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layout carpentry venue address country language latlng humandate humantime startdate enddate scw_project instructor helper email collaborative_notes eventbrite
workshop
sa2c
Swansea University
Zoom; link circulated by email
gb
en
Nov 10-11, 2021
9:30am - 1:00 pm
2021-11-10
2021-11-11
scw1389
Ed Bennett
Michele Mesiti
Tom Pritchard

{% comment %} See instructions in the comments below for how to edit specific sections of this workshop template. {% endcomment %}

{% comment %} HEADER

Edit the values in the block above to be appropriate for your workshop. If the value is not 'true', 'false', 'null', or a number, please use double quotation marks around the value, unless specified otherwise. And run 'make workshop-check' before committing to make sure that changes are good. {% endcomment %}

{% comment %} EVENTBRITE

This block includes the Eventbrite registration widget if 'eventbrite' has been set in the header. You can delete it if you are not using Eventbrite, or leave it in, since it will not be displayed if the 'eventbrite' field in the header is not set. {% endcomment %} {% if page.eventbrite %}

<iframe src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt" frameborder="0" width="100%" height="280px" scrolling="auto"> </iframe> {% endif %}

General Information

{% comment %} INTRODUCTION

Edit the general explanatory paragraph below if you want to change the pitch. {% endcomment %} {% if page.carpentry == "swc" %} {% include sc/intro.html %} {% elsif page.carpentry == "dc" %} {% include dc/intro.html %} {% elsif page.carpentry == "lc" %} {% include lc/intro.html %} {% elsif page.carpentry == "sa2c" %} {% include sa2c/intro.html %} {% elsif page.carpentry == "sa2c_mpi" %} {% include sa2c_mpi/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 page.carpentry == "swc" %} {% include sc/who.html %} {% elsif page.carpentry == "dc" %} {% include dc/who.html %} {% elsif page.carpentry == "lc" %} {% include lc/who.html %} {% elsif page.carpentry == "sa2c" %} {% include sa2c/who.html %} {% elsif page.carpentry == "sa2c_mpi" %} {% include sa2c_mpi/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://itouchmap.com/latlong.html to find the lat/long of an address. {% endcomment %} {% if page.latlng %}

Where: {{page.address}}. Get directions with OpenStreetMap or Google Maps.

{% endif %}

{% 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: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by {% if page.carpentry == "swc" or page.carpentry == "sa2c" or page.carpentry == "sa2c_mpi" %} Software Carpentry's {% elsif page.carpentry == "dc" %} Data Carpentry's {% elsif page.carpentry == "lc" %} Library Carpentry's {% endif %} Code of Conduct.

Registration: Tocyn Cymru

{% comment %} ACCESSIBILITY

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

Accessibility: We are committed to making this workshop accessible to everybody. Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. 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.

{% 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.

{% comment %} SURVEYS - DO NOT EDIT SURVEY LINKS {% endcomment %} {% if site.carpenty == "swc" or site.carpentry == "dc" or site.carpentry == "lc" %}

Surveys

{% endif %}

Please be sure to complete these surveys before and after the workshop.

{% if site.carpentry == "swc" %}

Pre-workshop Survey

Post-workshop Survey

{% elsif site.carpentry == "dc" %}

Pre-workshop Survey

Post-workshop Survey

{% elsif site.carpentry == "lc" %}

Pre-workshop Survey

Post-workshop Survey

{% endif %}

{% comment %} SCHEDULE

Show the workshop's schedule. Edit the items and times in the table to match your plans. You may also want to change 'Day 1' and 'Day 2' to be actual dates or days of the week. {% endcomment %}

Schedule

{% if page.carpentry == "swc" %} {% include sc/schedule.html %} {% elsif page.carpentry == "dc" %} {% include dc/schedule.html %} {% elsif page.carpentry == "lc" %} {% include lc/schedule.html %} {% elsif page.carpentry == "sa2c" %} {% include sa2c/schedule.html %} {% elsif page.carpentry == "sa2c_mpi" %} {% include sa2c_mpi/schedule.html %} {% endif %}

{% comment %} Collaborative Notes

If you want to use an Etherpad, go to

  http://pad.software-carpentry.org/YYYY-MM-DD-site

where 'YYYY-MM-DD-site' is the identifier for your workshop, e.g., '2015-06-10-esu'. {% endcomment %}

We will use ReCoN, the Swansea University Research Computing Network, for chatting, taking notes, and sharing URLs and bits of code.

{% comment %} SYLLABUS

Show what topics will be covered.

  1. If your workshop is R rather than Python, remove the comment around that section and put a comment around the Python section.
  2. Some workshops will delete SQL.
  3. Please make sure the list of topics is synchronized with what you intend to teach.
  4. You may need to move the div's with class="col-md-6" around inside the div's with class="row" to balance the multi-column layout.

This is one of the places where people frequently make mistakes, so please preview your site before committing, and make sure to run 'tools/check' as well. {% endcomment %} {% if page.carpentry != "sa2c_mpi" %}

Syllabus

{% if page.carpentry == "swc" %} {% include sc/syllabus.html %} {% elsif page.carpentry == "dc" %} {% include dc/syllabus.html %} {% elsif page.carpentry == "lc" %} {% include lc/syllabus.html %} {% elsif page.carpentry == "sa2c" %} {% include sa2c/syllabus.html %} {% endif %}

{% endif %}

{% 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 page.carpentry == "swc" %} Software Carpentry {% elsif page.carpentry == "dc" %} Data Carpentry {% elsif page.carpentry == "lc" %} Library Carpentry {% endif %} workshop, you will need access to the software 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.

{% if page.carpentry == "sa2c" %}

{% comment %} Start of 'shell' section. {% endcomment %}

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
      {% comment %} Git 2.18.0 Setup {% endcomment %}
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. Select “Use the nano editor by default” and click on “Next”.
      3. {% comment %} Adjusting your PATH environment {% endcomment %}
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
      4. {% comment %} Choosing the SSH executable {% endcomment %}
    4. Click on "Next".
      5. {% comment %} Configuring the line ending conversions {% endcomment %}
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
      6. {% comment %} Configuring the terminal emulator to use with Git Bash {% endcomment %}
    6. Select "Use Windows' default console window" and click on "Next".
      7. {% comment %} Configuring experimental performance tweaks {% endcomment %}
    7. Click on "Install".
      8. {% comment %} Installing {% endcomment %} {% comment %} Completing the Git Setup Wizard {% endcomment %}
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

macOS

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

{% comment %} End of 'shell' section. {% endcomment %}

{% elsif page.carpentry == "sa2c_mpi" %}

{% comment %} Start of 'mpi' section. {% endcomment %}

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly. In the MPI workshop, we will use it to interact with the Sunbird cluster.

Windows

  1. Download the Cygwin installer.
  2. Run the installer and follow the steps below:
      {% comment %} Git 2.18.0 Setup {% endcomment %}
    1. Click on "Next" six times. You don't need to change anything in the Information and location screens.
    2. In the select packages screen, select the latest version of the following packages
      1. ssh
      2. gcc-core and gcc-fortran
      3. openmpi, libopenmpi40, libopenmpihf08_40, libopenmpiusef08_40 and openmpi-devel
      4. make and cmake
      5. git
    3. Click "Next" twice.
    4. Click "Finish".

This will provide you with both the Cygwin Shell and OpenMPI.

macOS

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash.

MPI Worshop Requirements

OpenMPI is an open source implementation of the MPI standard. It is widely available and straightforward to install on most systems. However, when using using Visual Studio on Windows, it is easier to install and use the Microsoft implementation of MPI.

Follow the instruction on the workshop setup page. Install an implementation of MPI, CMocka or FRUIT, and the CubeGUI from the Scalasca section.

{% endif %}
{% comment %} Start of 'Git' section. GitHub browser compatability is given at https://help.github.com/articles/supported-browsers/{% endcomment %} {% comment %}

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Windows

Git should be installed on your computer as part of your Bash install (described above).

macOS

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Linux

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

{% endcomment %} {% comment %} End of 'Git' section. {% endcomment %}
{% comment %} Start of 'editor' section. {% endcomment %} {% comment %}

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

macOS

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

{% endcomment %}{% comment %} End of 'editor' section. {% endcomment %}
{% comment %} Start of 'Python' section. Remove the third paragraph if the workshop will teach Python using something other than the Jupyter notebook. Details at https://jupyter-notebook.readthedocs.io/en/stable/notebook.html#browser-compatibility {% endcomment %}

{% comment %}

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer. 

<p>
  Regardless of how you choose to install it,
  <strong>please make sure you install Python version 3.x</strong>
  (e.g., 3.6 is fine).
</p>

<p>
  We will teach Python using the <a href="https://jupyter.org/">Jupyter notebook</a>,
  a programming environment that runs in a web browser. For this to work you will need a reasonably
  up-to-date browser. The current versions of the Chrome, Safari and
  Firefox browsers are all
  <a href="https://jupyter-notebook.readthedocs.io/en/stable/notebook.html#browser-compatibility">supported</a>
  (some older browsers, including Internet Explorer version 9
  and below, are not).
</p>

Windows

Video Tutorial
  1. Open https://www.anaconda.com/download/#windows with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.

macOS

Video Tutorial
  1. Open https://www.anaconda.com/download/#macos with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.

Linux

  1. Open https://www.anaconda.com/download/#linux with your web browser.
  2. Download the Python 3 installer for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type 
    bash Anaconda3-
    and then press Tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with: 
    cd Downloads
    Then, try again.
  5. Press Return. You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.
{% comment %}

Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.

{% endcomment %}
{% endcomment %} {% comment %} End of 'Python' section. {% endcomment %}
{% comment %} Start of 'R' section. {% endcomment %} {% comment %}

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

macOS

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.

{% endcomment %} {% comment %} End of 'R' section. {% endcomment %}
{% comment %} Start of 'SQLite' section. {% endcomment %} {% comment %}

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

macOS

SQLite comes pre-installed on macOS.

Linux

SQLite comes pre-installed on Linux.

If you installed Anaconda, it also has a copy of SQLite without support to readline. Instructors will provide a workaround for it if needed.

{% endcomment %} {% comment %} End of 'SQLite' section. {% endcomment %}
{% comment %} Start of 'OpenRefine' section. {% endcomment %} {% comment %}

OpenRefine

For this lesson you will need OpenRefine and a web browser. Note: this is a Java program that runs on your machine (not in the cloud). It runs inside a web browser, but no web connection is needed.

Windows

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It will not run correctly in Internet Explorer.

Download software from http://openrefine.org/

Create a new directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".

Go to your newly created OpenRefine directory.

Launch OpenRefine by clicking openrefine.exe (this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).

If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

Mac

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It may not run correctly in Safari.

Download software from http://openrefine.org/.

Create a new directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory by double-clicking it.

Go to your newly created OpenRefine directory.

Launch OpenRefine by dragging the icon into the Applications folder.

Use Ctrl-click/Open ... to launch it.

If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

Linux

Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.

Download software from http://openrefine.org/.

Make a directory called OpenRefine.

Unzip the downloaded file into the OpenRefine directory.

Go to your newly created OpenRefine directory.

Launch OpenRefine by entering ./refine into the terminal within the OpenRefine directory.

If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

{% endcomment %} {% comment %} End of 'OpenRefine' section. {% endcomment %}

{% comment %} {% endcomment %}

Supercomputing Wales

In this workshop we will use the Supercomputing Wales facilities to learn to use High-Performance Computing. For this, you will need an account on the Supercomputing Wales facilities.

  1. Visit My Supercomputing Wales
  2. Sign in with your Swansea University email and password
  3. Fill in the form requesting a Supercomputing Wales account. Your aaccount request will be processed by an administrator.
  4. Once you receive an email indicating that your account has been created, then revisit My Supercomputing Wales, and log in again if necessary.
  5. Click the "Reset SCW Password" button, and enter a password that you will use to access the Supercomputing Wales hardware. (This does not have to be the same as your Swansea University password.) Click Submit.
  6. Under "Join a project", enter {{page.scw_project}} as the project code for this training session, and click "Join".
{% comment %} End of 'Supercomputing Wales' section. {% endcomment %}

{% if page.carpentry == "sa2c" %} {% comment %} {% endcomment %}

FileZilla

We will use FileZilla to transfer files to and from the Supercomputing Wales facilities.

Windows

  1. Open https://filezilla-project.org/download.php?platform=win64 with your web browser.
  2. Download and run the installer. You only need FileZilla, not FileZilla Pro.
  3. Follow the on-screen instructions. Note that while the installer may try to convince you to install additional software, you do not need to agree to this; if you do not agree to the additional license agreement, FileZilla will still install.
  4. FileZilla has been known to trigger some antivirus and anti-malware applications. You can also use WinSCP, which functions in the same way.

macOS

  1. Open https://filezilla-project.org/download.php?platform=osx with your web browser.
  2. Download and open the Client bundle. You only need FileZilla, not FileZilla Pro.
  3. Copy the FileZilla app to your Applications folder.

Linux

  1. Search for and install FileZilla in your distribution's package manager.
{% comment %} End of 'FileZilla' section {% endcomment %} {% endif %}

{% comment %}

Virtual Machine

Some instructors prefer to have learners use a virtual machine (VM) rather than install software on their own computers. If your instructors have chosen to do this, please:

  1. Install VirtualBox.
  2. Download our VM image. Warning: this file is 1.7 GByte, so please download it before coming to your workshop.
  3. Load the VM into VirtualBox by selecting "Import Appliance" and loading the .ova file.
{% endcomment %}

Install the videoconferencing client

{% comment %} Replace the paragraph below with the relevant installation instructions if you do not use Zoom {% endcomment %}

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

  • Two monitors: If you have two monitors, plan to have your terminal up on one monitor and the video conferencing software on the other.
  • Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
  • Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.
This blog post includes detailed information on how to set up your screen to follow along during the workshop.