General/Jupyternotebook - Revision history

Pysdlb at 08:10, 26 September 2023

2023-09-26T08:10:20Z

Pysdlb: /* Next Steps */

2023-09-14T10:09:00Z

‎Next Steps

Pysdlb at 15:52, 8 November 2022

2022-11-08T15:52:07Z

Pysdlb at 14:49, 9 June 2022

2022-06-09T14:49:10Z

Pysdlb at 09:40, 3 May 2022

2022-05-03T09:40:06Z

Pysdlb at 09:20, 24 May 2021

2021-05-24T09:20:44Z

Ccscj: /* Introduction */

2020-02-07T07:47:48Z

‎Introduction

Pysdlb at 15:39, 6 February 2020

2020-02-06T15:39:07Z

Pysdlb at 15:37, 6 February 2020

2020-02-06T15:37:53Z

Pysdlb at 15:16, 6 February 2020

2020-02-06T15:16:33Z

@@ Line 6: / Line 6: @@
 The Jupyter Notebook is an interactive computing environment that enables users to author notebook documents that include: - Live code - Interactive widgets - Plots - Narrative text - Equations - Images - Video.
-Jupyter notebooks are ideally suited for ''educational purposes only'', however, they have limitations across a network, particularly with the graphical interface. The university does provide a [[Jupyterhub|jupyterhub service]].
+Jupyter notebooks are ideally suited for ''educational purposes only'', however, they have limitations across a network, particularly with the graphical interface. The university does provide a [https://hullacuk.sharepoint.com/Services/JupyterHub/SitePages/Home.aspx JupyterHub service].
-* '''Important''': If you wish to carry out serious python development consider changing to an [[General/Interactive|interactive session]] and using a [[Applications/Miniconda|virtual environment]] within your account and using the editors [[Training/Linux_-_vi_editor|vi]] or [[Training/Linux_-_Nano_editor|nano]].
+* '''Important''': If you wish to carry out serious Python development consider changing to an [[General/Interactive|interactive session]] and using a [[Applications/Miniconda|virtual environment]] within your account and using the editors [[Training/Linux_-_vi_editor|vi]] or [[Training/Linux_-_Nano_editor|nano]].
-* '''Alternatively''', if you wish to edit files on your local machine there are many IDEs which provide a means for transferring python files across to Viper seamlessly, examples of these are [https://www.jetbrains.com/pycharm/ PyCharm] and [https://code.visualstudio.com/ Visual Studio Code]. (''All suitable for Linux, macOS and Windows'').
+* '''Alternatively''', if you wish to edit files on your local machine there are many IDEs which provide a means for transferring Python files across to Viper seamlessly, examples of these are [https://www.jetbrains.com/pycharm/ PyCharm] and [https://code.visualstudio.com/ Visual Studio Code]. (''All suitable for Linux, macOS and Windows'').
 ==Setting up==
@@ Line 111: / Line 111: @@
 module load python/anaconda/4.6/miniconda/3.7
-# Use the virtual environment for python customization (change <user>)
+# Use the virtual environment for Python customization (change <user>)
 source activate /home/user/.conda/envs/jupyter
@@ Line 199: / Line 199: @@
 ====SSH Tunneling with MobaXterm====
-In MobaXterm tunnels are set up independently to an SSH connection. To set up a tunnel, open the Tunneling menu by either going to ''Tools > MobaSSHTunnel (port forwarding)'' from the top menu or ''Tunneling'' from the button bar. In the new MobaSSHTunnel window, you can start an existing tunnel or add new tunnels, click ''New SSH Tunnel''. In the next window you want to set/select:
+In MobaXterm tunnels are set up independently to an SSH connection. To set up a tunnel, open the Tunneling menu by either going to ''Tools > MobaSSHTunnel (port forwarding)'' from the top menu or ''Tunneling'' from the button bar. In the new MobaSSHTunnel window, you can start an existing tunnel or add new tunnels, by clicking ''New SSH Tunnel''. In the next window, you want to set/select:
 * ''Local port forwarding''
 * Under "Local clients" enter the port that you will point your local web browser to in "<Forwarded port>" for example 5050 (it doesn't have to be the same as the port your Jupyter notebook is running on Viper, but it is easier if it is)
 * In "SSH server" enter "viper.hull.ac.uk" for SSH server and your username for "SSH login"
-* In "Remote server", under "<Remote server>" put the name of the compute node the Jupyter notebook is running on for example c048 (identity from squeue), and under "<Remote port>" enter the port your notebook is using, e.g. 5050 (either set manually or via your Jupyter config file).
+* In "Remote server", under "<Remote server>" put the name of the compute node the Jupyter notebook is running on, for example, c048 (identity from squeue), and under "<Remote port>" enter the port your notebook is using, e.g. 5050 (either set manually or via your Jupyter config file).
 * Save
 [[File:Sshtunnel.PNG]]
@@ Line 211: / Line 211: @@
 ====SSH Tunneling on Linux and Mac====
-To setup a port forwarding tunnel on Linux or Mac, simply run the following SSH command (replacing 5050 with your chosen port and c048 with your compute node name):
+To set a port forwarding tunnel on Linux or Mac, simply run the following SSH command (replacing 5050 with your chosen port and c048 with your compute node name):
 <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
@@ Line 221: / Line 221: @@
 ==Using jupyter configuration file==
-Jupyter notebook can be run using a configuration file to ease the number of command-line options needed.
+Jupyter Notebook can be run using a configuration file to ease the number of command-line options needed.
 Defaults for these options can also be set by creating a file named jupyter_notebook_config.py in your Jupyter folder. The Jupyter folder is in your home directory, ~/.jupyter.
@@ Line 240: / Line 240: @@
 </pre>
-To get your password you can use the following in python:
+To get your password you can use the following in Python:
 <pre>

@@ Line 252: / Line 252: @@
 ==Next Steps==
 * [https://www.anaconda.com/download/ Anaconda python]
 * [https://jupyter-notebook.readthedocs.io/en/stable/index.html Jupyter notebook]
 * [https://nbviewer.jupyter.org/ Jupyter viewer]
 ==Other Links==

@@ Line 8: / Line 8: @@
 Jupyter notebooks are ideally suited for ''educational purposes only'', however, they have limitations across a network, particularly with the graphical interface. The university does provide a [[Jupyterhub|jupyterhub service]].
-* '''Important''' : If you wish to carry out serious python development consider changing to an [[General/Interactive|interactive session]] and using a [[Applications/Miniconda|virtual environment]] within your account and using the editors [[Training/Linux_-_vi_editor|vi]] or [[Training/Linux_-_Nano_editor|nano]].
+* '''Important''': If you wish to carry out serious python development consider changing to an [[General/Interactive|interactive session]] and using a [[Applications/Miniconda|virtual environment]] within your account and using the editors [[Training/Linux_-_vi_editor|vi]] or [[Training/Linux_-_Nano_editor|nano]].
 * '''Alternatively''', if you wish to edit files on your local machine there are many IDEs which provide a means for transferring python files across to Viper seamlessly, examples of these are [https://www.jetbrains.com/pycharm/ PyCharm] and [https://code.visualstudio.com/ Visual Studio Code]. (''All suitable for Linux, macOS and Windows'').
@@ Line 138: / Line 138: @@
      Copy/paste this URL into your browser when you connect for the first time,
-     to login with a token:
+     to log in with a token:
          http://10.254.5.93:1487/?token=b71e38e053bd44e62ba340aff5a5b9b68c74cd0d0883d582
 [I 09:55:58.597 NotebookApp] 302 GET /?token=b71e38e053bd44e62ba340aff5a5b9b68c74cd0d0883d582 (10.254.5.247) 3.56ms
@@ Line 154: / Line 154: @@
 ===GPU Configuration===
-* the SLURM batch script would be slightly different
+* The SLURM batch script would be slightly different
 <pre>
@@ Line 250: / Line 250: @@
 </pre>
-==Resources==
+==Next Steps==
 * [https://jupyterhub.hull.ac.uk University's JupyterHub service]

@@ Line 15: / Line 15: @@
 ===Interactive mode (GPU)===
-Below is the console output of using jupyter notebook in an interactive session
+Below is the console output of using a '''jupyter notebook''' in an interactive session
@@ Line 196: / Line 196: @@
 ===SSH Tunneling for Jupyter===
-It is possible to run Jupyter on a compute node and connect to the notebook from your desktop browser. In order to do this you need to 'tunnel' a connection from your desktop/laptop over SSH to the node that Jupyter is running on.
+It is possible to run Jupyter on a compute node and connect to the notebook from your desktop browser. In order to do this, you need to 'tunnel' a connection from your desktop/laptop over SSH to the node that Jupyter is running on.
 ====SSH Tunneling with MobaXterm====

@@ Line 9: / Line 9: @@
 * '''Important''' : If you wish to carry out serious python development consider changing to an [[General/Interactive|interactive session]] and using a [[Applications/Miniconda|virtual environment]] within your account and using the editors [[Training/Linux_-_vi_editor|vi]] or [[Training/Linux_-_Nano_editor|nano]].
-* '''Alternatively''', if you wish to edit files on your local machine there are many IDEs which provide a means for transferring python file across to Viper seamlessly, examples of these are [https://www.jetbrains.com/pycharm/ PyCharm] and [https://code.visualstudio.com/ Visual Studio Code]. (''All suitable for Linux, macOS and Windows'').
+* '''Alternatively''', if you wish to edit files on your local machine there are many IDEs which provide a means for transferring python files across to Viper seamlessly, examples of these are [https://www.jetbrains.com/pycharm/ PyCharm] and [https://code.visualstudio.com/ Visual Studio Code]. (''All suitable for Linux, macOS and Windows'').
 ==Setting up==
@@ Line 144: / Line 144: @@
 </pre>
-* Going to a browser on visualization nodes or at time of writing login02.hpc.hull.ac.uk
+* Going to a browser on visualization nodes or at the time of writing login02.hpc.hull.ac.uk
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
@@ Line 154: / Line 154: @@
 ===GPU Configuration===
-* the SLURM batch script would slightly different
+* the SLURM batch script would be slightly different
 <pre>
@@ Line 199: / Line 199: @@
 ====SSH Tunneling with MobaXterm====
-In MobaXterm tunnels are set up independently to an SSH connection. To set up a tunnel, open the Tunneling menu by either going to ''Tools > MobaSSHTunnel (port forwarding)'' from the top menu or ''Tunneling'' from the button bar. In the new MobaSSHTunnel window, you can start an existing tunnel or add new tunnels, click ''New SSH Tunnnel''. In the next window you want to set/select:
+In MobaXterm tunnels are set up independently to an SSH connection. To set up a tunnel, open the Tunneling menu by either going to ''Tools > MobaSSHTunnel (port forwarding)'' from the top menu or ''Tunneling'' from the button bar. In the new MobaSSHTunnel window, you can start an existing tunnel or add new tunnels, click ''New SSH Tunnel''. In the next window you want to set/select:
 * ''Local port forwarding''
 * Under "Local clients" enter the port that you will point your local web browser to in "<Forwarded port>" for example 5050 (it doesn't have to be the same as the port your Jupyter notebook is running on Viper, but it is easier if it is)

@@ Line 8: / Line 8: @@
 Jupyter notebooks are ideally suited for ''educational purposes only'', however they have limitations across a network particularly with the graphical interface. The university does provide a [[Jupyterhub|jupyterhub service]].
-* '''Important''' : If you wish to carry out serious python development consider changing to an [[General/Interactive|interactive session]] and using a [[Applications/Miniconda|virtual environment]] within your account. If you wish to edit files on your local machine there are many IDEs which provide a means for transferring python file across to Viper seamlessly, examples of these are [https://www.jetbrains.com/pycharm/ PyCharm] and [https://code.visualstudio.com/ Visual Code]. (''All suitable for Linux, MacOS and Windows'').
+* '''Important''' : If you wish to carry out serious python development consider changing to an [[General/Interactive|interactive session]] and using a [[Applications/Miniconda|virtual environment]] within your account and using the editors [[Training/Linux_-_vi_editor|vi]] or [[Training/Linux_-_Nano_editor|nano]]. '''Alternatively''', if you wish to edit files on your local machine there are many IDEs which provide a means for transferring python file across to Viper seamlessly, examples of these are [https://www.jetbrains.com/pycharm/ PyCharm] and [https://code.visualstudio.com/ Visual Code]. (''All suitable for Linux, MacOS and Windows'').
 ==Setting up==