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JupyterLab section's contents
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= JupyterLab = | = JupyterLab = | ||
JupyterLab is now the recommended general-purpose user interface to use on a JupyterHub. | |||
From a JupyterLab server, you can manage your remote files and folders, | |||
and you can launch Jupyter applications like a terminal, (Python 3) notebooks, RStudio and a Linux desktop. | |||
== The JupyterLab Interface == | |||
When JupyterLab is ready to be used, the interface has multiple panels. | |||
[[File:JupyterLab_HomeTab.png|thumb|Default home tab when JupyterLab is loaded]] | |||
=== Menu bar on top === | |||
* In the ''File'' menu: | |||
** ''Hub Control Panel'': if you want to manually stop the JupyterLab server and the corresponding job on the cluster. This is useful when you want to start a new JupyterLab server with more or less resources | |||
** ''Log Out'': the JupyterHub session will end, which will also stop the JupyterLab server and the corresponding job on the cluster | |||
* Most other menu items are related to notebooks and Jupyter applications | |||
=== Tool selector on left === | |||
* ''File Browser'' (folder icon): | |||
** This is where you can browse in your home, project and scratch spaces | |||
** It is also possible to upload files | |||
* ''Running Terminals and Kernels'' (stop icon): | |||
** To stop kernel sessions and terminal sessions | |||
* ''Commands'' | |||
* ''Property Inspector'' | |||
* ''Open Tabs'': | |||
** To navigate between application tabs | |||
** To close application tabs - the corresponding kernels remain active | |||
[[File:JupyterLab_Softwares.png|thumb|Loaded modules and available modules]] | |||
* '''''Software''''' (blue diamond sign): | |||
** Compute Canada modules can be loaded and unloaded in the JupyterLab session. Depending on the module loaded, an icon directing to the [[#Prebuilt_Applications|Jupyter application]] will appear in the ''Launcher'' tab. | |||
** The search box can search for any [[Available software|available module]] and give the result in the ''Available Modules'' sub-panel. Note: some modules are hidden until their dependency is loaded - we recommend that you first look for a specific module with <code>module spider module_name</code> from a terminal. | |||
** The next sub-panel is the list of ''Loaded Modules'' in the whole JupyterLab session. Note: while <code>python</code> and <code>ipython-kernel</code> modules are loaded by default, additional modules must be loaded before launching some other applications or notebooks. For example: <code>scipy-stack</code>. | |||
** The last sub-panel is the list of ''Available modules'', similar to the output of <code>module avail</code>. By clicking on a module's name, detailed information about the module is displayed. By clicking on the ''Load'' link, the module will be loaded and added to the ''Loaded Modules'' list. | |||
=== Application area on right === | |||
* The ''Launcher'' tab is opened by default | |||
** It contains all available [[#Prebuilt_Applications|Jupyter applications and notebooks]], depending on which modules are loaded | |||
=== Status bar at the bottom === | |||
* By clicking on the icons, this brings you to the ''Running Terminals and Kernels'' tool. | |||
== Prebuilt Applications == | |||
JupyterLab offers access to a terminal, an IDE (Desktop), a Python console and different options to create text and Markdown files. This section presents only the main supported Jupyter applications that work with the Compute Canada software stack. | |||
=== Command Line Interpreters === | |||
[[File:JupyterLab_Launcher_Julia.png|thumb|Julia console launcher button]] | |||
[[File:JupyterLab_Launcher_Python.png|thumb|Python console launcher button]] | |||
[[File:JupyterLab_Launcher_Terminal.png|thumb|Terminal launcher button]] | |||
==== Julia Console ==== | |||
To enable the ''Julia 1.x'' console launcher, an <code>ijulia-kernel</code> module needs to be loaded. When launched, a Julia interpreter is presented in a new JupyterLab tab. | |||
==== Python Console ==== | |||
The ''Python 3.x'' console launcher is available by default in a new JupyterLab session. When launched, a Python 3 interpreter is presented in a new JupyterLab tab. | |||
==== Terminal ==== | |||
This application launcher will open a terminal in a new JupyterLab tab: | |||
* The terminal runs a (Bash) shell on the remote compute node without the need of an SSH connection | |||
** Gives access to the remote filesystems (<code>/home</code>, <code>/project</code>, <code>/scratch</code>) | |||
** Allows running compute tasks | |||
* The terminal allows copy-and-paste operations of text: | |||
** Copy operation: select the text, then press Ctrl+C | |||
*** Note: usually, Ctrl+C is used to send a SIGINT signal to a running process, or to cancel the current command. To get this behaviour in JupyterLab's terminal, click on the terminal to deselect any text before pressing Ctrl+C | |||
** Paste operation: press Ctrl+V | |||
=== Available Notebook Kernels === | |||
==== Julia Notebook ==== | |||
To enable the ''Julia 1.x'' notebook launcher, an <code>ijulia-kernel</code> module needs to be loaded. When launched, a Julia notebook is presented in a new JupyterLab tab. | |||
==== Python Notebook ==== | |||
[[File:JupyterLab_Softwares_ScipyStack.png|thumb|Searching for scipy-stack modules]] | |||
If any of the following scientific Python packages is required by your notebook, before you open this notebook, you must load the <code>scipy-stack</code> module from the JupyterLab ''Softwares'' tool: | |||
* <code>ipython</code>, <code>ipython_genutils</code>, <code>ipykernel</code>, <code>ipyparallel</code> | |||
* <code>matplotlib</code> | |||
* <code>numpy</code> | |||
* <code>pandas</code> | |||
* <code>scipy</code> | |||
* Other notable packages: <code>Cycler</code>, <code>futures</code>, <code>jupyter_client</code>, <code>jupyter_core</code>, <code>mpmath</code>, <code>pathlib2</code>, <code>pexpect</code>, <code>pickleshare</code>, <code>ptyprocess</code>, <code>pyzmq</code>, <code>simplegeneric</code>, <code>sympy</code>, <code>tornado</code>, <code>traitlets</code> | |||
* And many more (click on the <code>scipy-stack</code> module to see all ''Included extensions'') | |||
Note: you may also install needed packages by running for example the following command inside of a cell: <code>!pip install --no-index numpy</code> | |||
* For some packages (like <code>plotly</code>, for example), you may need to restart the notebook's kernel before importing the package. | |||
* The installation of packages in the default Python kernel environment is temporary to the lifetime of the JupyterLab session; you will have to reinstall these packages the next time you start a new JupyterLab session. For a persistent Python environment, you must configure a custom Python kernel. | |||
To open an existing Python notebook: | |||
* Go back to the ''File Browser'' | |||
* Browse to the location of the <code>*.ipynb</code> file | |||
* Double-click on the <code>*.ipynb</code> file: | |||
** This will open the Python notebook in a new JupyterLab tab | |||
** An IPython kernel will start running in background for this notebook | |||
To open a new Python notebook in the current ''File Browser'' directory: | |||
* Click on the ''Python 3.x'' launcher under the ''Notebook'' section: | |||
** This will open a new Python 3 notebook in a new JupyterLab tab | |||
** A new IPython kernel will start running in background for this notebook | |||
=== Other Applications === | |||
==== OpenRefine ==== | |||
[[File:JupyterLab_Launcher_OpenRefine.png|thumb|OpenRefine launcher button]] | |||
To enable the ''OpenRefine'' application launcher, an <code>openrefine</code> module needs to be loaded. Depending on the software environment version, the latest version of OpenRefine should be loaded: | |||
* With <code>StdEnv/2020</code>, load module: <code>openrefine/3.4.1</code> | |||
* With <code>StdEnv/2018.3</code>, load module: <code>openrefine/3.3</code> | |||
This ''OpenRefine'' launcher will open or reopen an OpenRefine interface in a new Web browser tab: | |||
* It is possible to reopen an active OpenRefine session after the Web browser tab was closed | |||
* The OpenRefine session will end when the JupyterLab session will end | |||
==== RStudio ==== | |||
[[File:JupyterLab_Launcher_RStudio.png|thumb|RStudio launcher button]] | |||
To enable the ''RStudio'' application launcher, the following three modules need to be loaded: | |||
# <code>gcc</code> | |||
# <code>r</code> | |||
# <code>rstudio-server</code> | |||
Depending on the software environment version, you should load the following two modules (<code>r</code> is loaded automatically): | |||
* With <code>StdEnv/2020</code>, it is not yet supported | |||
* With <code>StdEnv/2018.3</code>, load modules: <code>gcc/7.3.0</code>, <code>rstudio-server/1.2.1335</code> | |||
* With <code>StdEnv/2016.4</code>, load modules: <code>gcc/7.3.0</code>, <code>rstudio-server/1.2.1335</code> | |||
This ''RStudio'' launcher will open or reopen an RStudio interface in a new Web browser tab: | |||
* It is possible to reopen an active RStudio session after the Web browser tab was closed | |||
* The RStudio session will end when the JupyterLab session will end | |||
==== VS Code ==== | |||
[[File:JupyterLab_Launcher_VSCode.png|thumb|VS Code launcher button]] | |||
To enable the ''VS Code'' (Visual Studio Code) application launcher, a <code>code-server</code> module needs to be loaded. Depending on the software environment version, the latest version of VS Code should be loaded: | |||
* With <code>StdEnv/2020</code>, load module: <code>code-server/3.5.0</code> | |||
* With <code>StdEnv/2018.3</code>, load module: <code>code-server/3.4.1</code> | |||
This ''VS Code'' launcher will open or reopen the VS Code interface in a new Web browser tab: | |||
* For a new session, the ''VS Code'' session can take up to 3 minutes to complete its startup. | |||
* It is possible to reopen an active VS Code session after the Web browser tab was closed | |||
* The VS Code session will end when the JupyterLab session will end | |||
==== Desktop ==== | |||
[[File:JupyterLab_Launcher_Desktop.png|thumb|Desktop launcher button]] | |||
This ''Desktop'' launcher will open or reopen a remote Linux desktop interface in a new Web browser tab: | |||
* This is equivalent to running a [[VNC#Compute_Nodes|VNC server on a compute node]], then creating an [[SSH_tunnelling|SSH tunnel]] and finally using a [[VNC#Setup|VNC client]], but you need nothing of all this with JupyterLab! | |||
* It is possible to reopen an active desktop session after the Web browser tab was closed | |||
* The desktop session will end when the JupyterLab session will end | |||
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