Register event
54 events found

Content provider: VIB Bioinformatics Core  or PRACE 

  • Basic statistics in R, Ghent

    15 - 29 January 2019

    Ghent, Belgium

    Elixir node event
    Basic statistics in R, Ghent https://tess.elixir-europe.org/events/basic-statistics-in-r-ghent b'\nGet an idea of what R and Rstudio is\r\nUse R to handle data: creating, reading, reformatting and writing data\r\nUse R to create graphics\r\nUse basic statistical techniques in R : normality tests, t-tests, wilcoxon tests, chi square tests, correlations, survival analysis...\r\nWrite and use R scripts\n\r\n\n \nThis training gives an introduction to the use of the statistical software language R. R is a language for data analysis and graphics. This introduction to R is aimed at beginners. The training covers data handling, graphics, and basic statistical techniques. \r\nR is for free and for more information you can visit the site the CRAN web site.This training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents). A full overview of statistical analyses in R including regression, ANOVA will be given in the follow-up training Basic statistics in R, part II.\n\r\n \r\nRequirements\r\nThe training is intended for people who have no experience with R. However, understanding of basic statistical concepts is required, such as data types, normal distribution, descriptive statistics, tests for comparing groups... If you don\'t have sufficient statistical background you are strongly encouraged to attend the Basic statistics theorytraining. \r\nThis training is recommended for people with no experience in R who are planning to follow a training that requires some R background, like the mass spectrometry , the single cell RNA-Seq and the bulk RNA-Seq training....\n\r\n\n' 2019-01-15 09:30:00 UTC 2019-01-29 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Ghent, Belgium Bio-Accelerator Ghent Belgium 9052 [] [] [] [] [] []
  • 30th VI-HPS Tuning Workshop @ BSC

    21 - 25 January 2019

    30th VI-HPS Tuning Workshop @ BSC https://tess.elixir-europe.org/events/30th-vi-hps-tuning-workshop Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course convener:  Judit Gimenez, Tools Group Manager, Computer Sciences - Performance Tools, BSC Lecturers: List of lecturers to be confirmed. Additionally to BSC,  we have instructor commitments from MAQAO, Scalasca/Score-P, Vampir and TAU Objectives:  VI-HPS Tuning Workshops are the major training vehicle where around 30 participants receive instruction and guidance to become familiar with VI-HPS programming tools suite. During the training, we will explain the functionality of each tool and how they can be used. We will also give them hands-on assistance on how to apply VI-HPS tools to their own parallel application codes, along with advice for potential corrections and optimizations. Additionally, feedback to tools developers helps direct tools development to user needs, as well as improve tool documentation and ease of use. Learning Outcomes:  Understand common performance analysis and diagnosis techniques and how they can be employed in practice Make sense of the functionality of individual tools, and how to use them effectively Apply VI-HPS tools to their own parallel application codes Optimize their own codes thanks to the coaching of how to tune their measurement and analysis Level:  Basic knowledge on parallel programming. Attendees have to bring an application that can use on the hands-on. They need to have the source code and install it in the BSC machine. Agenda: Day 1: Monday 21 January 09:00 Welcome Introduction to VI-HPS & overview of tools [Judit Giménez, BSC] Introduction to parallel performance engineering Lab setup Computer systems and software environment [BSC] Building and running codes on MareNostrum-IV and CTE-POWER9 10:45 (break) 11:15 Paraver tracing tools suite [Judit Giménez, BSC] Paraver hands-on exercises 13:00 (lunch) 14:00 Hands-on coaching to apply tools to analyze participants' own code(s). 17:00 Review of day and schedule for remainder of workshop 17:30 (adjourn)   Day 2: Tuesday 22 January 09:00 Score-P instrumentation & measurement [Michael Knobloch, JSC] Score-P hands-on exercises CUBE profile explorer hands-on exercises [Michael Knobloch, JSC] Score-P analysis scoring & filtering   [Michael Knobloch, JSC] Measuring hardware counters and other metrics   10:45 (break)   11:15 TAU performance system [Sameer Shende, UOregon] TAU hands-on exercises 13:00 (lunch) 14:00 Hands-on coaching to apply tools to analyze participants' own code(s). 17:00 Review of day and schedule for remainder of workshop 17:30 (adjourn)   Day 3: Wednesday 23 January 09:00 Scalasca automated trace analysis [Michael Knobloch, JSC] Scalasca hands-on exercises 10:45 (break) 11:15 Extra-P automated scaling analysis [Alexandru Calotoiu, TUDarmstadt] Extra-P hands-on exercises 13:00 (lunch) 14:00 Hands-on coaching to apply tools to analyze participants' own code(s). 17:00 Review of day and schedule for remainder of workshop 17:30 (adjourn)   Day 4: Thursday 24 January 09:00 Vampir interactive trace analysis [Holger Brunst, TUDresden] Vampir hands-on exercises 10:45 (break) 11:15 MUST & ARCHER correctness checking of MPI usage & OpenMP [Joachim Protze & Simon Schwitanski, RWTH] MUST & ARCHER hands-on exercises 13:00 (lunch) 14:00 Hands-on coaching to apply tools to analyze participants' own code(s). 17:00 Review of day and schedule for remainder of workshop 17:30 (adjourn)   Day 5: Friday 25 January 09:00 MAQAO x86 performance analysis tools [Emmanuel Oseret & Cedric Valensi, UVSQ] MAQAO hands-on exercises 10:45 (break) 11:15 Intel Advisor and Roofline model [Egor Kazachkov, Intel] 12:30 Review of workshop 13:00 (lunch) 14:00 Hands-on coaching to apply tools to analyze participants' own code(s). 17:00 (adjourn)   https://events.prace-ri.eu/event/803/ 2019-01-21 08:30:00 UTC 2019-01-25 16:30:00 UTC [] [] [] workshops_and_courses [] []
  • Python in High-Performance Computing @ CSC

    23 - 25 January 2019

    Python in High-Performance Computing @ CSC https://tess.elixir-europe.org/events/python-in-high-performance-computing-csc-8f13c25c-4980-4639-8034-2e2a7c78d8d9 Thank you to those of you who have already registered for our "Python in High-Performance Computing @ CSC" training course! The course is now FULLY BOOKED! Due to the popularity of the Python course we are now operating a limited waiting list, 10 persons max. So, 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 at csc.fi. If you wish to be added to the waiting list please contact to patc at csc.fi. You will be notified via e-mail of your position on the waiting list. We will keep you further informed of whether you are enrolled into the course or not. Please note that the waiting list is handled on a first come/first serve basis. Welcome to the course! Description Python programming language has become popular in scientific computing due to many benefits it offers for fast code development. Unfortunately, the performance of pure Python programs is often sub-optimal, but fortunately this can be easily remedied. In this course we teach various ways to optimise and parallelise Python programs. Among the topics are performance analysis, efficient use of NumPy arrays, extending Python with more efficient languages (Cython), and parallel computing with  message passing (mpi4py) approach. Learning outcome After the course participants are able to analyse performance of Python program and use NumPy more efficiently optimize Python programs with Cython utilize external libraries in Python programs write simple parallel programs with Python Prerequisites Participants need some experience in Python programming, but expertise is not required. One should be familiar with Python syntax Basic builtin datastructures (lists, tuples, dictionaries) Control structures (if-else, for, while) Writing functions and modules Some previous experience on NumPy will be useful, but not strictly required. Agenda Day 1, Wednesday 23.1 Efficient use of NumPy Performance analysis Day 2, Thursday 24.1 Optimisation with Cython Interfacing with external libraries Day 3, Friday 25.1 Parallel computing with mpi4py Lecturers:  Jussi Enkovaara (CSC), Martti Louhivuori (CSC) Language:   English Price:          Free of charge https://events.prace-ri.eu/event/806/ 2019-01-23 07:00:00 UTC 2019-01-25 14:00:00 UTC [] [] [] workshops_and_courses [] []
  • VIB Interest Group Meeting - containers and workflows

    25 January 2019

    Gent, Belgium

    Elixir node event
    VIB Interest Group Meeting - containers and workflows https://tess.elixir-europe.org/events/vib-interest-group-meeting-containers-and-workflows 2019-01-25 09:30:00 UTC 2019-01-25 16:30:00 UTC VIB Bioinformatics Core Clemenspoort - zaal Seelos, Gent, Belgium Clemenspoort - zaal Seelos Gent Belgium 9000 [] [] [] [] [] []
  • Introduction to Hybrid Programming in HPC @ LRZ

    28 - 29 January 2019

    Introduction to Hybrid Programming in HPC @ LRZ https://tess.elixir-europe.org/events/introduction-to-hybrid-programming-in-hpc-lrz-112b005c-321c-495b-be52-91b7f62fe4a4 Overview Most HPC systems are clusters of shared memory nodes. Such SMP nodes can be small multi-core CPUs up to large many-core CPUs. Parallel programming may combine the distributed memory parallelization on the node interconnect (e.g., with MPI) with the shared memory parallelization inside of each node (e.g., with OpenMP or MPI-3.0 shared memory). This course analyzes the strengths and weaknesses of several parallel programming models on clusters of SMP nodes. Multi-socket-multi-core systems in highly parallel environments are given special consideration. MPI-3.0 has introduced a new shared memory programming interface, which can be combined with inter-node MPI communication. It can be used for direct neighbor accesses similar to OpenMP or for direct halo copies, and enables new hybrid programming models. These models are compared with various hybrid MPI+OpenMP approaches and pure MPI. Numerous case studies and micro-benchmarks demonstrate the performance-related aspects of hybrid programming. Hands-on sessions are included on both days. Tools for hybrid programming such as thread/process placement support and performance analysis are presented in a "how-to" section. This course provides scientific training in Computational Science, and in addition, the scientific exchange of the participants among themselves. The course is a PRACE Advanced Training Center event. It is organized by LRZ in cooperation with HLRS, RRZE, and VSC (Vienna Scientific Cluster). Agenda & Content (preliminary) 1st day 09:30 Registration 10:00 Welcome 10:05 Motivation 10:15 Introduction 10:45 Programming Models            - Pure MPI 11:15 Coffee Break 11:35  - Topology Optimization 12:00    Practical (application aware Cartesian topology) 13:00 Lunch 14:00  - MPI + MPI-3.0 Shared memory 14:45    Practical (replicated data) 15:30 Coffee Break 15:50  - MPI Memory Models and Synchronization 16:50    Practical (substituting pt-to-pt by shared memory) 17:30    Practical (substituting barrier synchronization by pt-to-pt) 18:00 End Social Event (self paying) 2nd day 09:00 Programming Models (continued)            - MPI + OpenMP 10:30 Coffee Break 10:50     Practical (how to compile and start) 11:30     Practical (hybrid through OpenMP parallelization) 13:00 Lunch 14:00  - Overlapping Communication and Computation 14:20     Practical (taskloops)  15:00 Coffee Break 15:20  - MPI + OpenMP Conclusions 15:30  - MPI + Accelerators 15:45 Tools 16:00 Conclusions 16:15 Q&A 16:30 End     https://events.prace-ri.eu/event/807/ 2019-01-28 08:30:00 UTC 2019-01-29 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Programming Distributed Computing Platforms with COMPSs @ BSC

    29 - 30 January 2019

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

    4 - 5 February 2019

    Introduction to Molecular Modelling (materials and bio) and Molecular dynamics in HPC @GRNET https://tess.elixir-europe.org/events/introduction-to-molecular-modelling-materials-and-bio-and-molecular-dynamics-in-hpc-grnet Introduction to Biomolecular modelling and Molecular dynamics in HPC (Classical and Quantum) 4 - 5 February 2019 Purpose of the course The purpose of this course is to present to existing and potential users of Molecular Dynamics packages the method, the necessary steps for a successful simulation, common practices, common mistakes. The steps for a complete simulation workflow i.e. system setup up to final properties evaluation will be presented using popular software packages. Outcomes After the course the participants should be able to efficiently use their prefered MD application (i.e. NAMD, GROMACS, LAMMPS, CP2K), for molecular modelling and molecular dynamics simulations,  how to create configuration files based on their needs, tuning the models, how to efficiently use the resources based on the simulation details, avoid common mistakes. Prerequisites Background in Physics/Chemistry/Biology. Programming skills, aware of Parallel environments. Bring your own laptop in order to be able to participate in the training hands on. Hands on work will be done in pairs so if you don’t have a laptop you might work with a colleague. Course language is English. Registration Registrations will be evaluated on a first-come, first-served basis. GRNET is responsible for the selection of the participants on the basis of the training requirements and the technical skills of the candidates. GRNET will also seek to guarantee the maximum possible geographical coverage with the participation of candidates from many countries. Venue GRNET headquarters Address: 2nd  Floor, 7, Kifisias Av. GR 115 23 Athens Information on how to reach GRNET headquarters ia available on GRNET website: https://grnet.gr/en/contact-us/   Accommodation options near GRNET can be found at: https://grnet.gr/wp-content/uploads/sites/13/2015/11/Hotels-near-GRNET-en.pdf ARIS - System Information ARIS is the name of the Greek supercomputer, deployed and operated by GRNET (Greek Research and Technology Network) in Athens. ARIS consists of 532 computational nodes seperated in four “islands” as listed here: 426 thin nodes: Regular compute nodes without accelerator. 44 gpu nodes: “2 x NVIDIA Tesla k40m” accelerated nodes. 18 phi nodes: “2 x INTEL Xeon Phi 7120p” accelerated nodes. 44 fat nodes: Fat compute nodes have larger number of cores and memory per core than a thin node. All the nodes are connected via Infiniband network and share 2PB GPFS storage.The infrastructure also has an IBM TS3500 library of maximum storage capacity of about 6 PB. Access to the system is provided by two login nodes. About Tutors Dr. Zoe Cournia (female) is a Researcher – Assistant Professor level at the Biomedical Research Foundation, Academy of Athens, where she works on anticancer drug design, design of drug delivery systems and biomolecular modeling using computational techniques. She graduated from the Chemistry Department, University of Athens in 2001 and completed her PhD at the University of Heidelberg in Germany in 2006. She then worked as a postdoctoral researcher at the Chemistry Department, Yale University, USA, on computer-aided drug design and in 2009 she became a lecturer at Yale College. She has been awarded the American Association for Cancer Research Angiogenesis Fellowship (2008), the "Woman of Innovation 2009" Award from the Connecticut Technology Council, USA, the Marie Curie Fellowship from the European Union (2010), the "Outstanding Junior Faculty Award" from the American Chemical Society (2014) and the first "Ada Lovelace Award" from the "Partnership for Advanced Computing in Europe" (2016). She is currently teaching at the Master’s program “Information Technologies in Technology and Medicine” at the Department of Informatics and Telecommunications, National University of  Athens. Dr. Dimitris Tsalikis (male) is a Research Associate at the Department of Chemical Engineering in the University of Patras. His research focuses on the physicochemical characterization and the rheology of polymers, polymer nanocomposites, nanofluidics and formulations via atomistic and mesoscopic simulations and to this he develops novel parallel computational methodologies. He received his Diploma in Chemical Engineering from the University of Patras in 2004 and his Ph.D. (titled: “Computational study of structural relaxation and plastic deformation of glassy polymers”) from the National Technical University of Athens in 2009 under the advisement of Prof. Doros N. Theodorou. In 2011 he joined the research team of Prof. Vlasis Mavrantzas in Patras as a Research Associate. Dr. Tsalikis has a solid experience with high performance computing since 2007 being an active user of Tier1 and Tier0 HPC systems available to scientific community under the frameworks of HPC-Europa, PRACE and LinkSCEEM projects. He is currently teaching at the Master’s program “Polymer Science and Technology” at University of Patras.  Dr. Dellis (Male) holds a B.Sc. in Chemistry (1990) and PhD in Computational Chemistry (1995) from the National and Kapodistrian University of Athens, Greece. He has extensive HPC and grid computing experience. He was using HPC systems in computational chemistry research projects on fz-juelich machines (2003-2005). He received an HPC-Europa grant on BSC (2009). In EGEE/EGI projects he acted as application support and VO software manager for SEE VO, grid sites administrator (HG-02, GR-06), NGI_GRNET support staff (2008-2014). In PRACE 1IP/2IP/3IP/4IP/5IP he was involved in benchmarking tasks either as group member or as BCO (2010-2017). Currently he holds the position of “Senior HPC Applications Support Engineer” at GRNET S.A. where he is responsible for activities related to user consultations, porting, optimization and running HPC applications at national and international resources. Dr Aristeidis Sotiropoulos received his BSc in Computer Science in 1998 from the University of Crete, Greece and his PhD in Parallel Processing and Cluster Computing in 2004 from the National Technical University of Athens, Greece. His interests mainly focus on the fields of Large Scale Computing & Storage Systems, System Software for Scalable High Speed Interconnects for Computer Clusters and Advanced Microprocessor Architectures. He has published several scientific papers in international journals and conference proceedings. He has received the IEEE IPDPS 2001 best paper award for the paper "Minimizing Completion Time for Loop Tiling with Computation and Communication Overlapping". He has worked in several European and National R&D programs in the field of High Performance Computing, Grid Computing, Cloud Computing and Storage. In 2013, he was appointed as the Head of Operations and Financial Management Services, in charge of 15 people. Currently, he is managing EC projects at GRNET SA, the Greek NREN responsible for the provision of advanced e-infrastructure services to the Greek Academic and Research Community. About GRNET GRNET provides Internet connectivity, high-quality e-Infrastructures and advanced services to the Greek Educational, Academic and Research community. Through its high-speed, high-capacity infrastructure that spans across the entire country, GRNET interconnects more than 150 institutions, including all universities and technological institutions, as well as many research institutes and the public Greek School Network. GRNET operates the National High Performance Computing system (a Tier-1 in the European HPC ecosystem) and offers user and application support services, that provide Greek scientists with the computing infrastructure and expertise they need for their research enabling them to perform large scale simulations. GRNET offers innovative IaaS cloud computing services to the Greek and global research & education communities: “ ~okeanos” and “okeanos global” allow users to create multi-layer virtual infrastructure and instantiate virtual computing machines, local networks to interconnect them, and a reliable storage space within seconds, with few, simple mouse clicks. GRNET aims at contributing towards Greece’s Digital Convergence with the EU, by supporting the development and encouraging the use of e-Infrastructures and services. The right and timely planning strategies, together with the long experience and know-how of its people, guarantee the continuation and enhancement of GRNET’s successful course. Greek Research and Technology Network – Networking Reserach and Education: www.grnet.gr, hpc.grnet.gr https://events.prace-ri.eu/event/795/ 2019-02-04 08:00:00 UTC 2019-02-05 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Analysis of single cell RNA-Seq data from 10x Genomics

    4 - 5 February 2019

    Ghent, Belgium

    Elixir node event
    Analysis of single cell RNA-Seq data from 10x Genomics https://tess.elixir-europe.org/events/analysis-of-single-cell-rna-seq-data-from-10x-genomics 2019-02-04 09:30:00 UTC 2019-02-05 17:00:00 UTC VIB Bioinformatics Core iGent Tower, Ghent, Belgium iGent Tower Ghent Belgium 9052 [] [] [] [] [] []
  • Big Data Analytics @ BSC

    5 - 8 February 2019

    Big Data Analytics @ BSC https://tess.elixir-europe.org/events/big-data-analytics-bsc-259ac7f9-7780-44d6-82f8-fdf33e6037d8 Registration is now open. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course Convener:  Maria-Ribera Sancho Objectives: The course brings together key information technologies used in manipulating, storing, and analysing data including: the basic tools for statistical analysis techniques for parallel processing tools for access to unstructured data storage solutions Learning outcomes: Students will be introduced to systems that can accept, store, and analyse large volumes of unstructured data. The learned skills can be used in data intensive application areas. Level: For trainees with some theoretical and practical knowledge AGENDA:  TBA Day 1 (Feb 5) 9:30 – 13:00 Introduction to Big Data (Vassil Alexandrov) Data Science current trends session will focus on results of the latest key studies both in Europe and the USA in the area of Data Science and will outline the major trends, findings and recommendations. 11:00 - 11:30 Coffee break Data Science definitions and mathematical foundations introduction. While tackling Big Data problems in many cases elementary or standard statistical approaches fail. New research methods are required to be developed to tackle such problems. Therefore, this session will focus key research methods and approaches for Data Science, ranging from theory creating and theory testing approaches to conceptual-analytical approaches and experimental ones, that are able to lead to discovering global properties on data. These will be mainly deterministic and hybrid (stochastic/deterministic) methods and algorithms. 13:00 – 14:00 Lunch Break 14:00 – 16:00 Introduction to Big Data (Vassil Alexandrov) This session will focus on several key methods and algorithms (both serial and parallel) that enable to discover global properties on data while dealing with Big Data: Network Science Multi Constrained and Multi-Objective Optimization Examples using the above approaches and some hands-on exercise 16:00 – 16:30 Coffee break 16:30 – 18:00 Harnessing the Power of Big Data and Simulation for Societal Challenges (Josep Casanovas and Isa Romanowska) The scale of challenges our societies face nowadays calls for innovative and creative methods and solutions. Here, we present the role of simulation in modern scientific practice and its complementarity to data driven applications. Focusing on a relatively novel technique – agent-based modelling we show how by using High Performance Computing enabled methods we can simulate large scale processes and mechanisms driving human societies at different scales. The marriage between Big Data and Agent-based modelling is a particularly promising avenue of research that should be explored further to advance our social science toolset. Day 2 (Feb 6) 9:30 – 13:00 Data Analytics with Apache Spark (Josep Lluis Berral) 11:00 - 11:30 Coffee break Apache Spark has become a consolidated technology for large-scale processing in a fast and general way, with “programmer-friendly” interfaces and official bindings for many of the most used languages (Java, Scala, Python and R), extensive documentation and development tools. This course introduces Apache Spark, as well as some of its core libraries for data manipulation, machine learning, data streams and graph analytics. 13:00 – 14:00 Lunch Break 14:00 – 16:00 Data Analytics with Apache Spark. Part 2 (Josep Lluis Berral) 16:00 – 16:30 Coffee break 16:30 – 18:00 Big IoT Project (Dr. Ernest Teniente)   Day 3 (Feb 7) 9:30 – 13:00 Big Data Management (Albert Abelló and Petar Jovanovic) : Big Data has many definitions and facets, we'll pay attention to the problems we have to face to store it and how we can process it. More specifically, we'll focus on the Apache Hadoop ecosystem and its two basic components, namely HBase and MapReduce engine. 11:00 - 11:30 Coffee break Hands-on exercise 13:00 – 14:00 Lunch Break 14:00 - 16:00 NoSQL databases (Oscar Romero) The relational model has dominated data storage systems since the mid 1970s. However, the changing storage needs over the past decade have given rise to new models for storing data, collectively known as NoSQL. In this presentation, we will focus on two of the most common types of NoSQL databases: document-oriented databases and graph databases and explain the use cases suitable for each of them. 16:00 - 16:30 Coffee break 16:30 - 18:00 Multidisciplinary research and data analytics: Smart Cities (Maria Cristina Marinescu)   Day 4 (Feb 8) 9:30 – 13:00 Practical Data Analytics for Solving Real World Problems (Carlos Carrasco) Data analytics has changed the way we make decisions. We see the benefits and the advances in many fields that go from financial to medical and industrial applications due to the integration of advanced data analytics. In this course we will propose practical tips gained through our experience at BSC in big data analytics projects. We will also discover how to overcome some of the most challenging tasks in practical data analytics. 11:00 - 11:30 Coffee break   END of COURSE     https://events.prace-ri.eu/event/761/ 2019-02-05 08:30:00 UTC 2019-02-08 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Data Management Plan @ MdlS/CINES

    6 - 8 February 2019

    Data Management Plan @ MdlS/CINES https://tess.elixir-europe.org/events/data-management-plan-mdls-cines Objective of the session: In the context of scientific research, Data Management Plans (DMP) are increasingly requested by project funders to describe the data lifecycle of projects from the craddle to the grave. The main difficulty is to fully understand what is exactly required to build such a document. The aim of this training is to assist researchers in putting together their own DMP, first by describing the important concepts to know before starting to draft one, then by having practical work sessions during which their own plan will be drafted with the support of experts. Day 1 : afternoon : Introduction, DMP + FAIR in theory, tools ; Day 2 : morning : Long term preservation (metadata, formats, principles),  DMP hands on ; afternoon : DMP hands on ; Day 3 : morning : EOSC-hub services, CINES visit. Prerequisites:  This training is intended for researchers who have a DMP to build as part of their research project. It is recommended that the participants come with an intended use case for which they need to develop a DMP.  Learning outcomes  Participants will understand the DMP structure and good practices, and have a first experience from a real use-case. Trainers Marjan Grootveld (DANS), Alexia de Casanove et Olivier Rouchon (CINES) https://events.prace-ri.eu/event/813/ 2019-02-06 13:00:00 UTC 2019-02-08 11:00:00 UTC [] [] [] workshops_and_courses [] []
  • 15th Advanced School on Parallel Computing @ Cineca

    11 - 15 February 2019

    15th Advanced School on Parallel Computing @ Cineca https://tess.elixir-europe.org/events/15th-advanced-school-on-parallel-computing-cineca Application deadline: January 16th, 2019 Description: In the roadmap toward next-generation supercomputers it is evident that heterogeneous architectures are taking an important share in the HPC market, and the consolidation of this kind of architectures requires an important effort in software development and applications refactoring. Moreover, in recent years Arm has started to emerge as a viable architecture for large scale HPC deployments, and more than one exascale projects being develop in the world are based on Arm architectures. This school focus on software development techniques to address the implementation of new HPC applications and the re-factory of existing ones, in the era of heterogeneous, energy efficient, massively parallel architectures, toward exascale. Two days of the school will be reserved for a workshop that will provide an introduction to, and hands on experience working with, the Arm HPC architecture and the accompanying ecosystem. It will be discussed the specifics of the Armv8 architecture, and their implications, and introduce some of the current HPC processors developed on this architecture. For the hands on exercises we will provide tutorials, to work through an introduction to the compiler and maths libraries, as well as the performance tools to be tested on the Arm cluster installed at Cineca. As a more advanced topic for the workshop we will introduce the upcoming vectorisation exstension SVE, and provide a guided tutorial on how to use the Arm instruction emulator to execute next generation code. Software engineering techniques and high productivity languages will complement lectures on parallel programming and porting toward new architectures, to allow the implementation of application that can be maintained across a complex and fast evolving HPC architectures. Topics: Heterogeneous architectures Arm HPC architecture Elements of software engineering Parallel programming techniques for throughput CPUs  (Nvidia and Intel) Parallel programming techniques for massively parallel applications Introduction to Python for high performance computing Models for applications integrating MPI, OpenMP OpenACC, CUDA and CUDA Fortran paradigms Target audience: The school is aimed at PRACE users, final year master students, PhD students, and young researchers in computational sciences and engineering, with different backgrounds, interested in applying the emerging technologies on high performance computing to their research. Pre-requisites: Good knowledge of parallel programming with MPI and/or OpenMP, knowledge of FORTRAN and C languages. Basic knowledge of parallel computer architectures. Admitted students: Attendance is free. A grant of 250 EUR (for students working abroad) and 150 EUR (for students working in Italy) will be available for participants not funded by their institution and not working or living in the Bologna area. Documentation will be required. Lunches for the 5 days will be provided by Cineca. Each student will be given a two month access to the Cineca's supercomputing resources. The number of participants is limited to 25 students. Applicants will be selected according to their experience, qualifications and scientific interest BASED ON WHAT WRITTEN IN THE REGISTRATION FORM. DUE TO PRIVACY REASON THE STUDENTS ADMITTED AND NOT ADMITTED WILL BE CONTACTED VIA EMAIL ON JANUARY, FRIDAY 18TH. IF YOU SUBMITTED AND DON'T RECEIVE THE EMAIL, PLEASE WRITE AT corsi.hpc@cineca.it.   Acknowledgement: The support of CINI for the software engineering module is gratefully acknowledged.   https://events.prace-ri.eu/event/836/ 2019-02-11 08:00:00 UTC 2019-02-15 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • RNA-Seq analysis for differential expression

    11 - 18 February 2019

    Leuven, Belgium

    Elixir node event
    RNA-Seq analysis for differential expression https://tess.elixir-europe.org/events/rna-seq-analysis-for-differential-expression-in-genepattern b'You will execute a complete analysis workflow in GenePattern, Galaxy or command line and R to detect differential expression between two conditions\n\r\n\r\n\n We\'ll go through the different steps of the workflow:\r\n\n \nQuality control of the sequence reads to detect biases or contaminating adapters.\r\nMapping of the reads to the reference genome with use of a transcript database model.\r\nQuality control  of the mapping results.\r\nAdjusting the mapping data to compensate for artefacts like duplicates.\r\nCalculate transcript counts usable for differential expression and merging of count tables \n\r\nComputing differential expression using  DESeq2.\n\r\n\r\n\n • fastQC • trimmomatic• Groomer • STAR• samtools• Picard • RSeQC• HTSeq• R - RStudio - Bioconductor - various packages \n\r\n\r\n\n  \r\nFamiliarity with \n \nRNA-seq assembly\r\nRNA-seq analysis for isoform detection\r\nRNA-seq analysis for detection of short RNA species\n\r\n\n \n.Organised by the VIB Bioinformatics Core​\n\r\n\n' 2019-02-11 09:30:00 UTC 2019-02-18 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • RNA-Seq analysis for differential expression, extra session

    12 - 25 February 2019

    Leuven, Belgium

    Elixir node event
    RNA-Seq analysis for differential expression, extra session https://tess.elixir-europe.org/events/rna-seq-analysis-for-differential-expression-extra-session b'You will execute a complete analysis workflow in GenePattern, Galaxy or command line and R to detect differential expression between two conditions\n\r\n\n We\'ll go through the different steps of the workflow:\r\n\n \nQuality control of the sequence reads to detect biases or contaminating adapters.\r\nMapping of the reads to the reference genome with use of a transcript database model.\r\nQuality control  of the mapping results.\r\nAdjusting the mapping data to compensate for artefacts like duplicates.\r\nCalculate transcript counts usable for differential expression and merging of count tables \n\r\nComputing differential expression using  DESeq2.\n\r\n\n • fastQC • trimmomatic• Groomer • STAR• samtools• Picard • RSeQC• HTSeq• R - RStudio - Bioconductor - various packages \n\r\n\n  \r\nFamiliarity with \n \nRNA-seq assembly\r\nRNA-seq analysis for isoform detection\r\nRNA-seq analysis for detection of short RNA species\n\r\n\n \n.Organised by the VIB Bioinformatics Core​\n\r\n​\n' 2019-02-12 09:30:00 UTC 2019-02-25 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Practical Deep Learning @ CSC

    13 - 14 February 2019

    Practical Deep Learning @ CSC https://tess.elixir-europe.org/events/practical-deep-learning-csc Thank you to those of you who have already registered for our PATC "Python in HPC @ CSC" training course! The course is now fully booked! 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 at csc.fi We have processed a LIMITED WAITING LIST (10 persons max). Please send your request to patc at csc.fi, and we will keep those on the waiting list informed of whether participation will be possible. Please note that registration/wait list is at a first come, first served basis. Welcome to the course! 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. Keras (https://keras.io/) and PyTorch (https://pytorch.org/) will be used in the exercise sessions. CSC's Notebooks (https://notebooks.csc.fi/) environment will be used on the first day of the course, and the Taito-GPU (https://research.csc.fi/taito-gpu) cluster 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, Wednesday 13.2    09.00 – 10.30 Lecture: Introduction to deep learning    10.30 – 11.00 Exercises: Introduction to Notebooks, Keras fundamentals    11.00 – 12.00 Lecture: Image data, multi-layer percepton networks, convolutional neural networks    12.00 – 13.00 Lunch    13.00 – 14.00 Exercises: Image classification with MLPs, CNNs    14.00 – 15.00 Lecture: Text data, embeddings, neural NLP, recurrent neural networks    15.00 – 16.00 Exercises: Text sentiment classification with CNNs, RNNs Day 2, Thursday 14.2    09.00 – 10.00 Lecture: GPUs, batch jobs, using Taito-GPU    10.00 – 12.00 Exercises: Image classification    12.00 – 13.00 Lunch    13.00 – 14.00 Exercises: Text categorization and labelling    14.00 – 15.00 Lecture: Cloud, GPU utilization, multiple GPUs    15.00 – 16.00 Exercises: Using multiple GPUs Coffee will be served both for the morning and afternoon sessions Lecturers:  Markus Koskela (CSC),  Mats Sjöberg (CSC)   Language:  English Price:          Free of charge https://events.prace-ri.eu/event/831/ 2019-02-13 07:00:00 UTC 2019-02-14 14:00:00 UTC [] [] [] workshops_and_courses [] []
  • Short course on HPC-based Computational Bio-Medicine @ BSC

    13 - 15 February 2019

    Short course on HPC-based Computational Bio-Medicine @ BSC https://tess.elixir-europe.org/events/short-course-on-hpc-based-computational-bio-medicine-bsc The registration to this course is now open. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course convener: Mariano Vazquez and Ruth Aris Lecturers: Mariano Vázquez (BSC), Marco Verdicchio (SURFsara), Okba Hamitou (Bull), Gábor Závodszky (UvA), João Damas (ACELLERA), Adrià Perez (UPF), Phil Tooley (USFD), Ricard Borrell (BSC), Jazmín Aguado-Sierra (BSC), Dr Alexander Heifetz (EVOTEC), Andrea Townsend-Nicholson (UCL), Guillermo Marín (BSC) and Paul Melis (SURFsara) Objectives:The objetive of this course is to give a panorama on the use of HPC-based computational mechanics in Engineering and Environment through the projects BSC are carrying on. This panorama includes the basics of what is behind the main tools: computational mechanics and parallelization. The training is delivered in collaboration with the center of excellence CompBioMed. Learning outcomes: The course gives a wide perspective and the latest trends of how HPC helps in industrial, clinical and research applications allowing to achieve more realistic multiphysics simulations.  In addition, the student has the opportunity of running Jobs in Marenostrum supercomputer. Level: INTERMEDIATE: For trainees with some theoretical and practical knowledge Agenda: Day 1 (Feb. 13) Session 1 / 9:00am – 1:00 pm (4 h lectures) 9:00-9:15 Welcome (Mariano Vázquez, BSC) 9:15-11:00 Introduction to HPC in Computational Modelling (Marco Verdicchio, SURFsara) 11:00-13:00 Compilation and Optimization in the HPC environment (Okba Hamitou, Bull) 13:00-14:00 Lunch Break Session 2 / 2:00pm – 6:00 pm (4 h lectures) 14:00-16:00 Zoom in on blood - Using supercomputers in hemodynamics (UvA) (Gábor Závodszky, UvA) 16:00-18:00 PlayMolecule: Cloud-based Applications for Molecular Discovery (João Damas, ACELLERA, Adrià Perez, UPF)   Day 2 (Feb. 14) Session 3 / 9:00am – 1:00 pm (4 h lectures) 9:00-11:00 Hands on Image Registration with pFIRE (Phil Tooley, USFD) 11:00-12:00 Parallel algorithms for Computational Mechanics (Ricard Borrell, BSC) 12:00-13:00 HPC Multi-scale computational modelling using Alya Red (Jazmín Aguado-Sierra, BSC) 13:00-14:00 Lunch Break Session 4 / 2:00pm – 6:00 pm (2 h lectures, 2 h practical) 14:00-15:00 Introduction to Computer-Aided Drug Design (CADD) and GPCR Modelling (Dr Alexander Heifetz, EVOTEC) 15:00-16:00 Innovations in HPC-training for medical, science and engineering students (Andrea Townsend-Nicholson, UCL) 16:00-18:00 Molecular Medicine: Hands On (Andrea Townsend-Nicholson, UCL)   Day 3 (Feb. 15) Session 5 / 9:00am – 1:00 pm (4 h lectures) 9:00-10:00 Data Visulization for Researchers Crash Course (Guillermo Marín, BSC) 10:00-12:00 Visualization applied to 2D/3D scientific datasets (Paul Melis, SURFsara) 12:00-13:00 Molecular Medicine (UCL) 13:00-14:00 Lunch Break Session 6 / 2:00pm – 4:00 pm 14:00-16:00 Visit to MareNostrum   END of COURSE   END of COURSE https://events.prace-ri.eu/event/762/ 2019-02-13 08:00:00 UTC 2019-02-15 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • High Performance Molecular Dynamics@CINECA

    18 - 20 February 2019

    High Performance Molecular Dynamics@CINECA https://tess.elixir-europe.org/events/high-performance-molecular-dynamics-cineca-c066f8d5-c323-4608-8001-abd223134c5b   Description: This course is designed for those users who wish run classical molecular dynamics programs such as GROMACS and NAMD on modern supercomputers. By understanding better the HPC infrastructures and the algorithms used to exploit them, the aim is to give researchers the tools to run simulations in the most efficient way possible on current and future supercomputers. The course will consist of presentations and practical sessions where students will be able to prepare and run examples of popular programs such as GROMACS and NAMD on the supercomputers of Cineca. Skills: By the end of the course each student should be able to: comprehend the basic principles of classical molecular dynamics (MD). understand the common algorithms for the optimization and parallelization of MD applications and the factors limiting the performance and parallel scaling. run and optimize MD simulations on advanced, multicore architectures equipped with both conventional processors and accelerators such as NVIDIA GPUs. design a simulation project for a computing resource application. Target Audience: Scientists with research interests in classical molecular dynamics in computational biology, chemistry or biophysics. Pre-requisites: Research interest in classical molecular dynamics with a focus on the simulation of biomolecular systems. Basic knowledge of UNIX and concepts of parallel computing. Grant: A grant of 300 EUR (for foreign students) and 150 EUR (for Italian students) will be available for participants not funded by their institution and not working in the Rome area. Some documentation will be required and the grant will be paid only after a certified presence of minimum 80% of the lessons and about 1 month after the ending of the course. For further information about how to submit for the grant, please wait the confirmation email that you are accepted to the course about 3 weeks before the date of the beginning of the lessons.  The lunch for the 3 days will be provided by Cineca. Coordinating Teacher: Dr. Andrew Emerson https://events.prace-ri.eu/event/829/ 2019-02-18 08:00:00 UTC 2019-02-20 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Node-Level Performance Engineering @ LRZ

    20 - 21 February 2019

    Node-Level Performance Engineering @ LRZ https://tess.elixir-europe.org/events/node-level-performance-engineering-lrz-9d1ccd4c-855b-4ad3-b4a1-44a0054656c5 This course teaches performance engineering approaches on the compute node level. "Performance engineering" as we define it is more than employing tools to identify hotspots and bottlenecks. It is about developing 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. Once the architectural requirements of a code are understood and correlated with performance measurements, the potential benefit of optimizations can often be predicted. We introduce a "holistic" node-level performance engineering strategy, apply it to different algorithms from computational science, and also show how an awareness of the performance features of an application may lead to notable reductions in power consumption. 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/821/ 2019-02-20 08:00:00 UTC 2019-02-21 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Energy Efficency in HPC @Cineca

    21 - 22 February 2019

    Energy Efficency in HPC @Cineca https://tess.elixir-europe.org/events/energy-efficency-in-hpc-cineca Description: With the steaming out of Moore's law and the end of Dennard's scaling the pace dictated on the performance increase of High Performance Computing Systems among generations has led to power constrained architectures and systems. In addition power consumption represents a significant cost factor in the overall HPC system economy. For this reasons in the recent years researchers, supercomputing centers and major vendors have developed new tools and methodologies to measure and optimize the energy consumption of large scale high performance system installation. Due to the link between energy consumption, power consumption and execution time of the application executed by the final user it is important for these tools and methodology to consider all these aspects empowering the final user and the system administrator with the capability of finding the best configuration given different high level objectives.  The school will give an introductory course on the fundamental concept of power consumption and energy efficiency in HPC systems. Then it will focuses on the mechanisms that today computing elements and systems provide in terms of monitoring and control the power and energy dissipation. Finally it will introduce and give hand ons on a set of tools for reducing the energy consumption in HPC devices.  The school is organized in four main sessions driving the audience from the physical and engineering principles underlying power consumption in supercomputing systems to the practical usage of state-of-the-art tools for monitoring and controlling the energy efficiency of supercomputing machines and workloads. The tools that will be covered are the MSR-SAFE (LLNL), MERIC (IT4I), COUNTDOWN (UNIBO), GEOPM (Intel) libraries.  Skills: By the end of the course, participants will be expected to: have a good understanding of the principles underlying the power consumption, energy dissipation in high performance computing nodes recognize trade-offs and implications of changing the power consumption in scientific computing systems during the execution of scientific computing applications have a clear view on the state-of-the-art and of practice in controlling the power consumption and energy efficiency of supercomputing nodes and processors. learn the internals and the usage of a set of user-space run-time libraries for controlling/optimizing the power consumption and energy efficiency in x86 computing nodes while executing user's applications. learn how to use these tools for optimize the energy consumption of your codes. Target Audience: Researchers, student, system administrator, application developers who may wish to limit the environmental impact of their computations, as well as reducing the cost of energy provisioning in supercomputing system - promoting a more sustainable supercomputing ecosystem. Pre-requisites: Knowledge of Fortran or C/C++. Elementary notions of Linux/Unix. Knowledge of computing architecture Experience in running HPC applications or systems Basic knowledge of parallel programming OpenMP and/or MPI    Grant The course is FREE of charge. The lunch for the two days will be offered to all the participants and some grants are available. The only requirement to be eligible is to be not funded by your institution to attend the course and to work and live in an institute outside the Bologna area. The grant  will be 200 euros for students working and living outside Italy and 100 euros for students working and living in Italy (outside Bologna area). Some documentation will be required and the grant will be paid only after a certified presence of minimum 80% of the lectures. Further information about how to request the grant, will be provided at the confirmation of the course: about 3 weeks before the starting date. https://events.prace-ri.eu/event/833/ 2019-02-21 08:00:00 UTC 2019-02-22 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Basic statistics theory

    22 February 2019

    Leuven, Belgium

    Elixir node event
    Basic statistics theory https://tess.elixir-europe.org/events/basic-statistics-theory b'After this basic statistics theory session, you should be able to:\r\nUnderstand basic statistical concepts and methods for statistical analysis of life sciences data\r\n\r\nChoose the correct statistical test for analyzing your data\n\r\n\n This training gives an introduction to the use of statistics for basic analyses of life sciences data. This training is a prerequisite introduction to a series of \r\nhands-on trainings on the statistical analysis of life sciences data: \r\n\'Basic statistics in R\' and \'Basic statistics in Graphpad Prism\'.\r\n If you want to follow one of these trainings, you have to follow this \r\nintroduction. Ít will give you all the theoretical background that you need. Those that already have a strong statistical background may register directly for the \'Basic statistics in R, part II\' training. \n\r\n\r\n\r\n\n No skills required. \n\r\n\n  9h30-12h30: Theoretical background\r\n\n' 2019-02-22 09:30:00 UTC 2019-02-22 16:30:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Parallel and Scalable Machine Learning @ JSC

    25 - 27 February 2019

    Parallel and Scalable Machine Learning @ JSC https://tess.elixir-europe.org/events/parallel-and-scalable-machine-learning-jsc-424a6e5f-64a6-471e-af99-5b940b60a8a4 The course offers basics of analyzing data with machine learning and data mining algorithms in order to understand foundations of learning from large quantities of data. This course is especially oriented towards beginners that have no previous knowledge of machine learning techniques. The course consists of general methods for data analysis in order to understand clustering, classification, and regression. This includes a thorough discussion of test datasets, training datasets, and validation datasets required to learn from data with a high accuracy. Easy application examples will foster the theoretical course elements that also will illustrate problems like overfitting followed by mechanisms such as validation and regularization that prevent such problems. The tutorial will start from a very simple application example in order to teach foundations like the role of features in data, linear separability, or decision boundaries for machine learning models. In particular this course will point to key challenges in analyzing large quantities of data sets (aka ‘big data’) in order to motivate the use of parallel and scalable machine learning algorithms that will be used in the course. The course targets specific challenges in analyzing large quantities of datasets that cannot be analyzed with traditional serial methods provided by tools such as R, SAS, or Matlab. This includes several challenges as part of the machine learning algorithms, the distribution of data, or the process of performing validation. The course will introduce selected solutions to overcome these challenges using parallel and scalable computing techniques based on the Message Passing Interface (MPI) and OpenMP that run on massively parallel High Performance Computing (HPC) platforms. The course ends with a more recent machine learning method known as deep learning that emerged as a promising disruptive approach, allowing knowledge discovery from large datasets in an unprecedented effectiveness and efficiency. Prerequisites: Knowledge on job submissions to large HPC machines using batch scripts, knowledge of mathematical basics in linear algebra helpful. Participants should bring their own notebooks (with an ssh-client). Learning outcome: After this course participants will have a general understanding how to approach data analysis problems in a systematic way. In particular this course will provide insights into key benefits of parallelization such as during the n-fold cross-validation process where significant speed-ups can be obtained compared to serial methods. Participants will also get a detailed understanding why and how parallelization provides benefits to a scalable data analyzing process using machine learning methods for big data and a general understanding for which problems deep learning algorithms are useful and how parallel and scalable computing is facilitating the learning process when facing big datasets. Participants will learn that deep learning can actually perform ‘feature learning’ that bears the potential to significantly speed-up data analysis processes that previously required much feature engineering. Application Applicants will be notified one month before the course starts, whether they are accepted for participitation. Instructors: Prof. Dr. Morris Riedel, Dr. Gabriele Cavallaro, JSC Contact For any questions concerning the course please send an e-mail to g.cavallaro@fz-juelich.de. https://events.prace-ri.eu/event/817/ 2019-02-25 08:00:00 UTC 2019-02-27 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Analyzing flow cytometry data in FlowJo

    25 February 2019

    Ghent (Sint-Denijs-Westrem), Belgium

    Elixir node event
    Analyzing flow cytometry data in FlowJo https://tess.elixir-europe.org/events/analyzing-flow-cytometry-data-in-flowjo b'Learn researchers how to analyze flow cytometry data in an efficient way using FlowJo v10,the world’s nr.1 analysis software tool for flow cytometry data.\r\n\n FlowJo version10 is a newly designed version of the famous FlowJo software. In contrast with previous versions (iOS only), version 10 is now a multi-platform software tool (Windows, iOS, Linux). It now has a very intuitive user interface designed to analyze your data in a very practical and fast way.\r\n\n Prior knowledge in general flow cytometry is required but the general principles will be repeated\r\n\n' 2019-02-25 09:30:00 UTC 2019-02-25 17:00:00 UTC VIB Bioinformatics Core Holiday Inn Gent Expo, Ghent (Sint-Denijs-Westrem), Belgium Holiday Inn Gent Expo Ghent (Sint-Denijs-Westrem) Belgium 9051 [] [] [] [] [] []
  • Introduction to Heterogeneous Memory Usage @ BSC

    26 February 2019

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

    26 February 2019

    Gent (Sint-Denijs-Westrem), Belgium

    Elixir node event
    Advanced FlowJo training https://tess.elixir-europe.org/events/advanced-flowjo-training b'\nParticipants must have experience with FlowJo. If you\'re new to the software you can attend our FlowJo introduction training​ first. ​\r\n\n \r\n\r\n\n' 2019-02-26 09:30:00 UTC 2019-02-26 17:00:00 UTC VIB Bioinformatics Core Holiday Inn Ghent Expo, Gent (Sint-Denijs-Westrem), Belgium Holiday Inn Ghent Expo Gent (Sint-Denijs-Westrem) Belgium 9051 [] [] [] [] [] []
  • Advanced Parallel Programming @ CSC

    27 February - 1 March 2019

    Advanced Parallel Programming @ CSC https://tess.elixir-europe.org/events/advanced-parallel-programming-csc-4c9c2989-610a-4d6d-ae2a-fa20776bd201 Description This course addresses hybrid programming by combining OpenMP and MPI, as well as more advanced topics in MPI. Also, parallel I/O is discussed and exemplified in the course. The course consists of lectures and hands-on exercises. Learning outcome After the course the participants should have an idea about more advanced techniques and best practices in parallel programming, and on how to scale up parallel applications and optimize them to different platforms. Prerequisites The PATC course Introduction to Parallel Programming or similar background knowledge together with fluency in Fortran and/or C programming languages will be assumed. Agenda (tentative) Day 1: Wednesday, February 27 09.00-09.45 Course intro, MPI & OpenMP recap 09.45-10.00 Coffee break 10.00-11.00 Exercises 11.00-11.30 Hybrid MPI + OpenMP programming I 11.30-12.00 Exercises 12.00-13.00 Lunch break 13.00-13.45 Hybrid MPI + OpenMP programming II 13.45-14.30 Exercises 14.30-14.45 Coffee break 14.45-15.15 Advanced MPI I: Communication topologies 15.15-16.15 Exercises 16.15-16.30 Summary of Day 1 Day 2: Thursday, February 28 09.00-09.45 Advanced MPI II: User-defined datatypes 09.45-10.00 Coffee break 10.00-11.15 Exercises 11.15-12.00 Advanced MPI III: One-sided communication 12.00-13.00 Lunch break 13.00-14.30 Exercises 14.30-14.45 Coffee break 14:45-15:15 Parallel I/O with Posix 15.15-16.15 Exercises 16.15-16.30 Summary of Day 2 Day 3: Friday, March 1 09.00-09.45 Parallel I/O with MPI 09.45-10.00 Coffee break 10.00-11.15 Exercises 11.15-12.00 Parallel I/O with MPI cont'd 12.00-13.00 Lunch break 13.00-14.15 Exercises 14.15-14.30 Coffee break 14.30-15.15 Parallel I/O with HDF5 15.15-16.15 Exercises 16.15-16.30 Summary of Day 3 Lecturers:  Jussi Enkovaara (CSC),  Martti Louhivuori (CSC)   Language:  English Price:          Free of charge https://events.prace-ri.eu/event/848/ 2019-02-27 07:00:00 UTC 2019-03-01 14:00:00 UTC [] [] [] workshops_and_courses [] []
  • Systems Workshop: Programming MareNostrum 4 @ BSC

    27 - 28 February 2019

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

    6 - 8 March 2019

    Parallel Programming with MPI and OpenMP @SURFsara https://tess.elixir-europe.org/events/parallel-programming-with-mpi-and-openmp-surfsara-eeb96613-54d8-4840-afd9-9523550d25ce The 3-days MPI/OpenMP course aims at giving people with some programming experience an introduction into the parallel programming models MPI and OpenMP. It starts on beginners level but also includes advanced features of the current standards. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the constructs of the Message Passing Interface (MPI) and the shared memory directives of OpenMP. The program will start with OpenMP on the first day, an introduction to MPI on the second day, and the advanced features in MPI-2.0 and MPI-3.0 standard on the third day. https://events.prace-ri.eu/event/828/ 2019-03-06 08:00:00 UTC 2019-03-08 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • High Performance Parallel IO and post-processing @ MdlS

    11 - 13 March 2019

    High Performance Parallel IO and post-processing @ MdlS https://tess.elixir-europe.org/events/high-performance-parallel-io-and-post-processing-mdls The increase in computational power goes hand in hand with an increase in the size of the data to be managed, both on the input and on the output sides. IO can easily become a bottleneck for large scale architectures. Understanding of parallel file system mechanisms and parallel IO concepts enables users to efficiently use existing high level libraries like HDF5. With the increasing performance gap between compute and storage, even the best use of IO bandwidth might not be enough and data reduction based on in-situ or in-transit post-processing becomes a requirement for large-scale codes. More and more libraries able to handle this become available. This course proposes an introduction to FlowVR, a technology developed at Inria dedicated to in-situ and in-transit post-processing. To handle the multiplication of libraries, this course will also introduce the Parallel Data Interface (PDI), a solution to couple simulation codes with libraries for I/O and post-processing based on simple annotations. PDI improves code quality with a) annotations independent of the library used, b) a choice of IO strategy at runtime in YAML and c) negligible overhead to access the full power of the underlying libraries. Agenda: Day 1: HDF5, pHDF5 and general parallel IO concepts (2x3h, including hands-on) Day 2: Lustre file system (1h30) Day 2: FlowVR (1h30 + 3h including hands-on) Day 3: Parallel Data Interface (3h including hands-on) Day 3: Diving deeper into HDF5, FlowVR or PDI, your choice ! (3h) Instructors: M. Haefele (Maison de la Simulation, CNRS), Thomas Leibovici (TGCC, CEA), Bruno Raffin (INRIA), Julien Bigot (Maison de la Simulation, CEA) Learning outcomes: After this course, participants should understand the trade-offs implied by using a parallel file-system, and know how to efficiently use parallel IO libraries. Participants will also have a basic understanding and practise of FlowVR and PDI. Prerequisites: Knowledge of C or Fortran programming languages, parallel programming with MPI   https://events.prace-ri.eu/event/814/ 2019-03-11 08:30:00 UTC 2019-03-13 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Basic statistics in R

    11 - 18 March 2019

    GENT, Belgium

    Elixir node event
    Basic statistics in R https://tess.elixir-europe.org/events/basic-statistics-in-r b'\n\nGet an idea of what R and Rstudio is\r\nUse R to handle data: creating, reading, reformatting and writing data\r\nUse R to create graphics\r\nUse basic statistical techniques in R : normality tests, t-tests, wilcoxon tests, chi square tests, correlations, survival analysis...\r\nWrite and use R scripts\n\r\n\r\n\n \nThis training gives an introduction to the use of the statistical software language R. R is a language for data analysis and graphics. This introduction to R is aimed at beginners. The training covers data handling, graphics, and basic statistical techniques. \r\nR is for free and for more information you can visit the site the CRAN web site.This\r\n training is an introduction to the use of R and RStudio and stops at very basic \r\nanalyses (t-tests and non-parametric equivalents). A full overview of statistical analyses in R including regression, \r\nANOVA will be given in the follow-up training Basic statistics in R, part II.\n\r\n \r\nRequirements\r\nThe training is intended for people who have no experience with R. However, understanding of basic statistical concepts is required, such as data types, normal distribution, descriptive statistics, tests for comparing groups... If you don\'t have sufficient statistical background you are strongly encouraged to attend the Basic statistics theory training. \r\nThis training is recommended for people with no experience in R who are planning to follow a training that requires some R background, like the mass spectrometry training, the single cell RNA-Seq and the bulk RNA-Seq training....\n\r\n\n' 2019-03-11 09:30:00 UTC 2019-03-18 17:00:00 UTC VIB Bioinformatics Core Clemenspoort, GENT, Belgium Clemenspoort GENT Belgium 9000 [] [] [] [] [] []
  • Introduction for Simulation Environments for Life Sciences @ BSC

    14 - 15 March 2019

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

    18 - 21 March 2019

    Advanced Topics in High Performance Computing @ LRZ https://tess.elixir-europe.org/events/advanced-topics-in-high-performance-computing-lrz-cfe82cd6-32b5-4187-b72a-b90b2c55c36d In this add-on course to the parallel programming course special topics are treated in more depth, in particular performance analysis, I/O and PGAS concepts. It is provided in collaboration of Erlangen Regional Computing Centre (RRZE) and LRZ within KONWIHR. The course is a PRACE Training event. Each day is comprised of approximately 5 hours of lectures and 2 hours of hands-on sessions. Tentative schedule: Day 1 (09:00-17:00) Processor-Specific Optimization (Eitzinger) Day 2 (09:00-17:00) 09:00-12:30 Parallel I/O with MPI IO (N.N.) 13:30-14:30 SuperMUC Tour (Weinberg) 14:30-17:00 Tuning I/O on LRZ's HPC systems / I/O Profiling: Darshan tool (Mendez) Day 3 (09:00-17:00) 09:00-12:30 Scientific Data Libraries: HDF5 / Scalable I/O library: SIONlib (Mendez) 13:30 - 17:00 Advanced OpenMP Programming (Weinberg) Day 4 (09:00-17:00) PGAS programming with coarray Fortran and Unified Parallel C (Bader) https://events.prace-ri.eu/event/822/ 2019-03-18 08:00:00 UTC 2019-03-21 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.