Computing Course November 2022

Name: Computing Course November 2022
Start: 2022-11-22T08:30:00+01:00
End: 2022-11-23T17:00:00+01:00
Location: WCW Congreszalen

22 Nov 2022, 08:30 → 23 Nov 2022, 17:00 Europe/Amsterdam

Z011 (WCW Congreszalen)

Z011

WCW Congreszalen

Science Park 125 1098 XG Amsterdam

Description

Join our two-day computing course (or parts of it) to learn about the following topics and more:

First day focus: 'You and computer resources'

Nikhef colleagues will talk about Nikhef's centralised services, give hands-on workshops, practical examples and do's and don'ts of which services (not) to use and how. This day will cover a broad range of topics, including but not limited to the following:

How to login; (protecting) ssh keys, proxy tunnels
General unix principles, basic scripting and programming
How to use interactive nodes, login servers and storage (dCache) and why
Using certificates, how to; security, how user environments work and analysis frameworks
Fall in love with Stoomboot, batch jobs, GPU's, system queues
Learn how to work with CVMFS, containers and Conda
Where to go for help (we don't bite, and we have cake!)

Second day focus: 'You and data'

Colleagues of Nikhef and CWI will take you through the world of Research Data Management, in a mix of theoretical and practical courses. The goal of the day is to give you the knowledge, setup and experience to intertwine RDM in your (daily) work/research. Including (but not limited to) the following topics:

FAIR principles, Dublin Core Metadata standard, create your own ORCID
How to fill in a (mock) data management plan & Code of Conduct
Adding licenses for data and software re-usability, and why this is crucial
Research information repositories (Zenodo, arXiv); how to use them
Importance of, and how to do (immutable) journal keeping
How to relate journal entries (and Jupyterhub) to corresponding data

*Note for PhD students: the second day of the course ('You and data') is mandatory to follow at least once during your PhD.

https://nikhef.zoom.us/j/93069538465?pwd=d2xGelRxaUNuSjFYaXUwZjNkTU5IUT09

Registration

Participants

Contact

cvaendel@nikhef.nl

+31628377405

Tuesday, 22 November
- Tue, 22 Nov
- Wed, 23 Nov
- 08:30 → 17:00
  Computing Course: You and computer resources
  - 08:30
    
    Walk-in & Coffee 30m
  - 09:00
    Welcome & Introduction 15m
    
    Introduction of the services that are going to be talked about in the Computing Course
    
    Know where to ask for help with questions or problems
    
    Know where to find documentation
    
    For newcomers: highlight the centralised services of Nikhef
    
    Speaker: Jeff Templon
    
    Nikhef-CompCourse-intro-2022.pdf
  - 09:15
    You and others; Security & Privacy 15m
    
    Understand why security is important for you and your colleagues
    
    Learn basic measures to work securely
    
    Understand what is meant with privacy: rights and responsibilities
    
    Speaker: Ronald Starink
    
    ComputingCourse-2022-Security-&-Privacy.pdf
  - 09:30
    You and a laptop 30m
    
    Know how to encrypt your harddrive
    
    Know how to backup your laptop
    
    Know how to setup EduVPN
    
    Know how to mount your home dir on your laptop; do’s and don’ts
    
    Know about different local storage areas; and which to use for what
    
    Speaker: Bart van der Wal
    
    You and A Laptop.pdf
  - 10:00
    You, your laptop, and somebody else; how to work together 1h
    
    Know how to send big files: SURF Filesender
    
    Know how to find and use SURFdrive and CernBox
    
    Understand which services are safe to use and which are not
    
    Know how to use Identity Services & Federated Login
    
    Know how to use Zoom and Mattermost
    
    Speaker: David Groep (Nikhef)
    
    NikhefCC-2022-Somebody-else.pdf
  - 11:00
    
    Coffee 20m
  - 11:20
    You, login and Linux 1h
    
    Know how to login; ssh keys, protecting ssh keys, do’s and don’t
    
    Understand basic principles of security with passwords
    
    Know how to setup and safely use (proxy) tunnels; do’s and don’ts
    
    Know how to manage your personal home page
    
    Understand and apply general unix principles
    
    Know about the basics of scripting and programming
    
    Know how to use the most common command line tools
    
    Understand file permissions and how to change them
    
    Understand how to use login servers and what they’re not intended for
    
    Speaker: Dennis van Dok
    
    You, login and linux
    
    backup
  - 12:20
    
    Lunch 1h 10m
  - 13:30
    You, Jupyter, submit nodes and interactive nodes 45m
    
    Understand shared resource etiquette for using interactive nodes
    
    Understand when to use your home directory, /project, /data, and /dcache for storage (Stoomboot)
    
    Know how to login and open Jupyter Notebooks on callysto.nikhef.nl (JupyterHub)
    
    Know how to setup a user environment to run group’s analysis framework (with conda in some cases)
    
    Know how to obtain a grid x509 proxy certificate and add it to a browser
    
    Understand basic principles of security with certificates
    
    Know how to view your Nikhef dcache storage from your browser
    
    Speakers: Mary Hester (Nikhef), Roel Aaij
    
    certs-walk-through.pdf
    
    jupyterhub-pres-nov-2022.pdf
    
    TCS-enduser-request-guide-NL.pdf
  - 14:15
    
    Coffee 30m
  - 14:45
    You, stoomboot, and a thesis as a present 55m
    
    Understand when and how to submit a (CPU) batch job
    
    Understand basic principles and use of CVMFS, Containers and Conda
    
    Know how batch system queues work and what resources are available
    
    Know how to write a job description file for a (local? Grid?) batch job
    
    Know how to write a batch script (script that runs non-interactively & what is diff with previous?)
    
    Know how to write data to dcache using data transfer protocols such as xrootd, webdav, gridftp
    
    Understand the pitfalls for scaling up batch jobs
    
    Speaker: Dennis van Dok
    
    You, stoomboot, and a thesis as a present
    
    backup
  - 15:40
    When the stoomboot is not enough 40m
    
    Understand when and how to submit a GPU job
    
    Know how to add VO information to grid proxy certificate (use grid-proxy-init / voms-proxy-init)
    
    Know how to write efficient code, and what not to do
    
    Know how to find your experiment framework (sft.cern.ch)
    
    Speaker: Roel Aaij
    
    Computing Course Docs
    
    Efficient_Coding.pdf
  - 16:20
    When you are in need of some help 20m
    
    Who are you going to call?
    
    Where to go when something is wrong
    
    Learn about basic troubleshooting tools
    
    Helpdesk, status.io, stbc users mailinglist
    
    Office Hours
    
    Speaker: Bart van der Wal
    
    When you are in need of some Help.pdf
Wednesday, 23 November
- Tue, 22 Nov
- Wed, 23 Nov
- 09:00 → 17:00
  Computing Course: You and data
  - 09:30
    
    Walk-in & Coffee 30m
  - 10:00
    You and your research data 30m
    
    Know about the FAIR principles and are able to assess your own data product with respect to these principles.
    
    Know the 5 Principles and know where to find the full text and the Standards for good research practices (section 3).
    
    Know about the Code of Conduct for Scientific integrity (2018) and its relation to reproducibility, documentation, reporting (including FAIR meta-data), and the prevention of CoIs.
    
    Know that students' reports are to be treated in confidence.
    
    Know about the Dublin Core meta-data elements
    
    Speaker: Reinder Radersma (Data Competence Center - CWI/NWO-I)
    
    Netherlands+Code+of+Conduct+for+Research+Integrity_2018_UK.pdf
    
    Nikhef-computing-course-2022-care-about-your-data.pdf
  - 10:30
    When your data becomes part of something bigger 1h 30m
    
    Know common persistent identifier schemes; at least DOI, hdnl.net and ORCID.
    
    Possess an ORCID identifier and know how to update basic information in their ORCID record.
    
    Know the importance of applying licenses to data and software for re-usability.
    
    Know the basic licenses for data and software, and know where to find guidance on license application and the main differences between licenses.
    
    Know the basic outline of a data management plan.
    
    Know how to fill in a mock data management plan in NWO format using the on-line tools.
    
    Speaker: David Groep (Nikhef)
    
    datainhdf5format.m
    
    NikhefCC-2022-Data-and-Software.pdf
  - 12:00
    
    Lunch 1h
  - 13:00
    When software enters the stage 2h
    
    Learn how to structure directories to manage processes, incoming, intermediate, and final research data, and to keep (persistent) references to data elements relative to its root.
    
    Learn about research information repositories, and at least get to know Zenodo and arXiv.
    
    Learn how to upload mock data or slides to Zenodo (in the sandbox.zenodo.org environment) and complete the meta-data requirements.
    
    Learn about the importance of (immutable) journal keeping and how to relate journal entries (and Jupyter notebooks) to the corresponding data
    
    Speaker: Roel Aaij
    
    Computing Course Docs
    
    Software_Stage.pdf
  - 15:00
    
    Coffee 20m
  - 15:20
    When you are in need of some help 1h 40m
    
    Know where to find research data management guidance at Nikhef (web pages, mail, in-person).
    
    Know where to find help & guidance for research issues and integrity at Nikhef
    
    Room for questions and in-depth help
    
    Speaker: David Groep (Nikhef)
    
    NikhefCC-2022-Need-Help.pdf
    
    stbc-users.png
    
    STBC-Users self-help Mattermost channel