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Content provider: PRACE  or European Bioinformatics Ins... 

  • [MOOC] A short introduction to MPI One-sided Communication @ HLRS & ASTRON & Surfsara

    25 October - 7 November 2020

    [MOOC] A short introduction to MPI One-sided Communication @ HLRS & ASTRON & Surfsara https://tess.elixir-europe.org/events/mooc-a-short-introduction-to-mpi-one-sided-communication-hlrs-astron-surfsara Overview This online course will start on the 26th of October and it will run for two weeks, with an estimated effort of 4 hours per week. It is provided as a MOOC (Massive Open Online Course). During this time you will be guided through the concepts of one-sided communication and learn to perform these data movements correctly and efficiently using MPI (with C and Fortran bindings). Several examples and exercises will illustrate their use and help to understand the benefits of these routines, and you also will be able to challenge your knowledge with some quizzes! This online course has been developed by HLRS, ASTRON and SURFsara with the sponsorship of PRACE, and the registration is done for free through FutureLearn in the indicated link below.   For further information and registration please visit the FutureLearn course page. https://events.prace-ri.eu/event/1079/ 2020-10-25 23:00:00 UTC 2020-11-07 23:00:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] High-performance scientific computing in C++ @ JSC

    26 - 29 October 2020

    [ONLINE] High-performance scientific computing in C++ @ JSC https://tess.elixir-europe.org/events/high-performance-scientific-computing-in-c-jsc-7577a0b2-ea9c-4d4d-831c-b75adb7ec714 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 by today's standards requires understanding and exploiting multiple levels of parallelism, and understanding C++ code from a 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 already familiar with C++17 (at the very least C++14), who wish to develop maintainable and fast applications. They will learn techniques to better utilize CPU caches, instruction pipelines, SIMD functionality and multi-threading. Shared memory parallel programming on multiple CPU cores will be introduced using parallel STL of C++17 and Intel (R) Threading Building Blocks. The participants will also learn basic GPGPU programming in C++ using NVidia CUDA and 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 16 October 2020, 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 This course was originally planned for 15-17 June 2020 as an in-person course. https://events.prace-ri.eu/event/984/ 2020-10-26 08:00:00 UTC 2020-10-29 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] Tools and techniques to quickly improve performances of HPC applications in Solid Earth@Cineca

    26 - 28 October 2020

    [ONLINE] Tools and techniques to quickly improve performances of HPC applications in Solid Earth@Cineca https://tess.elixir-europe.org/events/tools-and-techniques-to-quickly-improve-performances-of-hpc-applications-in-solid-earth-cineca It will be  shown a course targeted to improve the overall performance of a code in Solid Earth, currently in use at the CHEESE Center of Excellence H2020 project. Starting from a description of main architectures characterizing the HPC world,  parallel performance profiling tools will be provided on examples of the code to find the so-called performance bottlenecks. Starting from the profiling analysis, it will show how and where to intervene with respect to the hardware characterization of the HPC machine used for the investigation to improve the overall performance of serial and parallel codes.   Particular attention will be given to tools and techniques to improve the performance of the codes with respect to I / O and vectorization. Skills: At the end of the course the student will be able to: use a concrete methodology to improve the performance of a code in Solid Earth already in use in the context of ChEESE project find and solve all the main bottlenecks of an application with respect to appropriate computational metrics and the machine used Target audience:  Researchers in Solid Earth interested to learn and use all those techniques and related tools that may allow them to improve the performance of their code on current HPC architectures in the shortest possible time. Pre-requisites: Basic knowledge of LINUX/UNIX. Knowledge of C, FORTRAN, MPI or OpenMP is recommended. Notions of Parallel computing techniques and algorithms for Solid Earth applications   Coordinating Teachers: Dr. V Ruggiero, G.Amati.   https://events.prace-ri.eu/event/973/ 2020-10-26 08:15:00 UTC 2020-10-28 16:30:00 UTC [] [] [] workshops_and_courses [] []
  • The PRIDE database: storing, disseminating and integrating proteomics data in the public domain

    28 October 2020

    Elixir node event
    The PRIDE database: storing, disseminating and integrating proteomics data in the public domain https://tess.elixir-europe.org/events/the-pride-database-storing-disseminating-and-integrating-proteomics-data-in-the-public-domain This webinar will provide an introduction to proteomics approaches and the PRIDE database, followed by examples of PRIDE public data re-use, including “big data” approaches. 2020-10-28 15:30:00 UTC 2020-10-28 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • [ONLINE] Data Management with iRODS and Compute @SURFsara

    29 October 2020

    [ONLINE] Data Management with iRODS and Compute @SURFsara https://tess.elixir-europe.org/events/data-management-with-irods-and-compute-surfsara-11cb4922-2fd9-4e88-b5b0-1930d3c1afba Would you want to practice reproducible research in HPC and preserve your data for the future? Research Data Management is essential in effective and reproducible science. Due to ever increasing data volumes and complexity, researchers need modern tools to manage all stages of the data life cycle. Here we will use iRODS, a data management framework, to incorporate data management principles in compute pipelines.  What? In this course you will: - Learn about the the iRODS data management framework and icommands - Understand how to incorporate provenance in a compute workflow - Know about FAIR in data processing workflows Who? - Everyone interested in learning advanced data management tools for compute and data processing workflows Requirements - Basic knowledge of Linux and shell commands You should have - Your own laptop with an up-to-date browser and a terminal emulator. The use of the operating systems Linux and macOS is preferred, but not mandatory. For Windows users we recommend to download MobaXterm (portable version) as terminal emulator.   IMPORTANT INFORMATION: WAITING LIST If the course gets fully booked, no more registrations are accepted through this website. However, you can be included in the waiting list: for that, please send an email to training@surfsara.nl and you'll be informed when a place becomes available. https://events.prace-ri.eu/event/1058/ 2020-10-29 08:00:00 UTC 2020-10-29 16:30:00 UTC [] [] [] workshops_and_courses [] []
  • Introducing the new UniProt Disease Portal

    29 October 2020

    Elixir node event
    Introducing the new UniProt Disease Portal https://tess.elixir-europe.org/events/introducing-the-new-uniprot-disease-portal This webinar will provide an interactive introduction to the new UniProt Disease Portal: a single centralized resource of UniProt disease-centric information which has been developed with the help of our users to better serve the needs of the research community and facilitate protein discoverability. 2020-10-29 15:30:00 UTC 2020-10-29 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • Bioinformatics & Functional Genomics in Zebrafish

    2 - 5 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Bioinformatics & Functional Genomics in Zebrafish https://tess.elixir-europe.org/events/bioinformatics-functional-genomics-in-zebrafish-ff8f3fea-a89e-4b25-93b1-111191cae4b7 This course has been designed specifically for researchers working within the Zebrafish community, providing an introduction and practical knowledge of tools and resources for working with functional genomics data. 2020-11-02 09:00:00 UTC 2020-11-05 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Metagenomics bioinformatics

    2 - 6 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Metagenomics bioinformatics https://tess.elixir-europe.org/events/metagenomics-bioinformatics-91c48308-c2e6-48eb-b1ea-113f79da1edd This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data, including marker gene, whole gene shotgun (WGS) and assembly-based approaches. 2020-11-02 09:00:00 UTC 2020-11-06 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Marina Pujol [] [] [] [] HDRUK
  • Metagenomics bioinformatics (Virtual)

    2 - 6 November 2020

    Hinxton, United Kingdom

    Elixir node event
    Metagenomics bioinformatics (Virtual) https://tess.elixir-europe.org/events/metagenomics-bioinformatics-virtual Gain knowledge on the tools, processes and analysis approaches used in the field of metagenomics. 2020-11-02 09:00:00 UTC 2020-11-06 17:00:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Marina Pujol [] [] [] [] HDRUK
  • Europe PMC: Programmatic access

    3 November 2020

    Elixir node event
    Europe PMC: Programmatic access https://tess.elixir-europe.org/events/europe-pmc-programmatic-access This webinar will introduce the Europe PMC Articles RESTful API and show how to programmatically access publications and related information, such as citations, references, data links, or text-mined terms. 2020-11-03 14:00:00 UTC 2020-11-03 15:00:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • [ONLINE] Heterogeneous computing with performance modelling @ SNIC

    4 - 5 November 2020

    [ONLINE] Heterogeneous computing with performance modelling @ SNIC https://tess.elixir-europe.org/events/online-heterogeneous-computing-with-performance-modelling-snic Modern high core count CPUs and accelerators, such as GPUs, have been shown to provide significant performance benefits in many different applications. However, for a novice, or even for a moderately experienced scientist or programmer, it is not always clear which applications could potentially benefit from these resources and which do not. For example, a Nvidia V100 GPU can perform artificial intelligence (AI) related computations in a fraction of the time it takes a regular CPU to perform the same computations but ill-informed OpenACC compiler pragmas can actually make a code run slower. Why is this? When should one invest time in parallelization and/or GPU-acceleration? How much speedup can be expected with a given application? The main goal of this two-day course is to start answering these questions. The course also covers the basics of GPU programming and aims to provide the necessary information for avoiding the most common pitfalls. More information, schedule, and registration can be found on the course webpage at HPC2N, Umeå University. https://events.prace-ri.eu/event/1064/ 2020-11-04 08:00:00 UTC 2020-11-05 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Variant submission and data access at the European Variation Archive

    4 November 2020

    Elixir node event
    Variant submission and data access at the European Variation Archive https://tess.elixir-europe.org/events/variant-submission-and-data-access-at-the-european-variation-archive This webinar will cover how to access data using the EVA UI/API and the methodology of variant data submission to the EVA, specifically focusing on data transformation and formats. 2020-11-04 15:30:00 UTC 2020-11-04 16:30:00 UTC [] Ajay Mishra [] [] [] [] HDRUK
  • [ONLINE] Shared memory parallelization with OpenMP @ VSC Vienna

    5 - 6 November 2020

    [ONLINE] Shared memory parallelization with OpenMP @ VSC Vienna https://tess.elixir-europe.org/events/online-shared-memory-parallelization-with-openmp-vsc-vienna This course will be delivered as an ONLINE COURSE (using Zoom) for remote participation. REGISTRATION is strictly NECESSARY since the details to access the online course will be provided to the registered and accepted attendees only. Registration follows the "first come – first served" principle. For the online course we can take a maximum of 40 persons. Additional registrations will be added to a waiting list. Furthermore, accepted participants will be contacted a few days before the course and asked to do a short PRE-ASSIGNMENT that has to be completed before the course starts. For doing the HANDS-ON LABS all you need is a C/C++ or Fortran compiler that supports OpenMP. Participants can choose between using their own laptops or any system they have access to that provides an OpenMP enabled compiler, it's even possible to do the exercises in Google Colab. Alternatively, participants can ask for a training user account at the VSC for the duration of the course. Overview The focus of this 2 days course is on shared memory parallelization with OpenMP for dual-core, multi-core, shared memory, and ccNUMA platforms. This course teaches OpenMP starting from a beginners level. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the OpenMP directives, environment variables, and library routines. Race-condition debugging tools are also presented. Content Levels: Beginners = 6:00h (50%) + Intermediate = 4:00h (33%) + Advanced = 2:00h (17%) This course is a PRACE training event. It is organized by the VSC Research Center, TU Wien, in cooperation with the High-Performance Computing-Center Stuttgart (HLRS). Agenda & Content 1st day 08:45  Join online 09:00    Welcome 09:10    Introduction to modern hardware (talk) 10:10    An overview of OpenMP (talk) 10:35   Coffee 10:50    OpenMP programming and execution model (talk+practical) 12:30   Lunch 13:30    OpenMP worksharing directives (talk+practical)  15:00   Coffee 15:15    More OpenMP (talk+practical) 16:00    Summary (talk) + Q & A 16:30   End of first day 2nd day 08:45  Join online 09:00    How to write correct OpenMP programs (talk) 09:30    Intel Inspector XE (demo+practical) 10:30   Coffee 10:45    How to write efficient OpenMP programs (talk) 11:00    Heat equation (talk+practical) 12:30   Lunch 13:30    Heat equation (practical — continued) 14:00    Vectorization with OpenMP (talk) 14:25    Thread affinity in OpenMP (talk) 15:00   Coffee 15:15     The taskloop directive (talk+practical) 16:30   End of second day (course) https://events.prace-ri.eu/event/1076/ 2020-11-05 07:45:00 UTC 2020-11-06 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] Directive-based GPU programming with OpenACC @ JSC

    9 - 11 November 2020

    [ONLINE] Directive-based GPU programming with OpenACC @ JSC https://tess.elixir-europe.org/events/online-directive-based-gpu-programming-with-openacc-jsc GPU-accelerated computing drives current scientific research. Writing fast numeric algorithms for GPUs offers high application performance by offloading compute-intensive portions of the code to the GPU. The course will cover basic aspects of GPU architectures and programming. Focus is on the usage of the directive-based OpenACC programming model which allows for portable application development. Examples of increasing complexity will be used to demonstrate optimization and tuning of scientific applications. Topics covered will include: Introduction to GPU/Parallel computing Programming model OpenACC Interoperability of OpenACC with GPU libraries (like cuBLAS and cuFFT) and CUDA Multi-GPU Programming with MPI and OpenACC Tools for debugging and profiling Performance optimization The course consists of lectures and interactive hands-on sessions in C or Fortran (the attendee’s choice). This course will take place as an online event. The link to the online platform will be provided to the registrants only. Prerequisites: Some knowledge about Linux, e.g. make, command line editor, Linux shell (see for instance this overview), a little experience in C/Fortran Application Registrations are only considered until 2 November 2020, the maximal number of participants is limited. Applicants will be notified, whether they are accepted for participitation. Instructors: Dr. Andreas Herten, Dr. Thorsten Hater, Dr. Kaveh Haghighi-Mood, JSC; Markus Hrywniak, Jiri Kraus, NVIDIA Contact For any questions concerning the course please send an e-mail to a.herten@fz-juelich.de https://events.prace-ri.eu/event/1075/ 2020-11-09 08:00:00 UTC 2020-11-11 12:00:00 UTC [] [] [] workshops_and_courses [] []
  • Ensembl Browser workshop, University of California San Francisco, 9-10 November 2020

    9 - 10 November 2020

    Hinxton, United Kingdom

    Elixir node event
    Ensembl Browser workshop, University of California San Francisco, 9-10 November 2020 https://tess.elixir-europe.org/events/ensembl-browser-workshop-university-of-california-san-francisco-9-10-november-2020 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2020-11-09 17:00:00 UTC 2020-11-10 21:00:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Michal Szpak [] [] [] [] HDRUK
  • [ONLINE] Earth Sciences Simulation Environments @ BSC

    10 - 12 November 2020

    [ONLINE] Earth Sciences Simulation Environments @ BSC https://tess.elixir-europe.org/events/earth-sciences-simulation-environments-bsc-599900ce-5ae4-4c46-81cd-d14a424670dd 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: Marc Guevara, Carles Tena and Maria Teresa Pay Perez This training will be online via zoom. 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. 10) – 4.5h 10:00-10:15 Welcome and introduction of the BSC Earth Sciences Department. (Francisco Doblas-Reyes, Head of BSC-ES Department) 10:15-10:30 Technical and logistic information. (Marc Guevara and Carles Tena) 10:30-11:00 Introduction to earth science fundamentals and modelling. (Raffaele Bernardello) 11:00-11:30 Break 11:30-13:00 Introduction to Linux and HPC, BSC facilities, PRACE and RES + preparation/checks for hands-on tutorial after lunch break (Mario Acosta) 13:00-14:00 Lunch break 14:00-16:00 HPC hands-on tutorial. At the end of this tutorial, the students will be able to compile and execute jobs on Mare Nostrum 4. (Mario Acosta and Miguel Castrillo and Carles Tena) Day 2 (Nov 11) – 3.5h 9:30-10:00 Lecture on the EC-EARTH climate model. (Raffaele Bernardello) 10:00-10:30 Lecture on the NMMB-MONARCH atmosphere chemistry model. (Oriol Jorba) 10:30-11:00 Lecture on setting up and running the NMMB-MONARCH model with Autosubmit. (Francesca Macchia and Gilbert Montane) 11:00-11:30 Break 11:30-13:30 Model hands-on tutorial. Students will run a prepared case. (Francesca Macchia and Gilbert Montane and Carles Tena and Marc Guevara) Day 3 (Nov 12) – 3h 10:00-11:00 Introduction to analysis and visualisation tools for model outputs (s2dverification, MapGenerator, CDO, NCO, panoply, ncview) (Francesco Benincasa) 11:00-11:30 Break 11:30-13:30 Analysis hands-on tutorial. Students will apply tools for analysis and visualisation to the outputs created the day before. (Francesco Benincasa and Carles Tena and Marc Guevara) END of COURSE https://events.prace-ri.eu/event/1042/ 2020-11-10 08:30:00 UTC 2020-11-12 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] Introduction to Parallel Programming @GRNET

    11 - 13 November 2020

    [ONLINE] Introduction to Parallel Programming @GRNET https://tess.elixir-europe.org/events/online-introduction-to-parallel-programming-grnet [ONLINE] Introduction to Parallel Programming 11 - 13 November 2020 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 parallelization. The course ends with a section presenting profiling and code optimizations to understand the behavior and performance of parallelized codes. The 3 day course consist 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. Hands on sessions will run on participants computers. An HPC like environment with the necessary tools within a Virtual Machine image will be provided. Course language is English.   Venue ONLINE using zoom Timetable https://events.prace-ri.eu/event/1086/attachments/1344/2413/Timetable.pdf 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. In EGEE/EGI projects he acted as application support and VO software manager for SEE VO, grid sites administrator, NGI_GRNET support staff (2008-2014). In PRACE 1IP-6IP he was involved in benchmarking tasks either as group member or as BCO (2010-2020). Currently he holds the position of “HPC Team leader” at GRNET S.A.   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.   About GRNET   GRNET – National Infrastructures for Research and Technology, is the national network, cloud computing and IT e-Infrastructure and services provider. It supports hundreds of thousands of users in the key areas of Research, Education, Health and Culture. GRNET provides an integrated environment of cutting-edge technologies integrating a country-wide dark fiber network, data centers, a high performance computing system and Internet, cloud computing, high-performance computing, authentication and authorization services, security services, as well as audio, voice and video services. GRNET scientific and advisory duties address the areas of information technology, digital technologies, communications, e-government, new technologies and their applications, research and development, education, as well as the promotion of Digital Transformation. Through international partnerships and the coordination of EC co-funded projects, it creates opportunities for know-how development and exploitation, and contributes, in a decisive manner, to the development of Research and Science in Greece and abroad. National Infrastructures for Research and Technology – Networking Research and Education www.grnet.gr, hpc.grnet.gr https://events.prace-ri.eu/event/1086/ 2020-11-11 08:30:00 UTC 2020-11-13 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • CABANA Train the Trainer Workshop for XMXP20

    11 November 2020

    Elixir node event
    CABANA Train the Trainer Workshop for XMXP20 https://tess.elixir-europe.org/events/cabana-train-the-trainer-workshop-for-xmxp20 This virtual workshop takes place within the X-meeting eXperience 2020 symposium. It will provide new trainers with knowledge, skills, guidance and tips for developing and delivering training. 2020-11-11 09:00:00 UTC 2020-11-11 17:00:00 UTC Virtual format Virtual format [] Piraveen Gopalasingam [] [] [] [] HDRUK
  • MGnify today: analysing microbiome data

    11 November 2020

    Elixir node event
    MGnify today: analysing microbiome data https://tess.elixir-europe.org/events/mgnify-today-analysing-microbiome-data This webinar will describe how MGnify can assist you in your microbiome research by providing a broad overview of resources available in MGnify. During the webinar, we will cover what types of microbiome data are included, improvements we have made to our analysis pipeline, as well as ways to search for data. 2020-11-11 15:30:00 UTC 2020-11-11 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • [ONLINE] High-performance computing with Python @ JSC

    16 - 20 November 2020

    [ONLINE] High-performance computing with Python @ JSC https://tess.elixir-europe.org/events/high-performance-computing-with-python-jsc-8f572b9d-fe3d-4357-a015-1be3342e47a8 Python is increasingly used in high-performance computing projects. It can be used either as a high-level interface to existing HPC applications and libraries, as embedded interpreter, or directly. This course combines lectures and hands-on sessions. We will show how Python can be used on parallel architectures and how to optimize critical parts of the kernel using various tools. The following topics will be covered: Interactive parallel programming with IPython Profiling and optimization High-performance NumPy Just-in-time compilation with numba Distributed-memory parallel programming with Python and MPI Bindings to other programming languages and HPC libraries Interfaces to GPUs This course is aimed at scientists who wish to explore the productivity gains made possible by Python for HPC. Prerequisites: Good working knowledge of Python and NumPy Application Registrations are only considered until 6 November 2020. Applicants will be notified, whether they are accepted for participitation. Instructors: Dr. Jan Meinke, Dr. Olav Zimmermann, JSC Contact For any questions concerning the course please send an e-mail to j.meinke@fz-juelich.de https://events.prace-ri.eu/event/982/ 2020-11-16 08:00:00 UTC 2020-11-20 12:00:00 UTC [] [] [] workshops_and_courses [] []
  • CodeRefinery online workshop

    17 - 26 November 2020

    CodeRefinery online workshop https://tess.elixir-europe.org/events/coderefinery-online-workshop Course goals and format In this course, you will become familiar with tools and best practices for version control and reproducibility in modern research software development. The main focus is on using Git for efficiently writing and maintaining research software. We will not teach programming, but we teach the tools you need to use programming well. We assume that you are familiar with the programming language that you use in your work and research. We try to keep the course as language-independent as possible but we will show some basic code examples in Python. This is an informal and interactive event with type-along type of presentations, live coding, and demos. Short tutorials alternate with practical exercises. Prerequisites You should be able to navigate the file tree in a terminal session and edit text files in the terminal. This Linux shell crash course (video) contains the essentials. Basics in one or more programming languages. You need to install some software (see below). It is useful if you have a basic idea of how Git works. We will start from the basics anyway, but please go through this Git-refresher material for a basic overview and important configuration steps. Make sure that Git is configured, and verify the configuration (see below). Schedule All times are in Europe/Stockholm time Time converter The schedule includes frequent breaks. The schedule is subject to change. Pre-workshop installation help and verification times Nov 12 (Thu) 13:00 - 14:00 Nov 13 (Fri) 13:00 - 14:00 Join anytime during this (preferably not everyone at the very start and end) Day 1 (Nov 17, Tue) 9:00 - 9:20 Welcome and practical information  9:20 - 12:00 Introduction to version control - part 1/2 (“Motivation” to “Undoing”)  Day 2 (Nov 18, Wed) 9:00 - 12:00 Introduction to version control - part 2/2 (“Branching and merging” to “Inspecting history”)  Day 3 (Nov 19, Thu) 9:00 - 12:00 Collaborative distributed version control  Day 4 (Nov 24, Tue) 9:00 - 9:15 Mini-intro  9:00 - 11:00 Reproducible research and FAIR data  11:00 - 12:00 Social coding and open software  Day 5 (Nov 25, Wed) 9:00 - 10:30 Documentation  10:30 - 12:00 Jupyter  Day 6 (Nov 26, Thu) 9:00 - 10:30 Automated testing 10:45 - 11:45 Modular code development  11:45 - 12:00 Concluding remarks and where to go from here Software requirements You need to install some software before CodeRefinery (why we ask you to do this). Please do this - and check it - in advance, otherwise you’ll start off behind. Note that, e.g., a working Python executable on your laptop is not sufficient - a version greater than 3.4 is strongly recommended and a number of extra packages need to be installed as detailed on the Python installation page. You also need to check your git configuration (video: how to configure Git). If you have an institutional laptop with limited rights, start in advance and/or ask for help to translate these instructions to work on your system. Bash Editor Git, including some configuration (optional) Visual diff tools Python Jupyter and JupyterLab Snakemake Zoom You should either a) drop by one of our verification sessions in advance, or b) verify with your team’s helper before the workshop. How to join We are normally limited by number of helpers, thus why not allow groups to bring their own helper?: We have the concept of teams that bring their own breakout room. Anyone may register as a learner, we will try to take as many as we can. Or you can register as a helper. If you are somewhat comfortable with these tools, you can be a helper! (see below) Register as a team, one helper and 4-6 learners. We will accept all complete teams. Everyone on the team must register separately. Decide some team name, and when registering, everone enter this same name so that we can link you together. During the exercise sessions in breakout rooms, the helper has primary responsibility for their group’s hands-on exercises. Still, instructors drop by to check and help as needed, so don’t worry if you don’t know everything. This is a great opportunity to bring your friends and colleagues and prepare for the future together. If you’ve been to a CodeRefinery before and have used git some after that, you are definitely capable of being a helper. If you routinely use git and know Python somewhat well, you are also very qualified to be a helper. Registration Please visit the workshop webpage.  https://events.prace-ri.eu/event/1082/ 2020-11-17 08:00:00 UTC 2020-11-26 11:00:00 UTC [] [] [] workshops_and_courses [] []
  • Basics to advanced genome annotation at Ensembl and REST Application Programming Interfaces (APIs)

    17 - 20 November 2020

    Elixir node event
    Basics to advanced genome annotation at Ensembl and REST Application Programming Interfaces (APIs) https://tess.elixir-europe.org/events/basics-to-advanced-genome-annotation-at-ensembl-and-rest-application-programming-interfaces-apis Introduction to the Ensembl Genome Browser and REST API, in collaboration with NextGenHelper. 2020-11-17 18:00:00 UTC 2020-11-20 20:30:00 UTC Virtual format Virtual format [] Emily Perry [] [] [] [] HDRUK
  • MGnify API: accessing microbiome data computationally

    18 November 2020

    Elixir node event
    MGnify API: accessing microbiome data computationally https://tess.elixir-europe.org/events/mgnify-api-accessing-microbiome-data-computationally This webinar will provide an overview of the MGnify API. It will include how to utilise the API using a browser; where to find documentation; how to use filtering and pagination; available output formats; and scripting examples in Python. 2020-11-18 15:30:00 UTC 2020-11-18 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • Structural bioinformatics

    23 - 27 November 2020

    Cambridge, United Kingdom

    Elixir node event
    Structural bioinformatics https://tess.elixir-europe.org/events/structural-bioinformatics-de38d612-6cf9-481f-9a57-3a54511976de This course explores bioinformatics data resources and tools for the interpretation and exploitation of bio-macromolecular structures. 2020-11-23 09:00:00 UTC 2020-11-27 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Structural bioinformatics (Virtual)

    23 - 27 November 2020

    Hinxton, United Kingdom

    Elixir node event
    Structural bioinformatics (Virtual) https://tess.elixir-europe.org/events/structural-bioinformatics-virtual This course explores bioinformatics data resources and tools for the browsing, analysis and interpretation of bio-macromolecular structure information. 2020-11-23 09:00:00 UTC 2020-11-27 17:00:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • GPU Programming with CUDA @ EPCC Online

    23 - 26 November 2020

    GPU Programming with CUDA @ EPCC Online https://tess.elixir-europe.org/events/gpu-programming-with-cuda-epcc-online Outline This course will provide an introduction to GPU computing with CUDA aimed at scientific application programmers. The course will give a background on the difference between CPU and GPU architectures as a prelude to introductory exercises in CUDA programming. The course will discuss the execution of kernels, memory management, and shared memory operations. Common performance issues are discussed and their solution addressed. The course will also cover some of the alternatives to CUDA commonly available (OpenCL, OpenACC, and Kokkos) at the current time. A separate "Hackathon Day" will be available for attendees to try out their own problems (or a 'canned' extended example) with the help of staff from both EPCC and NVIDIA. Learning Outcomes At the end of the course, attendees should be in a position to make an informed decision on how to approach GPU parallelisation in their applications in an efficient and portable manner. Pre-requisites Attendees must be familiar with programming in C or C++ (a number of the baseline CUDA exercises are also available using CUDA Fortran). Some knowledge of parallel/threaded programming models would be useful. Access to a GPU machine will be supplied. Note: this course will not address machine learning or any machine learning frameworks. https://events.prace-ri.eu/event/1085/ 2020-11-23 10:00:00 UTC 2020-11-26 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • CABANA: Bioinformatics for plant biology

    30 November - 4 December 2020

    San Jose, Costa Rica

    Elixir node event
    CABANA: Bioinformatics for plant biology https://tess.elixir-europe.org/events/cabana-bioinformatics-for-plant-biology Please note this course will now be held in Costa Rica. It was previously due to run at EMBL-EBI in the UK. 2020-11-30 09:00:00 UTC 2020-12-04 17:00:00 UTC University of Costa Rica (UCR), San Jose, Costa Rica University of Costa Rica (UCR) San Jose Costa Rica CB10 1SD [] Marina Pujol [] [] [] [] HDRUK
  • CABANA: Bioinformatics for plant biology (Postponed until 2021)

    30 November - 4 December 2020

    San Jose, Costa Rica

    Elixir node event
    CABANA: Bioinformatics for plant biology (Postponed until 2021) https://tess.elixir-europe.org/events/cabana-bioinformatics-for-plant-biology-postponed-until-2021 This course was postponed from 2020. EMBL-EBI plans to deliver the majority of its 2021 events face-to-face with a small number of virtual events. Please note that some events that are currently listed as ‘on-site’ might need to be delivered virtually, depending on the prevailing status of the pandemic at the time. More courses will be added to this programme as our plans develop further. 2020-11-30 09:00:00 UTC 2020-12-04 17:00:00 UTC University of Costa Rica (UCR), San Jose, Costa Rica University of Costa Rica (UCR) San Jose Costa Rica [] Marina Pujol [] [] [] [] HDRUK
  • CABANA Workshop: Applied bioinformatics, molecular epidemiology, and the SARS-CoV-2 Pandemic

    1 - 4 December 2020

    Hinxton, United Kingdom

    Elixir node event
    CABANA Workshop: Applied bioinformatics, molecular epidemiology, and the SARS-CoV-2 Pandemic https://tess.elixir-europe.org/events/cabana-workshop-applied-bioinformatics-molecular-epidemiology-and-the-sars-cov-2-pandemic This workshop will provide training on the use of bioinformatic tools for the design and analysis of SARS-CoV-2 sequences. 2020-12-01 08:45:00 UTC 2020-12-04 12:00:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Piraveen Gopalasingam [] [] [] [] HDRUK
  • [ONLINE] Node-Level Performance Engineering @ LRZ

    2 - 4 December 2020

    [ONLINE] Node-Level Performance Engineering @ LRZ https://tess.elixir-europe.org/events/online-node-level-performance-engineering-lrz This online course covers performance engineering approaches on the compute node level. Even application developers who are fluent in OpenMP and MPI often lack a good grasp of how much performance could at best be achieved by their code. This is because parallelism takes us only half the way to good performance. Even worse, slow serial code tends to scale very well, hiding the fact that resources are wasted. This course conveys the required knowledge to develop a thorough understanding of the interactions between software and hardware. This process must start at the core, socket, and node level, where the code gets executed that does the actual computational work. We introduce the basic architectural features and bottlenecks of modern processors and compute nodes. Pipelining, SIMD, superscalarity, caches, memory interfaces, ccNUMA, etc., are covered. A cornerstone of node-level performance analysis is the Roofline model, which is introduced in due detail and applied to various examples from computational science. We also show how simple software tools can be used to acquire knowledge about the system, run code in a reproducible way, and validate hypotheses about resource consumption. Finally, once the architectural requirements of a code are understood and correlated with performance measurements, the potential benefit of code changes can often be predicted, replacing hope-for-the-best optimizations by a scientific process.   The course is a PRACE training event. Introduction Our approach to performance engineering Basic architecture of multicore systems: threads, cores, caches, sockets, memory The important role of system topology Tools: topology & affinity in multicore environments Overview likwid-topology and likwid-pin Microbenchmarking for architectural exploration Properties of data paths in the memory hierarchy Bottlenecks OpenMP barrier overhead Roofline model: basics Model assumptions and construction Simple examples Limitations of the Roofline model Pattern-based performance engineering Optimal use of parallel resources Single Instruction Multiple Data (SIMD) Cache-coherent Non-Uniform Memory Architecture (ccNUMA) Simultaneous Multi-Threading (SMT) Tools: hardware performance counters Why hardware performance counters? likwid-perfctr Validating performance models Roofline case studies Dense matrix-vector multiplication Sparse matrix-vector multiplication Jacobi (stencil) smoother Optional: The ECM performance model https://events.prace-ri.eu/event/1052/ 2020-12-02 08:00:00 UTC 2020-12-04 15:00:00 UTC [] [] [] workshops_and_courses [] []

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