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layout venue address country language latitude longitude humandate humantime startdate enddate instructor helper email collaborative_notes eventbrite
workshop
University of Arizona
online
us
en
0
0
June 3-4, 2024
9:00 am - 12:00 pm
20240603
20240604
Michele Cosi
Uwe Hilgert
KEYS Crew
KEYS Staff

INTRODUCTION TO SCIENCE COMPUTATION

General Information

{% comment %} INTRODUCTION {% endcomment %}

{% if site.carpentry == "swc" %} {% include swc/intro.html %} {% elsif site.carpentry == "dc" %} {% include dc/intro.html %} {% elsif site.carpentry == "lc" %} {% include lc/intro.html %} {% endif %}

{% comment %} AUDIENCE Explain who your audience is. (In particular, tell readers if the workshop is only open to people from a particular institution. {% endcomment %}

{% if site.carpentry == "swc" %} {% include swc/who.html %} {% elsif site.carpentry == "dc" %} {% include dc/who.html %} {% elsif site.carpentry == "lc" %} {% include lc/who.html %} {% endif %}

{% comment %} LOCATION This block displays the address and links to maps showing directions if the latitude and longitude of the workshop have been set. You can use https://www.latlong.net/ to find the lat/long of an address. {% endcomment %}

Where:This training will be delivered in hybrid format. The organizers will provide online participants with the information needed to connect to this workshop.

{% comment %} DATE This block displays the date and links to Google Calendar. {% endcomment %}

{% if page.humandate %}

When: {{page.humandate}}. {% include workshop_calendar.html %}

{% endif %}

{% comment %} SPECIAL REQUIREMENTS Modify the block below if there are any special requirements. {% endcomment %}

Requirements: {% if online == "false" %} Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. {% else %} Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. {% endif %} They should have a few specific software packages installed (listed below).

{% comment %} ACCESSIBILITY Modify the block below if there are any barriers to accessibility or special instructions. {% endcomment %}

Accessibility: {% if online == "false" %} We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

  • The room is wheelchair / scooter accessible.
  • Accessible restrooms are available.

Material will be provided in advance of the workshop. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

{% else %} We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you

{% endif %}

{% comment %} CONTACT EMAIL ADDRESS

Display the contact email address set in the configuration file. {% endcomment %}

Contact: Please email {% if page.email %} {% for email in page.email %} {% if forloop.last and page.email.size > 1 %} or {% else %} {% unless forloop.first %} , {% endunless %} {% endif %} {{email}} {% endfor %} {% else %} to-be-announced {% endif %} for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

{% comment%} CODE OF CONDUCT {% endcomment %}

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Report a Code of Conduct Incident

{% comment %} Collaborative Notes If you want to use an Etherpad, go to https://pad.carpentries.org/YYYY-MM-DD-site where 'YYYY-MM-DD-site' is the identifier for your workshop, e.g., '2015-06-10-esu'. Note we also have a CodiMD (the open-source version of HackMD) available at https://codimd.carpentries.org {% endcomment %}

{% if page.collaborative_notes %}

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

{% endif %}

Syllabus

(The listing below entails more material than can be taught during the short introductory workshops and can serve as resources to explore the topics in more detail.)

The Command Shell

The command shell (a.k.a. UNIX Shell, Bash Shell, Shell) is a power tool that allows computer users to do complex things with just a few keystrokes. Contrary to graphical user interfaces (GUI) it allows users to direct the computer from a more foundational level, using written commands. Even what happens when you click on items in GUIs is directed by written commands. Working in the 'Shell' helps users combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Shell proficiency is fundamental to using a wide range of other powerful tools and computing resources, including “high-performance computing” supercomputers.

Using the Bash Shell the workshop will introduce these concepts and procedures:

  • Graphical User Interface and Command Line
  • Navigation With Commands
  • Files and Directories
  • Directory Structure
  • Data Cleanup
  • Proprietary Data Formats
  • History and Tab Completion
  • Pipes and Redirection
  • Creating and Running Shell Scripts
Additional Resources:

Remote Computing

Commercial-grade computers are great tools for daily tasks: note taking, word editing, light computation, web searching, and communication. The research world, however, requires machines with larger computational power such as the University of Arizona’s HPC (High-Performance Computing) system. HPCs are used to simulate, compute, extrapolate and generate data using popular research-grade software or novel tools maintained by scientists all around the world.

This section covers the basics for understanding the structure of the UA HPC, including navigation, storage, and job submission. Additionally, we are going to cover GitHub, a powerful platform that researchers and scientists use to communicate and develop scientific software used for research. The Remote Computing section introduces:

  • Creating and connecting to the HPC using Secure Shell
  • The UA HPC structure
  • The SLURM workload manager and commands
  • GitHub and introductory Git commands
Additional Resources:

Syllabus subject to change if necessary.

{% comment %} SETUP

Delete irrelevant sections from the setup instructions. Each section is inside a 'div' without any classes to make the beginning and end easier to find.

This is the other place where people frequently make mistakes, so please preview your site before committing, and make sure to run 'tools/check' as well. {% endcomment %}

Setup

To participate in a {% if site.carpentry == "swc" %} Software Carpentry {% elsif site.carpentry == "dc" %} Data Carpentry {% elsif site.carpentry == "lc" %} Library Carpentry {% endif %} workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

{% comment %} For online workshops, the section below provides:

  • installation instructions for the Zoom client
  • recommendations for setting up Learners' workspace so they can follow along the instructions and the videoconferencing

If you do not use Zoom for your online workshop, edit the file _includes/install_instructions/videoconferencing.html to include the relevant installation instructions. {% endcomment %} {% if online != "false" %} {% include install_instructions/videoconferencing.html %} {% endif %}

{% comment %} These are the installation instructions for the tools used during the workshop. {% endcomment %}

{% if site.carpentry == "swc" %} {% include swc/setup.html %} {% elsif site.carpentry == "dc" %} {% include dc/setup.html %} {% elsif site.carpentry == "lc" %} {% include lc/setup.html %} {% elsif site.carpentry == "incubator" %} Please check the "Setup" page of [the lesson site]({{ site.incubator_lesson_site }}) for instructions to follow to obtain the software and data you will need to follow the lesson. {% endif %}