JupyterLab: Difference between revisions

From Alliance Doc
Jump to navigation Jump to search
(App introduction reviewed, new sections)
(No more translation for this page.)
 
(43 intermediate revisions by 5 users not shown)
Line 1: Line 1:
{{draft}}
#REDIRECT [[Jupyter#JupyterLab]]
 
== Introduction ==
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 subsection [[JupyterHub#JupyterHub_on_clusters|JupyterHub on clusters]] contains the list of available Jupyter hubs at Compute Canada.
 
== Launching a JupyterLab server as a job ==
[[File:JupyterHub_Server_Options.png|thumb|''Server Options'' form on Béluga's JupyterHub]]
On [[JupyterHub#JupyterHub_on_clusters|Béluga and Hélios]], once the authentication is done on [[JupyterHub#JupyterHub_on_clusters|JupyterHub]], your Web browser is redirected to either a) a previously launched Jupyter server or b) a form that allows you to configure and submit a new interactive session on the cluster. In any case, the JupyterLab server is running on dedicated compute resources.
 
In the ''Server Options'' form, you can:
* Set all [[JupyterHub#Compute_resources| compute resources]] options you need for the session
* Select ''JupyterLab'' as the ''[[JupyterHub#User_Interface|User Interface]]''
* Start the JupyterLab server by clicking the ''Start'' button
 
== 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'':
** 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]]
* ''Softwares'' (blue cubic icon):
** Compute Canada modules can be loaded and unloaded in the JupyterLab session
** The search box can search for [[Available software|available modules]] and give the result in the ''Available Modules'' 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 and 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.
 
=== Application area on right ===
* The ''Launcher'' tab is opened by default
** It contains all available [[#Jupyter_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.
 
== Jupyter 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.
 
=== Terminal ===
 
[[File:JupyterLab_Launcher_Terminal.png|thumb|Terminal launcher button]]
This 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
 
=== Python 3.x (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'')
 
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
 
=== OpenRefine ===
 
=== RStudio ===
 
[[File:JupyterLab_Launcher_RStudio.png|thumb|RStudio launcher button]]
To enable the ''RStudio'' 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 working
* 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 ===
 
=== 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

Latest revision as of 16:21, 11 January 2022

Redirect to:

Retrieved from "https://docs.alliancecan.ca/mediawiki/index.php?title=JupyterLab&oldid=109719"