Windows for Research

Unlike Linux and macOS, Windows runs on a completely different OS. Many coding environments are adapted to Linux, so Windows users must properly configure their machine to prepare it for a project. This is of special importance when working in environments supporting distributed cyberinfrastructure. Here in many cases Linux is required.

Setting Up the Python Environment

Often you need a specific version of Python. If in doubt, please install the newest one. At time of writing this document it is Python 3.10.5.

Please download and install it from python.org. We recommend that you uninstall Anaconda if you used that before and use the verison from python.org instead.. Development is easier when using a native Python installation instead of anaconda/conda.

To uninstall anaconda, press the Windows key and type “Add or remove programs”. Then, press Enter and search for conda in the “Search this list” box. Remove everything related to anaconda. Note that anaconda may have set some environment variables or added configuration scripts to your .bashrc files in case you use gitbash. Please, remove them and make sure your Python version from python.org works as expected.

To code in Python, we recommend using PyCharm and not VSCode.

Pycharm and Git Bash can be installed with the instructions found in Install.

Installation may be simplified while using chocolatey.

This includes

• gitbash
• pycharm
• emacs
• docker

Before installing docker however you have to set up the appropriate hypervisor at boot time. PLease let us know how you set them for your machine, so we can add some information here. You will likely have to research it.

Please also know that you MUST uninstall virtualbox before you install docker, as old versions of virtualbox are incompatible with docker and it is just easier to uninstall virtualbox and reinstall it.

Next we summarize the installations using chocolatey.

Before installing anything, we recommend that you read the entire section. Especially when installing docker and if you do not have a brand new computer.

Install Chocolatey

To install chocolatey, follow the tutorial at https://github.com/cybertraining-dsc/cybertraining-dsc.github.io/blob/main/content/en/docs/tutorial/reu/chocolatey/index.md

Install Git Bash

Git Bash must be installed with specific configurations, as the discrepancy between Windows and other operating systems can cause errors during runtime, if not properly configured. If Git Bash is already installed, uninstall it by pressing the Windows key and typing Add or remove programs (and press Enter). Then locate and uninstall Git Bash.

To install Git Bash with chocolatey, issue the following command:

$ choco install git.install --params "/GitAndUnixToolsOnPath \
        /Editor:Nano /PseudoConsoleSupport /NoAutoCrlf" -y

The /NoAutoCrlf sets it so that the files are not downloaded via git with Windows line endings. If it were downloaded with such line endings, then it would cause programming bugs. Programmers should Commit As-Is to avoid conflicts.

Install PyCharm, emacs, and Docker

Uninstall PyCharm Community version if already installed on the computer by pressing the Windows key and typing Add or remove programs (and press Enter). Then locate and uninstall PyCharm.

The following command installs PyCharm Professional, among other necessary development programs. To install these programs in an easy manner, issue the following command (you must have chocolatey installed):

$ choco install pycharm emacs docker-desktop -y

PyCharm is advantageous over other IDEs such as VSCode because students receive the professional version of PyCharm for free. Furthermore, PyCharm offers robust features such as Refactor and Inspect Code.

A guide to activating PyCharm with a free professional license is available at https://youtu.be/QPESX-VBnEU

Configure PyCharm

Set hard wrap

Press Ctrl + Alt + S in PyCharm and expand the Editor menu on the left-hand side. Then, click on Code Style and enter 79 in the Hard wrap at: box. Also, check the Wrap on typing checkbox.

This is done so that the text in files is uniformly indented at 79 columns.

Makefile Tab configuration and formatting

To change what the Tab key does in a Makefile, open a Makefile in PyCharm and click on Tab in the bottom right of the PyCharm interface. If you cannot find the Tab button, then click on View in the top-right, go to Appearance, and make sure Status Bar is checked.

After clicking the Tab button in the bottom-right, click on Configure Indents for Makefile... Tab size should be 4.

If PyCharm fails to render your Makefile correctly, right-click on the Makefile in your open files tabs and click Override File Type. If you cannot find Makefile in the list, you must install the Makefile Language plugin for PyCharm.

Preparing for Virtualization

Docker

To enable virtualization for Docker on Windows machines, some preparations must be made. First, if the user has VirtualBox installed it is suggested that they uninstall it and reinstall later if necessary. Some older versions of VirtualBox do not support other virtual images like Windows Subsystem for Linux (WSL).

Next, the BIOS settings must be changed to enable virtualization. To do this, search Advanced startup in the Windows Search Bar and click Restart now. Click Troubleshoot and Advanced startup options and then UEFI Firmware Settings to get into the BIOS. NOTE: These are not exhaustive instructions because computer brands and hardware differ vastly. The main objective is to get into the BIOS and search for any Virtualization or Hyper V options in Windows BIOS configuration. For example, Lenovo brand laptops have a Configure tab in the BIOS and the virtualization settings must be enabled under that menu. Then, the user must exit the BIOS while saving changes.

Better documentation on enabling virtualization, which is recommended by Docker and created by Berkeley, is located at https://bce.berkeley.edu/enabling-virtualization-in-your-pc-bios.html

Lastly, check Windows features with Turn Windows features on or off. For Docker, Hyper-V and Containers must be enabled.

WSL

WSL is a Linux virtual image designed for Windows. WSL 2 is typically used as opposed to WSL 1. To install, type this into administrative PowerShell:

PS> wsl --install

To install a particular distribution, use wsl --install -d <DistroName> instead. The available distributions can be found with

PS> wsl --list --online

After WSL is installed, it can be accessed by typing wsl in Powershell. More documentation can be found in the Microsoft Official Documentation.

Directories in WSL

WSL creates a Linux environment in your Windows directory. To access your directories with WSL, a special syntax is used. For example, your home directory, typically C:\Users\USERNAME and abbreviated to ~ is the following with WSL: /mnt/c/Users/USERNAME/. So to change directories to the Desktop in WSL, use this command:

$ cd /mnt/c/Users/USERNAME/Desktop

where USERNAME is to be replaced with the name of the user.

bashrc

env=~/.ssh/agent.env

agent_load_env () { test -f "$env" && . "$env" >| /dev/null ; }

agent_start () {
    (umask 077; ssh-agent >| "$env")
    . "$env" >| /dev/null ; }

agent_load_env

# agent_run_state: 0=agent running w/ key; 1=agent w/o key; 2=agent not running
agent_run_state=$(ssh-add -l >| /dev/null 2>&1; echo $?)

if [ ! "$SSH_AUTH_SOCK" ] || [ $agent_run_state = 2 ]; then
    agent_start
    ssh-add
elif [ "$SSH_AUTH_SOCK" ] && [ $agent_run_state = 1 ]; then
    ssh-add
fi

unset env

source ~/ENV3/Scripts/activate
cd ~/cm