Register event
31 events found

Content provider: PRACE  or de.NBI 

  • [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 [] []
  • Ontologies - statistics, biases, tools, networks, and interpretation

    26 - 29 October 2020

    Ontologies - statistics, biases, tools, networks, and interpretation https://tess.elixir-europe.org/events/ontologies-statistics-biases-tools-networks-and-interpretation Educators: Bálint Mészáros, Matt Rogon, Renato Alves (HD-HuB) Date: 26 - 29 October 9:00 - 12:30 Location: Online Meeting (connection details after registration) Content: Ontologies are the primary means to store biological data about genes, proteins, and other biological entities in an accessible and unambiguous way. These ontologies are hierarchical collections of descriptive terms, typically represented as networks (graphs), serving as a fundamental structure to store biological knowledge. The use of ontology-based enrichment and network representations to infer biological properties of gene and protein sets identified in experiments, is now ubiquitous. Consequently, a solid understanding and fluency in ontology-based approaches is an essential skill in a wide range of biological fields. Learning goals: During this 4-day online course participants will learn how to access and utilize biological ontologies (mainly Gene Ontology) to arrive at sound biological inferences using standard and customized enrichment analyses and network visualization. During the course you will learn how to: - access gene and pathway ontologies to build high-quality maps for data interpretation and visualisation; - customize query data as well as databases themselves to deal with a wide range of biases and produce reliable results using online tools, Cytoscape, and R packages; - explore Gene Ontology, KEGG and Reactome databases; - understand, utilize and create sub-ontologies to address specific biological questions by executing enrichment analyses; - Use R-based packages to automate, accelerate and create reproducible analyses; - be able to interpret and assess the quality of GeneOntology analyses in publications by understanding the strengths and limitations of enrichment calculations. After the course you will be able to independently extract data from public resources, assess their quality, annotate your own networks and biomolecules in Cytoscape, extract data using R, and critically interpret the results. Prerequisites: This course is an introduction to ontologies, however we require: - working knowledge of Cytoscape (e.g. introductory level course by Matt Rogon from EMBL CBNA https://git.embl.de/rogon/introduction-to-cytoscape-and-network-biology) - basic knowledge of R (data structures, file operations etc.) - e.g. introductory level course by EMBL CSDA (https://git.embl.de/klaus/tidyverse_R_intro) or EMBL Bio-IT (https://bio-it.embl.de/events/introduction-to-r/) Keywords: Ontologies ,statistics, biases, tools, networks, interpretation, R, Cytoscape 2020-10-26 09:00:00 UTC 2020-10-29 12:30:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • [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 [] []
  • 5th Differential analysis of quantitative proteomics data using R

    2 November 2020

    5th Differential analysis of quantitative proteomics data using R https://tess.elixir-europe.org/events/5th-differential-analysis-of-quantitative-proteomics-data-using-r Educators: Michael Turewicz (bioinformatician) and Karin Schork (biostatistician) (BioInfra.Prot) Date: Monday, 2nd Nov 2020 Location: Online Contents: This course will impart knowledge about how to conduct a differential analysis of high-throughput quantitative proteomics data using R. As we start with a basic introduction to the popular statistical programming language, no prior knowledge on R is required. The statistical background on utilized methods is explained in order to enable the participants to assess their own as well as published workflows critically. In this regard the course will touch upon • statistical inference: hypotheses, type I and II error • location tests (t-test) • multiple testing Learning goals: • Independent usage of basic R functions including - data import and export - basic plots - statistical tests • Deeper understanding of statistical methods applied in differential analyses Prerequisites: • Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; • No prior knowledge on R required • Computer with stable internet connection, headset and camera Keywords: R; high-throughput data; omics; proteomics; differential analysis Tools: download and more information on R here: https://cran.r-project.org/ We recommend using an editor such as RStudio, see www.rstudio.com 2020-11-02 09:00:00 UTC 2020-11-02 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • [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 [] []
  • [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 [] []
  • 2nd Advanced analysis of quantitative proteomics data using R

    9 November 2020

    2nd Advanced analysis of quantitative proteomics data using R https://tess.elixir-europe.org/events/2nd-advanced-analysis-of-quantitative-proteomics-data-using-r Educators: Michael Turewicz (bioinformatician) and Karin Schork (biostatistician) (BioInfra.Prot) Date: Monday, 9th Nov 2020 Location: Online Contents: In this course you will learn about using R for the analysis of proteomics data. We will focus on data preprocessing methods and advanced methods for data analysis. In this regard the cpurse will touch upon: • data normalization • quality control, handling of missing values • clustering, heatmaps • ROC-curves Please be aware that basic knowledge of R and methods for differential analysis of proteomics data are taught in our course “Differential analysis of quantitative proteomics data” the previous day (Monday, 2nd Nov 2020, http://goo.gl/forms/mpKHnbT1Um) Learning goals: • Independent usage of R functions for - Data preprocessing - Plots and graphs - Statistical methods for data analysis - Use of additional R packages • Deeper understanding of statistical methods applied in differential analyses Prerequisites: • Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; • Basic knowledge of R (e.g. data import, basic plots, t-test, for loop) and basic knowledge of differential analysis of proteomics data. Both can for example be gained from our course “Differential analysis of quantitative proteomics data” the previous day (Monday, 2nd Nov 2020, http://goo.gl/forms/mpKHnbT1Um). • Computer with stable internet connection, headset and camera Keywords: R; high-throughput data; omics; proteomics; data analysis, graphics, data preprocessing Tools: download and more information on R here: https://cran.r-project.org/ We recommend using an editor such as RStudio, see www.rstudio.com 2020-11-09 09:00:00 UTC 2020-11-09 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • [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 [] []
  • [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 [] []
  • de.NBI Crop Analysis Tool Suite (Part I) training course – Explore the barley genome

    16 November 2020

    de.NBI Crop Analysis Tool Suite (Part I) training course – Explore the barley genome https://tess.elixir-europe.org/events/de-nbi-crop-analysis-tool-suite-part-i-training-course-explore-the-barley-genome Educators: Uwe Scholz (GCBN), Sebastian Beier (GCBN) Date: 16th November 2020, 10:00 a.m. – 11:30 a.m. Location: Online Contents: Complex plant genomes impose high demands on analytical software and the knowledge of biologists to interpret these results. The service centre GCBN offers CATS (Crop Analysis Tool Suite), which provides various tools for sequence analysis. In this first of three courses the main focus is on the operation of the BLAST Server and the integration with BARLEX (Barley Genome Explorer). There will be two short presentations on the two topics and two online live demonstrations with examples. Together the whole training course will last about 90 minutes. Learning goals: The primary objective of this training course is to introduce tools for sequence analysis for crops (in particular barley). The theoretical basics as well as some examples will be shown by using online demonstrations, which will enable the participants to design and perform their own analyses. Prerequisites: The training course is designed for early career scientists such as PhD students and postdocs, but also for experienced scientists who want to learn more about the analysis and handling of sequence data for complex plant genomes like barley. Keywords: Sequence analysis, genomics, transcriptomics, annotation, Morex v2 assembly Tools: IPK WebBlast - https://webblast.ipk-gatersleben.de/barley_ibsc/ BARLEX - http://barlex.barleysequence.org/ 2020-11-16 10:00:00 UTC 2020-11-16 11:30:00 UTC de.NBI [] [] [] 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 [] []
  • de.NBI – e!DAL-PGP training course – Sharing and Publishing Comprehensive Plant Research Data

    19 November 2020

    de.NBI – e!DAL-PGP training course – Sharing and Publishing Comprehensive Plant Research Data https://tess.elixir-europe.org/events/de-nbi-e-dal-pgp-training-course-sharing-and-publishing-comprehensive-plant-research-data Educator: Daniel Arend (GCBN) Date: 19th November 2020, 10:00 a.m. – 11:30 a.m. Location: Online Contents: In the context of a growing global demand for food and feed the need for improved crop yield and the identification of more efficient and better adapted crops to answer the world's growing population is an important driving force for high-throughput plant genotyping and phenotyping studies which comprise comprehensive and data-intense experiments. As formulated in current funding policies, research data should be published under consideration of the FAIR (findable, accessible, interoperable, and reusable) data principles. Contrarily, they remain frequently unpublished due to organizational reasons or missing infrastructures. Therefore, the reproducibility and the preservation of research data depend on the scientists or the journal to which they want to publish their results. The eDAL-PGP repository provide a powerful infrastructure to easily share and publish comprehensive and cross-domain plant research data. Learning goals: The major goal of this trainings course is to get a general understanding how to publish plant research data that do not fit into the scope of existing databases in a FAIR way by using the eDAL-PGP repository. Prerequisites: The training course is designed for early career scientists such as PhD students and postdocs, but also for experienced scientists who want to learn more about the analysis and handling of sequence data for complex plant genomes like barley. Keywords: FAIR research data, Digital Object Identifier, Research Data Publication, Genomics, Phenomics Tools: e!DAL-PGP - http://edal-pgp.ipk-gatersleben.de/ 2020-11-19 10:00:00 UTC 2020-11-19 11:30:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • de.NBI Crop Analysis Tool Suite (Part II) training course – Working with repetitive sequences

    20 November 2020

    de.NBI Crop Analysis Tool Suite (Part II) training course – Working with repetitive sequences https://tess.elixir-europe.org/events/de-nbi-crop-analysis-tool-suite-part-ii-training-course-working-with-repetitive-sequences Educator: Sebastian Beier (GCBN) Date: 20th November 2020, 10:00 a.m. – 11:30 a.m. Location: Online Contents: Complex plant genomes impose high demands on analytical software and the knowledge of biologists to interpret these results. The service centre GCBN offers CATS (Crop Analysis Tool Suite), which provides various tools for sequence analysis. In this second of three courses the main focus is on the operation of repeat analysis and masking with the tools Kmasker plants (mathematically defined repeats) and MISA-Web (microsatellites). There will be two short presentations on the two topics and two online live demonstrations with examples. Together the whole training course will last about 90 minutes. Learning goals: The primary objective of this training course is to introduce tools for sequence analysis for crops. The theoretical basics as well as some examples will be shown by using online demonstrations, which will enable the participants to design and perform their own analyses. Prerequisites: The training course is designed for early career scientists such as PhD students and postdocs, but also for experienced scientists who want to learn more about the repeat analysis and masking of sequence data for complex plant genomes. Keywords: Microsatellite, Mathematically Defined Repeat, K-mer, SSR Tools: Kmasker Plants - https://kmasker.ipk-gatersleben.de/ MISA-Web - https://webblast.ipk-gatersleben.de/misa/ 2020-11-20 10:00:00 UTC 2020-11-20 11:30:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Introduction to the Cloud for Proteomics Analyses

    23 November 2020

    Introduction to the Cloud for Proteomics Analyses https://tess.elixir-europe.org/events/introduction-to-the-cloud-for-proteomics-analyses Educators: Dominik Kopczynski, Markus Stepath, Michael Turewicz and Julian Uszkoreit (BioInfra.Prot) Date: Monday, 2020-11-23 Location: online Contents: In this one day course we will show some of BioInfra.Prot's tools provided by de.NBI, namely “PIA - Protein Inference Algorithms”, “BIONDA – A Free Biomarker Database” and “CalibraCurve”. Besides the tool based sessions we offer a "Proteomics in the Cloud" session where we show advantages of cloud based bioinformatics and give a tutorial how to access the de.NBI cloud. PIA allows to inspect and combine the results of proteomics search engines. The main focus lays on the integrated inference algorithms for identification and quantification purposes. BIONDA is a free, up-to-date and user-friendly biomarker and biomarker candidate database that facilitates any kind of research on protein biomarkers and the corresponding diseases. CalibraCurve is a tool intended for the generation of calibration curves in the context of MRM (targeted proteomics) experiments. Such calibration curves are necessary for the selection of suitable transitions. In addition the web service STAMPS will be part of this course. It is a pathway-centric service for the development of targeted proteomics assays. In combination with Skyline, it offers a streamlined pipeline for identification and quantification in targeted proteomics analyses and development of targeted proteomics assays. Learning goals: Attendees of the course will learn how to use the tools PIA, BIONDA, CalibraCurve and STAMPS effectively for their daily proteomics tasks. Additionally they will learn how to use the de.NBI cloud. Prerequisites: This course is for all researches in the field of proteomics. The attendees should have basic knowledge of LC-MS proteomics, but no prior bioinformatics skills are required. Basic knowledge of how to analyse LC-MS data are sufficient. Attendees are required to bring their own laptops. If this is not possible or laptops have very low computing capacities, please contact the organizers. Keywords: Proteomics; Data Analysis; Assay Development; Biomarkers; de.NBI Cloud 2020-11-23 09:00:00 UTC 2020-11-23 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Applied Metaproteomics Workshop 2020

    23 - 27 November 2020

    Magdeburg, Germany

    Applied Metaproteomics Workshop 2020 https://tess.elixir-europe.org/events/applied-metaproteomics-workshop-2020 Educators: Dirk Benndorf, Stephan Fuchs, Robert Heyer, Kay Schallert (BiGi/MetaProtServ) Date: 23.11.2020 – 27.11.2020 Location: Magdeburg, Germany (Universitätsplatz 2, Building 28.205) Contents: Microbiome research is rapidly increasing. Meta-Omics data provide insights into microbial community influencing human health and biochemical cycle. Metaproteomics focusses on proteins representing the expressed genes and functions. In contrast to metagenomics or metatranscriptomics, the extraction and the analysis of proteins from human or environmental samples is challenging. The de.NBI course on Applied Metaproteomics trains the participants to apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Maximum 10 participants are strongly encouraged to analyze their own samples to start their own metaproteomics project. The workshop takes place at chair of bioprocess engineering at Otto-von-Guericke University Magdeburg. The team of microbial communities head by Dr. Dirk Benndorf is well experienced in metaproteomics. The samples will be measured on newly purchased timsTOF Pro MS. His group devellopes the MetaProteomAnalyzer service facilitating the analysis of of metaproteomic data. The provision of service is supported by the German Network for Bioinformatics Infrastructure - de.NBI. Monday 09:00-10:00 Arrival 10:00-11:00 Introduction to metaproteomics (lecture: Dirk Benndorf) 11:00-12:00 Design of experiments and sample preparation (lecture: Robert Heyer) 12:00-13:00 Lunch 13:00-18:00 Sample preparation I (protein extraction, protein quantification: Robert Heyer) during the afternoon short presentations of participant´s about their samples (each participant max. 10 min) Tuesday 08:00-11:00 Sample preparation II (FASP digest, SDS-PAGE: Robert Heyer) 11:00-13:00 Introduction to high resolution mass spectrometry (lecture: Dirk Benndorf) 13:00-14:00 Lunch 13:00-14:00 Sample preparation II (peptide extraction: Robert Heyer) 14:00-16:00 Introduction to the MPA 2.0 (lecture: Kay Schallert) non-stop: measurement of participant’s samples I Wednesday non-stop: measurement of participant’s samples I: Dirk Benndorf, Patrick Hellwig 09:00-11:00 MPA 2.0 exercise I (working with a small reference dataset, db searching, metaprotein concept: Kay Schallert, Robert Heyer) 11:00-13:00 MPA 2.0 exercise II (loading user db, BLAST search of unknown hits, quantitative comparison of datasets, visualization and data export: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Prophane workflow (lecture and training: Stefan Fuchs, external speaker) Thursday 09:00-13:00 MPA 2.0 exercise III (analyzing own data: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Training at MS (calibration, setup of LC-MS methods, solvent exchange, trouble shooting, Patrick Hellwig) Friday 08:00-10:00 MPA 2.0 exercise IV (visualization of data: Robert Heyer) 10:00-12:00 Individual discussion of results and preparation of presentations (Dirk Benndorf, Robert Heyer, Kay Schallert) 12:00-13:00 Short presentations of participant‘s results and conclusion 13:00 Lunch and departure Learning goals: To apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Prerequisites: Fee: 30 € Keywords: Microbiome, MPA, Metaproteomics, MetaProteomeAnalyzer, Tools: MetaproteomeAnalyzer 2020-11-23 09:00:00 UTC 2020-11-27 17:00:00 UTC de.NBI Magdeburg, Magdeburg, Germany Magdeburg Magdeburg Germany [] [] [] workshops_and_courses [] []
  • 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 [] []
  • de.NBI Crop Analysis Tool Suite (Part III) training course – Explore barley diversity

    24 November 2020

    de.NBI Crop Analysis Tool Suite (Part III) training course – Explore barley diversity https://tess.elixir-europe.org/events/de-nbi-crop-analysis-tool-suite-part-iii-training-course-explore-barley-diversity Educator: Patrick König (GCBN) Date: 24th November 2020, 10:00 a.m. – 11:30 a.m. Location: Online Contents: The service centre GCBN offers CATS (Crop Analysis Tool Suite), which includes a web application for exploratory data analysis of the genomic diversity data derived from studies based on the concept of gene bank genomics. The concept of gene bank genomics is about to gain insight into the diversity of genetic resources stored in gene banks and to allow the utilisation of this mainly untapped diversity for breeding and further research and exploitation. BRIDGE is an interactive web tool for exploratory data analysis of a gene bank genomics study of more than 20,000 barley accessions. The tool helps researchers and breeders to keep the overview about the massive amount of data and to derive a benefit from diversity data through context-based data visualisation and data export. Learning goals: The goal of this training course is to provide an introduction into the BRIDGE web application, its available data domains and its use for data visualisation, exploratory data analysis and data export for different use cases of specific research interests. Prerequisites: The training course is aimed at young scientists such as PhD students and postdocs, but also at experienced scientists who want to learn more about exploratory data analysis, visualization and exploitation of plant diversity data for use in breeding and research. Keywords: Barley, Gene bank genomics, Exploratory data analysis, Visual analytics, Data visualisation, Data warehouse, Tools: BRIDGE (https://doi.org/10.3389/fpls.2020.00701 2020-11-24 10:00:00 UTC 2020-11-24 11:30:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • de.NBI - CeBiTec Nanopore Workshop 2020 - Best Practice and SARS-CoV-2 applications

    30 November - 4 December 2020

    de.NBI - CeBiTec Nanopore Workshop 2020 - Best Practice and SARS-CoV-2 applications https://tess.elixir-europe.org/events/de-nbi-cebitec-nanopore-workshop-2020-best-practice-and-sars-cov-2-applications Educators: Stefan Albaum, Jan-Simon Baasner, Sebastian Jünemann, Nils Kleinbölting, Alexander Sczyrba, Alex Walender (BiGi), Daniel Wibberg (CAU), David Brandt, Christian Rückert, Jörn Kalinowski (CeBiTec) Date: 30 November – 4 December 2020 Location: Online Content: Aim of this workshop is to familiarize the participants with the Nanopore sequencing technology, its applications, the "Best Practice" bioinformatics workflows and the analysis of SARS-CoV-2 genomes. The Nanopore technology has greatly facilitated the assembly of prokaryotic, viral and eukaryotic genomes. Therefore, the workshop is focused on the establishment of finalized genome sequences, ranging from basecalling, quality assessment over assembly to sequence polishing and finally assembly evaluation. A focus in this years workshop is on the analysis of Nanopore sequenced SARS-CoV-2 genomes and a suitable workflow for resequencing based on the ARTIC bioinformatics protocol. The course will start with a one day webinar on best practices for the lab work on sequencing SARS-CoV2 and a “guided tour” showing the necessary bioinformatics steps. This part of the workshop is open to a large number of applicants. The following 4 days will be a mixture of talks and practical sessions in the de.NBI cloud introducing, in more detail, the Nanopore sequencing technology and bioinformatics processing tools, as, for instance, base calling, assembly and polishing.This part of the workshop is, however, limited to a smaller number of applicants. Learning goals: This workshop aims to teach basic skills and best practices to researchers working with Nanopore data, e.g. SARS-CoV-2. The full course will include all necessary steps from raw sequencing data to finalized genomes (1) with a de novo assembly and (2) with re-sequencing and mapping to a reference. Prerequisites: This workshop is intended for PhD students and postdocs with molecular biology background in genomics or SARS-CoV2 background. Good understanding of command line tools is a plus, but not required. Tools: minimap2, canu, pilon, guppy, porechop, medaka, poretools, nextstrain, quast, ARTIC pipeline Keywords: Nanopore sequencing, genome assembly, genomics, SARS-CoV2, 2020-11-30 09:00:00 UTC 2020-12-04 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • [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 [] []
  • [ONLINE] GPU Programming with CUDA @ JSC

    7 - 11 December 2020

    [ONLINE] GPU Programming with CUDA @ JSC https://tess.elixir-europe.org/events/online-gpu-programming-with-cuda-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 an NVIDIA GPU. The course will cover basic aspects of GPU architectures and programming. Focus is on the usage of the parallel programming language CUDA-C which allows maximum control of NVIDIA GPU hardware. 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 CUDA GPU libraries like CuBLAS and CuFFT Tools for debugging and profiling Performance optimizations Prerequisites: Some knowledge about Linux, e.g. make, command line editor, Linux shell, experience in C/C++ Dates: 7-11 December 2020, 09:00-13:00 each day Application Registrations are only considered until 30November 2020, the maximal number of participants is limited. Applicants will be notified, whether they are accepted for participitation. Instructors: Dr. Jan Meinke, Jochen Kreutz, Dr. Andreas Herten, JSC; Jiri Kraus, Markus Hrywniak, NVIDIA Contact For any questions concerning the course please send an e-mail to j.meinke@fz-juelich.de https://events.prace-ri.eu/event/1083/ 2020-12-07 08:00:00 UTC 2020-12-11 12:00:00 UTC [] [] [] workshops_and_courses [] []
  • Data visualization using R

    7 December 2020

    Data visualization using R https://tess.elixir-europe.org/events/data-visualization-using-r Educators: Markus Stepath, Karin Schork, Nils Hoffmann (BioInfra.Prot / LIFS) Date: Monday, 7th Dec 2020 Location: Online training Contents: In this course you will learn how to use the ggplot2 package in R to create informative and beautiful figures to communicate your omics data and analysis results. We will cover the following topics: - Usage of the tidyverse for data preprocessing - Usage of the ggplot2 R package - Presentation of different types of graphics and when to use them - Customization of graphics Please be aware that basic knowledge of R is taught in our course “Differential analysis of quantitative proteomics data” on Monday, 2nd Nov 2020 (http://goo.gl/forms/mpKHnbT1Um). Learning goals: - Using the ggplot2 R package to create graphics for omics data - Decide which type of graph is appropriate for the given data - Ability to costumize the graphics using ggplot2 Prerequisites: - Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; - Basic knowledge of R (e.g. data import, basic plots. This can for example be gained from our course “Differential analysis of quantitative proteomics data” (Monday, 2nd Nov 2020, http://goo.gl/forms/mpKHnbT1Um). - Computer with stable internet connection, headset and camera Keywords: R; tidyverse; ggplot2; high-throughput data; omics; proteomics; data analysis, graphics, data preprocessing Tools: Download and more information on R here: https://cran.r-project.org/ We recommend using an editor such as RStudio, see www.rstudio.com 2020-12-07 09:00:00 UTC 2020-12-07 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • [ONLINE] CUDA 4 Dummies @ VSC Vienna

    10 - 11 December 2020

    [ONLINE] CUDA 4 Dummies @ VSC Vienna https://tess.elixir-europe.org/events/online-cuda-4-dummies-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. The HANDS-ON LABS will be done on VSC-3, all participants will get a training user account at the VSC for the duration of the course. Overview CUDA is the standard API for code development targeting the GPU and a number of impressive examples have already been given in diverse areas from particle physics to computational biology. CUDA allows simple extensions of standard C/C++/Fortran code with GPU-specific functions. In this way thousands of cores available on the GPU can be leveraged to work in parallel and thus carry out significant fractions of the computational workload on the device rather than the CPU. There is also a vast set of auxiliary tools available to the developer including libraries, code templates, building blocks, analysis tools, developmental frameworks and in general a vivid community making up the CUDA Developer Zone. It is often for this multifaceted support environment that the interested beginner is feeling overwhelmed and unsettled about which particular first steps should best be taken to gain a straightforward introduction into the subject. For exactly this reason the present course is offering a systematic step-by-step introduction into GPU computing from the perspective of the newcomer. Basic design principles will be established, central programming techniques acquired and a number of state-of-the-art workflows examined that efficiently employ the GPU and are frequently used in scientific computing. This course provides lectures, demos, and hands-on labs. This course is a PRACE training event. It is organized by the VSC Research Center, TU Wien. Agenda & Content (tentative) 1st day – 10 December 2020 Basic design principles, getting started with simple CUDA routines, mastering the CUDA environment; Memory Hierarchy with a focus on CUDA managed unified memory; Practical exercise: all the pitfalls one can run into when porting a dummy code to CUDA. 08:45 - 09:00    join online 09:00 - 13:00    lectures and hands-on labs (with breaks: 11:00-11:15) 13:00 - 14:00    lunch break 14:00 - 17:00    lectures and hands-on labs (with breaks: 15:15-15:30) 2nd day – 11 December 2020 Selected examples to demonstrate CUDA capabilities and GPU operation, e.g., bandwidthTest, simpleAssert, simpleStreams, etc.; CUDA libraries, CUBLAS, CUSolver, considering numerical precision, gaining insight into the runtime; Practical exercise: CUDA in everyday life (of a scientist). 08:45 - 09:00    join online 09:00 - 13:00    lectures and hands-on labs (with breaks: 11:00-11:15) 13:00 - 14:00    lunch break 14:00 - 17:00    lectures and hands-on labs (with breaks: 15:15-15:30) https://events.prace-ri.eu/event/1078/ 2020-12-10 07:45:00 UTC 2020-12-11 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] Practical Deep Learning @ CSC

    17 - 18 December 2020

    [ONLINE] Practical Deep Learning @ CSC https://tess.elixir-europe.org/events/online-practical-deep-learning-csc This course will be delivered as an ONLINE EVENT for remote participation due to the COVID-19 measures enforced by most European governments. Description This course gives a practical introduction to deep learning, convolutional and recurrent neural networks, GPU computing, and tools to train and apply deep neural networks for natural language processing, images, and other applications. The course consists of lectures and hands-on exercises. TensorFlow 2, Keras, and PyTorch  will be used in the exercise sessions. CSC's Notebooks environment will be used on the first day of the course, and the GPU-accelerated Puhti supercomputer on the second day. Learning outcome After the course the participants should have the skills and knowledge needed to begin applying deep learning for different tasks and utilizing the GPU resources available at CSC for training and deploying their own neural networks. Prerequisites The participants are assumed to have working knowledge of Python and suitable background in data analysis, machine learning, or a related field. Previous experience in deep learning is not required, but the fundamentals of machine learning are not covered on this course.  Basic knowledge of a Linux/Unix environment will be assumed. Agenda (tentative) Day 1, Thursday 17.12    09.00 – 11.00 Introduction to deep learning and to Notebooks    11.00 – 12.00 Multi-layer perceptrons                12:00 - 13:00  Lunch    13.00 – 14.30 Image data and convolutional neural networks    14.30 – 16.00 Text data and recurrent neural networks Day 2, Friday 18.12    09.00 – 10.30 Deep learning frameworks, GPUs, batch jobs    10.30 – 12.00 Image classification exercises                12:00 - 13:00  Lunch    13.00 – 14.30 Attention and text categorization exercises    14.30 – 16.00 Cloud, using multiple GPUs Lecturers:  Markus Koskela (CSC),  Mats Sjöberg (CSC) Language:  English Price:           Free of charge (2 training days) REGISTRATION is OBLIGATORY since the details to access the online course will be provided to the registered and accepted attendees only. If you have registered to this course and you are not able to attend, please CANCEL your registration in advance by sending an email to patc@csc.fi https://events.prace-ri.eu/event/1087/ 2020-12-17 07:00:00 UTC 2020-12-18 14:00:00 UTC [] [] [] workshops_and_courses [] []
  • [FORMAT TBD] Programming Distributed Computing Platforms with COMPSs @ BSC

    26 - 27 January 2021

    [FORMAT TBD] Programming Distributed Computing Platforms with COMPSs @ BSC https://tess.elixir-europe.org/events/format-tbd-programming-distributed-computing-platforms-with-compss-bsc Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course convener: Rosa Badia, Workflows and Distributed Computing Group Manager, Computer Sciences - Workflows and Distributed Computing Department Lecturers:  Rosa M Badia, Workflows and Distributed Computing Group Manager, Computer Sciences - Workflows and Distributed Computing Department, BSC Javier Conejero, Senior Researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Jorge Ejarque, Researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Daniele Lezzi, Senior Researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Objectives: The objective of this course is to give an overview of the COMPSs programming model, which is able to exploit the inherent concurrency of sequential applications and execute them in a transparent manner to the application developer in distributed computing platform. This is achieved by annotating part of the code as tasks, and building at execution a task-dependence graph based on the actual data used consumed/produced by the tasks. The COMPSs runtime is able to schedule the tasks in the computing nodes and take into account facts like data locality and the different nature of the computing nodes in case of heterogeneous platforms. Additionally, recently COMPSs has been enhanced with the possibility of coordinating Web Services as part of the applications. COMPSs supports Java, C/C++ and Python as programming languages. Learning Outcomes:  In the course, the COMPSs syntax, programming methodology and an overview of the runtime internals will be given. The attendees will get a first lesson about programming with COMPSs that will enable them to start programming with this framework. A hands-on with simple introductory exercises will be also performed. The students who finish this course will be able to develop simple COMPSs applications and to run them both in a local resource and in a distributed platform (initially in a private cloud). The exercises will be delivered in Python and Java. In case of Python, Jupyter notebooks will be used in some of the exercises. Level: for trainees with some theoretical and practical knowledge. INTERMEDIATE: for trainees with some theoretical and practical knowledge; those who finished the beginners course ADVANCED: for trainees able to work independently and requiring guidance for solving complex problems Prerequisites: Programming skills in Java and Python  Agenda:  Day 1 (January 26th, 2021) 9:30 - 10:00 - Welcome and round table (30') 10:00 - 10:30 - Session 1: Introduction to COMPSs (30') 10:30 - 11:15 - Session 2: PyCOMPSs: Writing Python applications (45') 11:15 - 11:45 - Coffee break 11:45 - 13:00 - Session 3: Python Hands-on using Jupyter notebooks (1h15') 13:00 - 14:30 - Lunch break 14:30 - 15:00 - Session 4: Machine learning with dislib (30') 15:00 - 16:30 - Session 5: Hands-on with dislib (1h30') Day 2 (January 27th, 2021) 9:30 - 11:00 - Session 6: Java & C++ (1h30') 11:00 - 11:30 - Cofee break 11:30 - 13:00 - Session 7: COMPSs Advanced Features (1h30') 13:00 - 14:30 - Lunch break 14:30 - 16:30 - Session 8: Cluster Hands-on (MareNostrum) (2h) 16:30 - 16:45 - Session 9: COMPSs Installation & Final Notes (15') END of COURSE https://events.prace-ri.eu/event/1054/ 2021-01-26 08:30:00 UTC 2021-01-27 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • [FORMAT TBD] Managing distributed data with Hecuba and dataClay @ BSC

    28 January 2021

    [FORMAT TBD] Managing distributed data with Hecuba and dataClay @ BSC https://tess.elixir-europe.org/events/format-tbd-managing-distributed-data-with-hecuba-and-dataclay-bsc Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course conveners: Department and Research group: Computer Science - Workflows and Distributed Computing Yolanda Becerra, Data-driven Scientific Computing research line, Senior researcher Anna Queralt, Distributed Object Management research line, Senior researcher Course Lecturers: Department and Research group: Computer Sciences - Workflows and Distributed Computing Alex Barceló, Distributed object Management research line, Researcher Yolanda Becerra, Data-driven Scientific Computing research line, Senior researcher Adrián Espejo, Data-driven Scientific Computing research line, Junior research engineer Daniel Gasull, Distributed object Management research line, Research engineer Pol Santamaria, Data-driven Scientific Computing research line, Junior developer Anna Queralt, Distributed object Management research line, Senior researcher Objectives: The objective of this course is to give an overview of BSC storage solutions, Hecuba and dataClay. These two platforms allow to easily store and manipulate distributed data from object-oriented applications, enabling programmers to handle object persistence using the same classes they use in their programs, thus avoiding time consuming transformations between persistent and non-persistent data models. Also, Hecuba and dataClay enable programmers to transparently manage distributed data, without worrying about its location. This is achieved by adding a minimal set of annotations in the classes. Both Hecuba and dataClay can work independently or integrated with the COMPSs programming model and runtime to facilitate parallelization of applications that handle persistent data, thus providing a comprehensive mechanism that enables the efficient usage of persistent storage solutions from distributed programming environments. Both platforms offer a common interface to the application developer that facilitates using one solution or the other depending on the needs, without changing the application code. Also, both of them have additional features that allow the programmer to take advantage of their particularities. Learning Outcomes:   In the course, the Hecuba and dataClay syntax, programming methodology and an overview of their internals will be given. Also, an overview of COMPSs at user level will be provided in order to take advantage of the distribution of data with both platforms. The attendees will get a first lesson about programming with the common storage interface that will enable them to start programming with both frameworks. A hands-on with simple introductory exercises will be also performed for each platform, with and without COMPSs to distribute the computation. The students who finish this course will be able to develop simple Hecuba and dataClay applications and to run them both in a local resource and in a distributed platform (initially in a private cloud) Prerequisites: Basic programming skills in Python and Java. Previous attendance to PATC course on programming distributed systems with COMPSs is recommended.   Tentative Agenda (TBC):  Day 1 (Jan 28th, 2021) Session 1 / 9:30 – 13:00 9:30-10:00 Round table. Presentation and background of participants 10:00-11:00 Motivation, introduction and syntax of BSC storage platforms 11:00-11:30 Coffee break 11:30-12:15 Hands-on with storage API 12:15-13:00 COMPSs overview and how to parallelize a sequential application 13:00-14:30 Lunch break Session 2/ 14:30 – 18:00 14:30-16:00 Hecuba specifics and hands-on 16:00-16:30 Break 16:30-18:00 dataClay specifics and hands-on END of COURSE       https://events.prace-ri.eu/event/1055/ 2021-01-28 08:30:00 UTC 2021-01-28 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] OpenMP Programming Workshop @ LRZ

    17 - 19 February 2021

    [ONLINE] OpenMP Programming Workshop @ LRZ https://tess.elixir-europe.org/events/online-openmp-programming-workshop-lrz With the increasing prevalence of multicore processors, shared-memory programming models are essential. OpenMP is a popular, portable, widely supported, and easy-to-use shared-memory model. Since its advent in 1997, the OpenMP programming model has proved to be a key driver behind parallel programming for shared-memory architectures.  Its powerful and flexible programming model has allowed researchers from various domains to enable parallelism in their applications.  Over the more than two decades of its existence, OpenMP has tracked the evolution of hardware and the complexities of software to ensure that it stays as relevant to today’s high performance computing community as it was in 1997. This workshop will cover a wide range of  topics, reaching from the basics of OpenMP programming using the "OpenMP Common Core" to really advanced topics. During each day lectures will be mixed with hands-on sessions. Day 1 The first day will cover basic parallel programming with OpenMP. Most OpenMP programmers use only around 21 items from the specification. We call these the “OpenMP Common Core”. By focusing on the common core on the first day, we make OpenMP what it was always meant to be: a simple API for parallel application programmers. In this hands-on tutorial, students use active learning through a carefully selected set of exercises, to master the Common Core and learn to apply it to their own problems. Day 2 and 3 Day 2 and 3 will cover advanced topics like: Mastering Tasking with OpenMP, Taskloops, Dependencies and Cancellation Host Performance: SIMD / Vectorization Host Performance: NUMA Aware Programming, Memory Access, Task Affinity, Memory Management Tool Support for Performance and Correctness, VI-HPS Tools Offloading to Accelerators Other Advanced Features of OpenMP 5.0 Future Roadmap of OpenMP Developers usually find OpenMP easy to learn. However, they are often disappointed with the performance and scalability of the resulting code. This disappointment stems not from shortcomings of OpenMP but rather with the lack of depth with which it is employed. The lectures on Day 2 and Day 3 will address this critical need by exploring the implications of possible OpenMP parallelization strategies, both in terms of correctness and performance. We cover tasking with OpenMP and host performance, putting a focus on performance aspects, such as data and thread locality on NUMA architectures, false sharing, and exploitation of vector units. Also tools for performance and correctness will be presented. Current trends in hardware bring co-processors such as GPUs into the fold. A modern platform is often a heterogeneous system with CPU cores, GPU cores, and other specialized accelerators. OpenMP has responded by adding directives that map code and data onto a device, the target directives. We will also explore these directives as they apply to programming GPUs. OpenMP 5.0 features will be highlighted and the future roadmap of OpenMP will be presented. All topics are accompanied with extensive case studies and we discuss the corresponding language features in-depth. Topics might be still subject to change. For the hands-on sessions participants need to use their own laptops or systems with a C/C++ or Fortran compiler supporting at least OpenMP 4.5 installed (see https://www.openmp.org/resources/openmp-compilers-tools/). The course is organized as a PRACE training event by LRZ in collaboration with the OpenMP ARB and RWTH Aachen. Lecturers Dr. Michael Klemm holds an M.Sc.  and a Doctor of Engineering degree from the Friedrich-Alexander-University Erlangen-Nuremberg, Germany.  His areas of interest include compiler construction, design of programming languages, parallel programming, and performance analysis and tuning.  Michael Klemm joined the OpenMP organization in 2009 and was appointed CEO of the OpenMP ARB in 2016. Dr. Christian Terboven is a senior scientist and leads the HPC group at RWTH Aachen University. His research interests center around Parallel Programming and related Software Engineering aspects. Dr. Terboven has been involved in the Analysis, Tuning and Parallelization of several large-scale simulation codes for various architectures. He is responsible for several research projects in the area of programming models and approaches to improve the productivity and efficiency of modern HPC systems. He is further co-author of the new book “Using OpenMP – The Next Step“, https://www.openmp.org/tech/using-openmp-next-step/ https://events.prace-ri.eu/event/1084/ 2021-02-17 09:00:00 UTC 2021-02-19 16:00:00 UTC [] [] [] workshops_and_courses [] []

Note, this map only displays events that have geolocation information in TeSS.
For the complete list of events in TeSS, click the grid tab.