You will need some way to manage files, connect to SLAC computers and open display windows. Generally that will be a combination of using terminal windows and an X-windows systems for graphics.
There are two primary approaches you can take here:
- Do everything "natively" in Windows—this may be more straightforward, but may be a bit more difficult as you get to more advanced topics.
- Use the Windows Subsystem for Linux—this takes a bit more work to setup, but will give you a development environment more similar to what is often used in labs (i.e., unix-based, as opposed to Windows).
Both of these options are valid, but using the Windows Subsystem for Linux may make it easier to follow documentation in the future.
As of Build 2020, Microsoft has released Windows Terminal 1.0, which can be installed from the Microsoft Store.
Windows Terminal includes many modern terminal emulator features and is generally recommened over cmd.exe or older solutions like Cygwin.
As of Windows 10 build 14328 (released in 2016), it is now possible to set up a Unix-like terminal on Windows, using the following guide:
You can choose from a number of Linux systems, though Ubuntu is recommended, unless you have previous experience with a specific Linux system.
Following these instructions will set-up a Linux system within your Windows laptop. A few notes regarding this:
- Your Linux home directory will be:
/home/<your_linux_username>. - Since you have a Linux system, installation of new programs should be done following Linux installation
instructions and using the Linux terminal tools such as
apt-get. - Your Windows files will be located at:
/mnt/c/Users/<your_windows_username>/. Here you can find your usual "Documents", "Pictures", "Downloads", etc. folders you should be familiar with.
The X Windows system is a very common way to open connections to and send graphics from processes running on remote computers. It is generically useful and we recommend you install it if you are using a windows laptop.
Download and run the installer to install VcXsrv. You will need to make sure the installed VcXsrv application is running to use the window forwarding features; if you shut down/restart your computer, you will need to restart the application.
You are going to need some way to edit files. I strongly recommend that you do not use Notepad, WordPad, or other built-in Windows editors to try and edit software files.
There are many different options, here is a summary of some of your choices:
The Windows 10 Linux shell should already have 'vim' installed and accessible from within a Linux shell terminal; you can verify by typing
which vim
which should print:
/usr/bin/vim
If you wish to use emacs instead, I recommend you install via your Linux terminal:
sudo apt-get emacs
The tools that you are most likely to need on your personal computer in order to do research "git", which is a file versioning system and "conda", which is a combination of python and a software package management system.
Note that the following documentation assumes you are using the Linux shell via the Windows Subsystem for Linux.
git is a versioning system that is pretty ubiquitous in our work. It lets many users work together to manage a large set of files. This can be set of software, or a paper draft, or some documentation, or pretty much any kind of files.
I recommend using the instructions under using "Installing Git on Ubuntu" on the page below:
Running the following command in a terminal window will setup git and use it to "clone" this Bootcamp:
# Install git using apt-get
sudo apt-get update
sudo apt-get install git
# "Clone" this repository into a directory called "BootCamp"
git clone https://github.com/KIPAC/BootCamp.git
(The lines that start with '#' are comments.)
conda is a combination of python and a software package management system. You can either install the full anaconda package or your can install miniconda, a minimal installer that bootstraps itself and only installs the package you need.
Note that the full anaconda distribution comes with a lot of tutorials and extra things, so you might want to install that version.
You can download the Linux version of anaconda from here:
I recommend installing anaconda under your home directory '~/Applications/' or whevever is equivalent on your distribution.
Once you have installed anaconda you can also set up your terminal windows to activate conda for that terminal by doing this:
# Activate conda
. ~/Applications/anaconda3/etc/profile.d/conda.sh
# "Activate" the "base" conda environment
conda activate
(The lines that start with '#' are comments.)
You can download miniconda from there, (make sure to get the python 3 version):
If you go the route of installing miniconda there are a number of packages, such as jupyter notebooks that you will likely need to install.
Running the following commands in a terminal window will install a minimal set of packages to let you run jupyter notebooks locally.
# Activate conda, if you ran conda init when you installed
# miniconda you don't need to do this
. /Users/echarles/miniconda3/etc/profile.d/conda.sh
# Create a conda environment to work these examples
conda create --name kipac python
# Install the stuff you need (from the conda-forge software 'channel')
conda install --name kipac -c conda-forge numpy scipy jupyter
# "Activate" the kipac environment
conda activate kipac
(The lines that start with '#' are comments.)
Alternatively, you can run
conda env create -f kipac-env.yaml
conda activate kipac
to create and activate an environment named kipac that has been prepared in advance.
Note that you will need to run
conda activate kipac
each time you begin a new session (i.e., open a terminal).
You will need to perform a few extra steps to get Jupyter to use your favorite web browser when displaying notebooks.
You need to define a BROWSER variable. To do this open up ~/.bashrc using your text editor and add the following line:
export BROWSER="/mnt/c/Program Files (x86)/Google/Chrome/Application/chrome.exe"
If you are using a different web browser than Chrome (example above) you will need to modify the path to point to the appropriate executable.
Next enter the following commands:
jupyter notebook --generate-config
echo c.NotebookApp.use_redirect_file = False >> ~/.jupyter/jupyter_notebook_config.py
You may need to close and restart your terminal for the changes to take effect.
If you want to start a notebook you can then do:
# Start a notebook server in the current directory that you are in
jupyter notebook
Once you have started a notebook server you will want to navigate to the notebook that you want to run. Let's start with the basic python / notebook tutorial. In your browser you can selection that notebook to open it.
BootCamp ->Python -> Python (1).ipynb
Note. You can get you notebook browser to start up in a different folder in a few different ways. For example you could:
# Version one, go to a directory and start the notebook server there
cd ~/BootCamp/Python
jupyter notebook
# Version two, use the --notebook-dir option
jupyter notebook --notebook-dir="BootCamp/Python"