The NCC Netherlands

Introduction Scientific Visualisation with Blender: Data, Lights, Camera, Action!
2024-10-15 09:30 - 17:00 UTC | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands
Would you like to make 3D visualizations that are visually more attractive than what ParaView or VisIt can provide? Do you need an image for a grant application that needs to look spectacular? Would you like to create a cool animation of your simulation data? Then this course may be for you!
Sign up

What will you learn?
The goal of this course is to provide you with hands-on knowledge to produce great images and basic animations from 3D scientific data. We will be using the open-source package Blender (http://www.blender.org), which provides good basic functionality, while also being usable for advanced usage and general editing of 3D data. It is also a lot of fun to work with (once you get used to its graphical interface).
Example types of relevant scientific data are 3D cell-based simulations, 3D models from photogrammetry, (isosurfaces of) 3D medical scans, molecular models and earth sciences data. Note that we don’t focus on information visualization of abstract data, such as graphs (although you could convert those into a 3D model first and then use them in Blender).
We like to encourage participants to bring along the data they normally work with, or a sample thereof, and would like to apply the course knowledge to.
For whom?
Anyone interesting in learning how to design attractive visualizations. We assume the context to be an academic setting, but it is don’t make many assumptions on use cases for Blender, and we are happy to help to how we can use Blender to make attractive visuals of the data.
Prerequisites
It helps to have some familiarity with basic 3D graphics concepts (transformations, rendering), but it is not mandatory.
You will need to have a laptop, preferably with an acceptable GPU, where you can install Blender during the course.

Introduction to Supercomputing, part III
2024-10-10 13:00 - 17:00 | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands
If you are comfortable submitting jobs on HPC systems and managing input and output data on the file systems, this course will help you utilize the system’s computing capacity by running parallel jobs effectively.
Sign up

What will you learn in this training?
In this training, you will:

learn the fundamentals of performance analysis
understand the key Slurm parameters for parallel job scheduling, including threads, cores, sockets, nodes, and processes
perform practical exercises on the national supercomputer Snellius to execute tightly coupled parallel tasks
learn about the characteristics of embarrassingly parallel jobs and techniques to efficiently handle concurrency
engage in practical exercises using QCG Pilotjob.

For whom?
This course is suitable for anyone with a basic understanding of cluster computing who wants to improve their ability to run parallel jobs efficiently on supercomputers.
Prerequisites
Participation in the course Introduction to Supercomputing Part I (Unix shell and remote access to supercomputers), and optionally Part II too.
The language of instruction is English.

Introduction to Supercomputing, part II
2024-10-09 13:00 - 17:00 | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands
If you have a basic understanding of clusters and supercomputers, know how to access the system, and can run basic jobs, this course will enhance your interaction with file systems and improve your input and output operations in your jobs.
Sign up

What will you learn in this training?
In this training, you will:

understand the differences between different file systems
learn how to manage data on supercomputing systems
engage in practical exercises involving input and output operations on the national supercomputer Snellius

For whom?
This course is suitable for anyone familiar with the basics of cluster computing and who wants to develop their skills further by learning how to manage files on supercomputers.
Prerequisites
Participation in the course Introduction to Supercomputing, Part I (Unix shell and remote access to supercomputers).
The language of instruction is English.

Introduction to Supercomputing, part I
2024-10-08 13:00 - 16:30, 2024-09-03 13:00 - 16:30, 2024-08-06 09:00 - 12:30 | Online
If you need to perform many calculations, or analyses that are too big for your own system, clusters and supercomputers will provide the computing power you need. In this course, you will learn how to work with these large computing systems!
Sign up

What will you learn in this training?
In this training you will:
• understand what is high-performance computing (HPC)
• learn basic details on clusters and supercomputers
• do practical exercises on the national supercomputer Snellius effectively
• apply the essential best practices on how to work effectively with large HPC systems
For whom?
Anyone who wants to know how to perform very large computing tasks.
This course is organized in collaboration with the UvA via the shared HPC program, see more on https://hpc.uva.nl.
Prerequisites
Basic knowledge of Unix shell is useful.
Language
This webinar will be in English

Cluster Computing for Social Scientists with R
2024-09-27 09:00 - 17:00 | Amsterdam Science Park, Science Park 904, Amsterdam, 1098XH, Netherlands
Want to learn how to work with a supercomputer? And how to translate your R workflow from a graphical user interface (GUI) on your desktop to a scripting/automated workflow for a supercomputer?Sign up

What will you learn?
In this course, you will learn the basics of supercomputing. The day starts with an introduction to supercomputer architecture, including a hands-on session focused on running jobs on a supercomputer.
The second half of the programme focuses on translating your R workflow from a GUI (Rstudio) workflow on your desktop to a scripting/batch environment on the supercomputer. Topics covered here include: efficient programming, parallel computing, and using the SLURM job manager to send your job/analysis to the supercomputer.
In this course you will:

Do practical exercises to learn how to effectively use the national supercomputer Snellius and how to complete your tasks with minimal effort in the shortest possible time.
Experience how to achieve high performance with R by using the supercomputing facilities at SURF

Prerequisites:

Basic knowledge of Linux (Unix shell) is useful
Basic knowledge of R is useful

You must have:
A personal laptop with an up-to-date browser and a terminal emulator (Putty is perfectly fine for users of the OSSC/CBS RA environment). Using the operating systems Linux and macOS is preferred but not mandatory. For Windows users, we recommend downloading MobaXterm (portable version) as a terminal emulator. If you are limited in your choice, Putty also works.
Costs
Participation is free of charge
The language of instruction is English

Introduction to SURF Research Cloud
2024-09-17 09:00 - 13:00 | Amsterdam Science Park, Science Park 904, Amsterdam, 1098XH, Netherlands
This training explains cloud computing in general. The accompanying hands-on approach introduces you to (some of) the many features of SURF Research Cloud. You will learn how to create and manage your own virtual computing environment(s).
Sign up

For whom?
Anyone who wants to use a flexible and customized environment to run powerful applications.The language of instruction is English.
Requirements:
1. Bring your own laptop.
2. A browser (Chrome or Firefox is good enough).
3. Experience with Linux commands helps, but is not a requirement.

High-Performance Deep Learning
2024-09-09 09:30 - 2024-09-10 17:00 | Amsterdam Science Park, Science Park 904, Amsterdam, 1098XH, Netherlands
Our online course on high-performance machine learning provides the necessary skills to train neural networks and extract the most relevant information from datasets.
Sign up

The first day will focus on basic deep learning knowledge and skills. The second day will focus on training neural networks on high-performance computing clusters.
What?
On day 1 of this course you will:

Understand the fundamental theories of machine learning and the intuitions/ideas behind the algorithms
Work with a high-level machine learning API (Keras)
Explore hyperparameter space to improve a neural network
Understand the pitfalls of classic machine learning algorithms

On day 2 of this course you will learn:

How to set up your software environment
About the technical capabilities of modern day CPUs and GPUs
How to identify bottlenecks in your code

9th of September: 9:30 – 17:00
10th of September: 9:30 – 17:00
Who?
Everyone interested in getting familiar with machine learning at scale, from the beginning up to more advanced topics
Prerequisites

Basic knowledge on statistics
Basic knowledge on linear algebra
Basic knowledge on Python programming. Some experience with the use of Jupyter Notebooks is desirable, but not essential.

* Basic knowledge on parallel computing is helpful, but not required.
* This workshop will be in English

Introduction to SURF Research Cloud
2024-07-25 13:00 - 17:00 | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands
Do you want to create and manage your own work environment and run powerful applications on it? SURF Research Cloud opens the door to cloud computing on different platforms. During this training, your workload runs on the SURF HPC Cloud platform in Amsterdam.
Sign up

This training explains cloud computing in general. The accompanying hands-on approach introduces you to (some of) the many features of SURF Research Cloud. You will learn how to create and manage your own virtual computing environment(s). By the end, you will feel comfortable enough to install your own applications, and benefit from the power of cloud computing.
For whom?
Anyone who wants to use a flexible and customized environment to run powerful applications.
The language of instruction is English.
This course is organized in collaboration with the UvA via the shared HPC program, see more: https://hpc.uva.nl.
Requirements
Bring your own laptop.
A browser (Chrome or Firefox is good enough).
Experience with Linux commands helps, but is not a requirement.

Introduction to Data Management, Research Drive and Yoda
2024-07-22 13:00 - 17:00 | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands
This workshop will provide you with the knowledge you need to make your research data FAIR (findable, accessible, interoperable and reusable) using various services and tools. In particular, you will learn how to work with the data sharing and storage tool Research Drive, or also with Yoda, an integral support tool for the whole data life cycle.
Sign up

Nowadays, this is a complicated task because of the heterogeneity of information and the requirements to share certain data with specific groups of people. After this training, you will be a lot more agile in managing your data!
For whom
Anyone who wants to learn to store research data in an efficient and scalable way.
This course is organized in collaboration with the UvA via the shared HPC program, see more: https://hpc.uva.nl.

High-Performance Deep Learning
2024-07-08 13:00 - 2024-07-11 17:00 | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands
Our online course on high-performance machine learning provides the necessary skills to train neural networks and extract the most relevant information from datasets.
Sign up

The first day will focus on basic deep learning knowledge and skills. The second day will focus on training neural networks on high-performance computing clusters.
What?
On day 1 of this course you will:

Understand the fundamental theories of machine learning and the intuitions/ideas behind the algorithms
Work with a high-level machine learning API (Keras)
Explore hyperparameter space to improve a neural network
Understand the pitfalls of classic machine learning algorithms

On day 2 of this course you will learn:

How to set up your software environment
About the technical capabilities of modern day CPUs and GPUs
How to identify bottlenecks in your code

Who?
Everyone interested in getting familiar with machine learning at scale, from the beginning up to more advanced topics
This course is organized in collaboration with the UvA via the shared HPC program, see more: https://hpc.uva.nl.
Prerequisites

Basic knowledge on statistics
Basic knowledge on linear algebra
Basic knowledge on Python programming. Some experience with the use of Jupyter Notebooks is desirable, but not essential.

* Basic knowledge on parallel computing is helpful, but not required.

Introduction to Supercomputing, part II
2024-07-05 09:00 - 13:00 | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands
Using a high-performance computing system in the most effective and efficient way is not an easy task. Therefore, this course brings a follow-up to the first introductory Supercomputing course (part I), where you can take a deeper dive into the use of supercomputers with a special focus on efficiency and good practices and a very practical approach.
Sign up

What will you learn in this course?
This course is a follow-up to the first introductory Supercomputing course, where you can take a deeper dive into the use of supercomputers with a special focus on efficiency and good practices and a very practical approach.
The format of this course includes the following modules:

Fundamentals of performance analysis. This introductory technical presentation introduces high-performance hybrid systems, abstractly covering the architecture and configuration of the system. Our aim is to enhance the understanding of HPC complexity before delving deeper into the importance of performance analysis models. Special attention is paid to the Roofline model.

Abstract Modelling hybrid supercomputers. Presenting an abstract modelling approach for hybrid supercomputers, condensing their complexity into three key parameters: peak performance, memory and network bandwidth.
Performance analysis. Explore performance analysis, starting with an overview of different models and going deeper into the specifics of the roofline model.
The roofline model. Describing the roofline model and presenting its practical application through clear explanations and demonstrations.

File systems. This practical session covers the proper use of file systems on HPC systems, especially on Snellius.
Slurm hybrid tasks. Slurm, a widely used job scheduler for high-performance computing (HPC) systems, has been introduced in earlier sections for a basic understanding. This module covers the specific resource allocation parameters for hybrid jobs with shared and distributed memory.

Nodes, cores and tasks. This segment covers the fundamental concepts of nodes, cores and tasks, and highlights their role within the context of HPC systems.
Bindings. The concept of bindings is explored, providing insight into how tasks are associated with specific resources, improving participants’ understanding of resource allocation mechanisms.
Hands on. We will run the vector optics kernel with multiple configurations using a set of scripts.

QCG pilot job. In some cases, users need to run a large number of lightweight cases. However, the nodes of supercomputers are too powerful and only allow relatively large partitions. For example, the smallest possible allocation on Snellius is 1/4 of a node: 32 cores and 64 GB. Job concurrency is a common strategy to efficiently launch multiple lightweight jobs on such large partitions.

Fundamentals of job concurrency. This segment discusses the basic principles underlying job concurrency. Job concurrency is a methodological approach that allows the simultaneous execution of multiple smaller jobs within a larger allocated partition. The goal is to optimise resource utilisation and improve efficiency in scenarios where lighter tasks are executed on nodes designed for heavier workloads.
Hands-on QCG PilotJob. This hands-on session provides participants with hands-on experience of the QCG Pilotjob framework. Participants will gain practical insights into the strategies and techniques of using job concurrency to launch and manage multiple lightweight jobs within the context of bulky node partitions.

Prerequisites
Participation in the course Introduction to Supercomputing, Part I
The language of instruction is English

Introduction to Supercomputing, part I
2024-07-04 13:00 - 17:00 | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands

FIRE: FPGA Iannovation Research Exchange: Tools and Platforms for Accelerating AI Workloads
2024-06-27 09:30 - 17:00
On June 27, 2024, the HW Acceleration Network community and SURF organize a HW acceleration workshop focused on tools and HW platforms for accelerating AI workloads. This workshop is part of the “FIRE: FPGA Innovation Research Exchange“ series of events.
Sign up

What to expect?
The event features a lineup of discussions centered around cutting-edge computing technologies for AI workload acceleration showcasing multiple industrial players such as Innatera and Groq as well as developers of HW acceleration platforms such as AMD and Altera. In addition, the workshop features two keynote talks on future computing platforms dedicated to quantum computing as well as cellular automata.
Practical information
Where: SURF Utrecht (Moreelsepark 48, 3511 EP, Utrecht)
When: June 27, 2024, 9.30-17.00
The outline of the program of the event is as follows.
09.30 – 09.45: Welcome&Coffee
09.45 – 10.00: Introduction and updates
10.00 – 11.00: Keynote 1
11.00 – 12.30: Platforms for AI acceleration session
12.30 – 13.30: Lunch
13.30 – 14.30: Keynote 2
14.30 – 15.00: Flash talks
15.00 – 15.30: Coffee break
15.30 – 17.00: Tools for accelerator platforms session
17.00 – 17.30: Drinks

HPC Advanced course
2024-06-20 12:30 - 17:00 | Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, Netherlands
Did you recently start using the High Performance Computing Cluster (HPC Anunna)? Do you have some basic Linux knowledge but want to know more about how things work on Anunna? Join the free 5 hours course on the basics of the HPC. You will be set to work on computing tasks to gain insight and experience with Anunna. The course is organized by SRF and WDCC with contributions from WUR scientists experienced on Anunna.
Read more

Organised by
WUR FB-IT and WUR Shared Research Facilities

Date
Thu 20 June 2024 12:30 to 17:00
Thu 21 November 2024 12:30 to 17:00
*These dates are for the full course. Unable to attend the first session? Don’t worry, you’ll have another opportunity on the second date!

Room
TBA

Price description
The courses are free when you already have a user account on our HPC or if your group has a commitment on the HPC. If you do not have an account or a commitment, the fee is 250 euros. This amount will be reduced from your first bill once you start using the HPC after the course.

Bring your own laptop
Please bring your own laptop to the course.
The course is also open for interested people outside WUR.

HPC basic course
2024-06-13 12:30 - 17:00 | Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, Netherlands
Did you recently start using the High Performance Computing Cluster (HPC Anunna)? Do you have some basic Linux knowledge but want to know more about how things work on Anunna? Join the free 5 hours course on the basics of the HPC. You will be set to work on computing tasks to gain insight and experience with Anunna. The course is organized by SRF and WDCC with contributions from WUR scientists experienced on Anunna.
Read more

Organised by
WUR FB-IT and WUR Shared Research Facilities

Date
Thu 13 June 2024 12:30 to 17:00
Tue 12 November 2024 12:30 to 17:00
*These dates are for the full course. Unable to attend the first session? Don’t worry, you’ll have another opportunity on the second date!

Room
TBA

Price description
The courses are free when you already have a user account on our HPC or if your group has a commitment on the HPC. If you do not have an account or a commitment, the fee is 250 euros. This amount will be reduced from your first bill once you start using the HPC after the course.

Bring your own laptop
Please bring your own laptop to the course.
The course is also open for interested people outside WUR.

Introduction to Supercomputing, part I
2024-06-11 09:00 - 12:30 | Online
If you need to perform many calculations, or analyses that are too big for your own system, clusters and supercomputers will provide the computing power you need. In this course, you will learn how to work with these large computing systems!
Sign up

What will you learn in this training?
In this training you will

understand what is high-performance computing (HPC)
learn basic details on clusters and supercomputers
do practical exercises on the national supercomputer Snellius effectively
apply the essential best practices on how to work effectively with large HPC systems

For whom?
Anyone who wants to know how to perform very large computing tasks.
Basic knowledge of Unix shell is useful.

Harnessing High-Performance Computing for Industrial Innovation
2024-06-10 13:00 - 14:00 | Webinar
Are you an R&D driven tech company or start up? 🌟 Join us on June 10th for the webinar Driving National Growth: Harnessing High-Performance Computing for Industrial Innovation.
During this webinar we will highlight the transformative power of High-Performance Computing (HPC). Explore practical use cases and strategies for leveraging supercomputing in R&D-driven tech companies.
📅 Date: June 10, 2024
🕓 Time: 13:00 – 14:00 (Online)
🎙️ We have great speakers lined up for you:
1️⃣ Dr. Marijn Martens, Synaptica
2️⃣ Professor Gábor Závodszky – UvA & Dutch HPC Coalition
3️⃣ Carlos Teijeiro Barjas, EuroCC Netherlands
Marijn Martens will talk about Predicting the functional consequence of ion channel mutations. Understanding the functional consequences of genetic mutations is key for early diagnosis and precision medicine. For only around 2% of potential pathogenic ion channel mutations, the gain or loss of function effects are known and well quantified. Using these known mutations, Synaptica has trained a machine learning model of all missense mutations in many of the disease-related ion channels. HPC now allows the simulation of molecular dynamics and 3D structures of the individual mutated protein sequences, allowing for deep feature extraction.
Using this approach, Synaptica provides predictions on gain or loss of function for ion channel mutations. Synaptica is currently running a clinical proof of concept clinical trial for a familial case of epilepsy. The results are aimed at medical use in clinical trial screening and treatment for channelopathies, such as epilepsy, muscle and heart diseases.
Gábor Závodszky will give insights about big simulations (road to exascale). During his talk he will also give examples of an extreme detailed simulation of a heart disease and a large-scale (330+ CPU core) cellular blood flow simulation. On top of that he will also review the energy consumption of these large simulations. And what can we predict how they will look like in an exascale execution and on new CPU architectures (with contribution from Eviden. To wrap up his talk, he will share how this fits the national landscape and the forming Dutch HPC Coalition.
Carlos Teijeiro Barjas will be your host and HPC Specialist from EuroCC Netherlands.
Gain valuable insights to elevate your organization’s innovation game.
Register now on linkedin

Introduction to SURF Research Cloud
2024-06-03 09:00 - 12:00 | TU Delft Library, Prometheusplein 1, Delft, Netherlands
This training explains cloud computing in general. The accompanying hands-on approach introduces you to (some of) the many features of SURF Research Cloud. You will learn how to create and manage your own virtual computing environment(s).
Sign up

For whom?
Anyone who wants to use a flexible and customized environment to run powerful applications.The language of instruction is English.
Requirements:
1. Bring your own laptop.
2. A browser (Chrome or Firefox is good enough).
3. Experience with Linux commands helps, but is not a requirement.

Sign up

MPI and OpenMP in Scientific Software Development
2024-05-27 09:00 - 2024-05-29 17:00 | Online
This advanced course describes different everyday challenges that developers of parallel code must face in everyday work and provides working solutions for them.
Sign Up

Each of these sessions includes hands-on exercises to facilitate the understanding of the different constructs. Moreover, you will also obtain some insight on useful parallel libraries and routines for scientific code development, like ParMETIS and PETSc.
Prerequisites:
As a participant for this course, you already have basic knowledge on parallel programming with MPI and OpenMP using the C programming language. If you are not very familiar with these basic concepts, please consider registering for our basic MPI and OpenMP course, where you can get all the required background! If you are a programmer of Fortran or Python, please note that the hands-on codes for this advanced course are written in C/C++, so you may need to have some understanding for the language syntax.

Please bring your own laptop (with a ssh client installed) for the hands-on sessions!
Knowledge of Linux/Unix commands is necessary.
Knowledge of C or C++ (or good understanding of the syntax of these programming languages) is necessary.
Basic knowledge of MPI and OpenMP concepts is necessary.

Sign up

Basic Parallel Programming with MPI and OpenMP
2024-05-21 09:00 - 2024-05-22 17:00 | Online
This basic course is focused on introducing parallel programming using the most widely used approaches: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP).
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Each session includes hands-on exercises to facilitate the understanding of the different constructs. As a participant, you have already some familiarities with C, Fortran, or Python programming, and in these two days you will be able to start the development of your own parallel application.
The materials for this course have been developed at HLRS by Dr. Rolf Rabenseifner.
Prerequisites:

Please bring your own laptop (with a ssh client installed) for the hands-on sessions!
Knowledge of Linux/Unix commands is necessary.
Knowledge of either C/C++, Fortran or Python programming language is necessary.

Sign up

Linux basic course
2024-05-16 09:00 - 13:30 | Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, Netherlands
Are you interested in using the High Performance Computing Cluster (HPC) but lack the basic Linux knowledge? Join the free 5 hours course on the basics of Linux for working on the HPC. You will learn the Linux commands and skills needed to create repetitive tasks. The course is organized by FB-IT and SRF with contributions from WUR scientists experienced on the HPC.
Read more

Organised by
WUR FB-IT and WUR Shared Research Facilities

Date
Thu 16 May 2024 09:00 to 13:30
Thu 17 October 2024 09:00 to 13:30
*These dates are for the full course. Unable to attend the first session? Don’t worry, you’ll have another opportunity on the second date!

Room
TBA

Price description
The courses are free when you already have a user account on our HPC or if your group has a commitment on the HPC. If you do not have an account or a commitment, the fee is 250 euros. This amount will be reduced from your first bill once you start using the HPC after the course.

The course is also open for interested people outside WUR.
Bring your own laptop
Please bring your own laptop to the course.

2nd BioExcel Conference on Advances in Biomolecular Simulations
2024-05-08 08:00 - 17:00
Registration for the 2nd BioExcel Conference on Advances in Biomolecular Simulations is now open!
Date: 20 – 23 October 2024
Venue: Brno, Czech Republic
Following the success of the first BioExcel conference on Advances and Challenges in Biomolecular Simulations, we are pleased to announce our second BioExcel conference on Advances in Biomolecular Simulations. The event gathers the biomolecular research community to explore the latest trends, updates and challenges in the fields of integrative modelling, free energy and drug design, workflows, automation and data integration.
Important dates:
15 March 2024: Abstract submission opens (see instructions under ‘Registration’)
15 April 2024: Registration opens
15 June 2024: Early bird registration closes
15 June 2024: Oral presentation submission closes
20 July 2024: Notification of selected oral presentations
30 September 2024: Registration closes (payment and poster deadline)
Program, speakers and more information via the button!
Read more

Introduction to Supercomputing, part I
2024-05-07 09:00 - 12:30 | Online
If you need to perform many calculations, or analyses that are too big for your own system, clusters and supercomputers will provide the computing power you need. In this course, you will learn how to work with these large computing systems!
Sign up

What will you learn in this training?
In this training you will:
• understand what is high-performance computing (HPC)
• learn basic details on clusters and supercomputers
• do practical exercises on the national supercomputer Snellius effectively
• apply the essential best practices on how to work effectively with large HPC systems
For whom?
Anyone who wants to know how to perform very large computing tasks.
Prerequisites
Basic knowledge of Unix shell is useful.
Language
This webinar will be in English

Sign up

Supercomputing with LUMI
2024-05-02 09:45 - 2024-05-03 16:45 | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands
This two-day hybrid course serves as an introduction to the LUMI architecture and setup. It will include lessons about the hardware architecture, compiling, using software and running jobs efficiently. After the course you will be able to work effectively on both the CPU (LUMI-C) as well as GPU partition (LUMI-G).
Sign Up

What will you learn in this training?
In this training you will:
• connect to LUMI and transfer data from and to the cluster
• understand LUMI’s hardware and effectively compile software on it
• utilize the module system and EasyBuild for software management
• submit and manage jobs with Slurm, including the use of job arrays and GPU/CPU binding
• identify and mitigate I/O bottlenecks in the LUSTRE file system
• create Python environments and run containers on LUMI
For whom?
Anyone who wants to know how to perform very large computing tasks, specifically if you intend to use the LUMI supercomputer in the future.
Prerequisites:
Basic knowledge of the Unix shell and general HPC cluster computing is necessary.
Familiarity with a programming language (C, Fortran, or Python) is highly recommended.
Agenda
Day 1:
09:45 – Course introduction
10:00 – Hardware architecture (40 min)
10:40 – Cray Programming Environment (45 min)
11:25 – Break
11:55 – How to access LUMI (35 min)
12:30 – Lunch break
13:30 – Exercises (30 min)
14:00 – Modules (35 min)
14:35 – Exercises: Exploring the modules (15 min)
14:50 – Break
15:20 – Software (55 min)
16:15 – Exercises (30 min)
16:45 – Wrap-up of the day and free Q&A
Day 2:
9:45 – Short welcome, recap and plan for the day
10:00 – Slurm 1 (75 minutes)
11:15 – Break
11:45 – Slurm 2: Binding (45 minutes)
12:30 – Lunch break
13:30 – Slurm exercises (30 minutes)
14:00 – Using Lustre (30 minutes)
14:30 – Containers on LUMI (60 minutes including demo or exercises)
15:30 – Break
16:00 – LUMI support and documentation (20 minutes)
16:20 – LUMI in The Netherlands (15 minutes)
16:35 – What else do we offer and what did we not cover and how can I learn about it? (10 minutes)
16:45 – Q&A and wrap-up
Cannot participate onsite in Amsterdam?
Don’t worry! We are also setting up an online option for participation, so you are also welcome to participate from home (only with potentially limited support for exercises).

Sign up

Advanced Topics in Scientific Visualization with Blender: Geometry, Scripts, Animation, Action!
2024-04-25 10:00 - 2024-05-03 12:00 | Online
This course is a follow-up to our introductory Blender course. We assume you are familiar with working with Blender and have some experience with topics such as the Blender UI, 3D meshes, materials, lighting and cameras.
Sign up

Course Setup
In this course you will learn a number of advanced Blender topics:
* The basics of the Python API that is available in Blender. You will learn how the API is structured and eventually start making some simple geometry with code. This can be used, for example, for writing custom import scripts or to perform operations that you would otherwise do manually.
* The node-based shader editor that is used to create and edit materials. In our introductory Blender course we did go into detail on materials, but without describing the node-based shader networks that are the basis of materials. Here, we go deeper into these node network and how to edit them.
* More advanced animation topics, such as shape keys.
Another important part of the course is that you will work on a visualization based on your own research or other endeavors.
The basis of the course is self-paced training during 10 days, using course materials that we provide (videos and exercises) and with some short online sessions. During the course period you can work on the materials in your own pace. We provide a Discord communication channel with the course teachers that you can use for questions and feedback during the course. We use a small number of online plenary sessions spread over the indicated two-week period, beginning with an introductory webinar of two hours and follow-up feedback sessions. These are used to discuss your projects and make sure you are able to make progress.
Prerequisites

Basic knowledge of Blender: getting around the interface, making and adding geometry, some basics on materials
Basic knowledge of Python
An idea and/or some data for your own project to work on during the course.
You will need to have your own laptop with Blender installed (http://www.blender.org)

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Introduction Scientific Visualisation with Blender: Data, Lights, Camera, Action!
2024-04-23 09:00 - 17:00 | SURF Amsterdam, Science Park 140, Amsterdam, 1098 XG, Netherlands
Would you like to make 3D visualizations that are visually more attractive than what ParaView or VisIt can provide? Do you need an image for a grant application that needs to look spectacular? Would you like to create a cool animation of your simulation data? Then this course may be for you!
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Goal
The goal of this course is to provide you with hands-on knowledge to produce great images and basic animations from 3D scientific data. We will be using the open-source package Blender (http://www.blender.org), which provides good basic functionality, while also being usable for advanced usage and general editing of 3D data. It is also a lot of fun to work with (once you get used to its graphical interface).
Example types of relevant scientific data are 3D cell-based simulations, 3D models from photogrammetry, (isosurfaces of) 3D medical scans, molecular models and earth sciences data. Note that we don’t focus on information visualization of abstract data, such as graphs (although you could convert those into a 3D model first and then use them in Blender).
We like to encourage participants to bring along the data they normally work with, or a sample thereof, and would like to apply the course knowledge to.
For whom?
Anyone interesting in learning how to design attractive visualizations. We assume the context to be an academic setting, but it is not make many assumptions on use cases for Blender, and we are happy to help to how we can use Blender to make attractive visuals of the data.
Prerequisites:
It helps to have some familiarity with basic 3D graphics concepts (transformations, rendering), but it is not mandatory.
You will need to have a laptop, preferably with an acceptable GPU, where you can install Blender during the course.

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ParaView for (remote) visualizations
2024-04-19 09:00 - 14:00 | Eindhoven University of Technology, De Zaale 32, Eindhoven, Netherlands
In this course you will get to know the fundamentals of scientific visualisation using ParaView. The main topics will cover the 3D data manipulation model and pipelines, learning how to work with simulation data effectively. Practical exercises with different scientific examples will help you to apply these concepts.
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Prerequisites

You will need to have your own laptop with ParaView installed (https://www.paraview.org/)

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Energy Aware Simulations
2024-04-18 09:00 - 14:00 | Eindhoven University of Technology, De Zaale 32, Eindhoven, Netherlands
Did you know that an optimal use of applications or code development can have an impact in the environment? The energy usage of computing infrastructure is becoming an increasingly prominent topic for computing systems design and usage. In this course you will learn about the basics behind energy efficient computing.
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What?
This course will present some tools and technologies that allow a user/software-developer to understand their energy usage in terms of energy analysis of the software that is being deployed on the system. You will get an overview on how to optimize the use of computing systems and application development for the purpose of energy efficiency, rather than keeping a focus on performance or memory usage. You will learn how to do green coding and work with applications in a sustainable way. Some of the main topics will include:

Overview of the data center energy footprint
Energy usage and energy-aware computing on HPC systems

Who?

Everyone interested in learning how to understand energy usage of their software.

Requirements:

Basic knowledge of Linux
Basic programming experience is recommended

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.

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