870/ 2019-06-11 07:00:00 UTC 2019-06-12 15:30:00 UTC [] [] [] workshops_and_courses [] []
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