Computing Course November 2022

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

Z011 (WCW Congreszalen)

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

Tuesday, 22 November

Computing Course: You and computer resources

08:30 Walk-in & Coffee

1 Welcome & Introduction

• 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

2 You and others; Security & Privacy

• 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

3 You and a laptop

• 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

4 You, your laptop, and somebody else; how to work together

• 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

5 You, login and Linux

• 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 You, login, and linux.pdf

12:20 Lunch

6 You, Jupyter, submit nodes and interactive nodes

• 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

7 You, stoomboot, and a thesis as a present

• 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 You, Stoomboot, and a thesis as a present.pdf

8 When the stoomboot is not enough

• 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

9 When you are in need of some help

• 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

Computing Course: You and data

09:30 Walk-in & Coffee

10 You and your research data

• 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

11 When your data becomes part of something bigger

• 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

12 When software enters the stage

• 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

13 When you are in need of some help

• 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