====== Jupyter Notebook Python Virtual Environment======
The following steps will walk you through setting up an Anaconda virtual environment with Python 3 and Jupyter Notebook. It will also cover the steps of requesting a compute note to run a Jupyter Notebook session on Caviness. Lastly, it will explain how to set up SSH connections to be able to connect to the Jupyter Notebook session running on a compute node. This setup will be done in the ''it_css'' workgroup directory. This will allow all users in the ''it_css'' workgroup to use the Jupyter Notebook virtual environment. If your workgroup has already created a Jupyter Notebook virtual environment and a corresponding VALET package, then proceed to [[technical:recipes:jupyter-notebook#using-jupyter-notebook-virtual-environment|using Jupyter Notebook Virtual Environment]].
These directions are geared towards setting up and running Jupyter Notebook on Caviness. However, these directions can easily be used on DARWIN, although references to directory paths and software versions will be different.
Before starting, make sure you set your workgroup and change to the directory where you would like to store your Jupyter Notebook virtual environment. In this example, a general directory ''anaconda-envs'' will be created for Anaconda virtual environments that can be shared with everyone in the workgroup ''it_css'' in the ''sw'' directory.
If you do not have a ''sw'' or ''sw/valet'' directory, please consult with your PI (stakeholder of the workgroup) on how to setup for your workgroup software installs [[abstract:caviness:install_software:workgroup-sw|Workgroup Directory]] on Caviness before proceeding with these instructions. On DARWIN, [[abstract:darwin:install_software:workgroup-sw|workgroup directories]] for ''sw'' and ''sw/valet'' are automatically created as part of the allocation.
[traine@login00 ~]$ workgroup -g it_css
[(it_css:traine)@login00 ~]$ cd $WORKDIR/sw
[(it_css:traine)@login00 it_css]$ mkdir anaconda-envs
[(it_css:traine)@login00 it_css]$ chmod 02775 anaconda-envs
===== Create Jupyter Notebook Virtual Environment =====
As stated above, in this example we will be using Anaconda version ''2024.02''. This was the latest version available on the Caviness Cluster in August 2024.
(it_css:traine)@login00 ~$ vpkg_require anaconda/2024.02
Adding package `anaconda/2024.02` to your environment
After loading the Anaconda software, we will want create the Jupyter Notebook virtual environment. In this example we will call it ''jupyter-notebook'', but you are welcome to call it anything you would like. Before creating it, we will want to see what "default" version of Python 3 is available on as part of Anaconda.
[(it_css:traine)@login00 ~]$ which python3
/opt/shared/anaconda/2024.02/bin/python3
[(it_css:traine)@login00 ~]$ python3 --version
Python 3.11.7
Now that we know the version of python3 loaded into our environment is ''3.11.7'', we can run the commands to create a virtual environment. We will also specify a version directory by date ''20240801'' for the installation of the August 2024 Jupyter Notebook virtual environment. This is needed for setting up a VALET package definition, and allows for multiple versions to be installed based on need. You will be asked to ''Proceed ([y]/n)?'' and you will want to choose ''y'' as this is advising you that prerequisite software is also going to be installed.
[(it_css:traine)@login00 ~]$ conda create --prefix $WORKDIR/sw/anaconda-envs/jupyter-notebook/20240801 -c jupyter python=3.11.7
Channels:
- jupyter
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /work/it_css/sw/anaconda-envs/jupyter-notebook/20240801
added / updated specs:
- python=3.11.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2024.7.2 | h06a4308_0 127 KB
pip-24.0 | py311h06a4308_0 3.3 MB
python-3.11.7 | h955ad1f_0 32.8 MB
setuptools-69.5.1 | py311h06a4308_0 1.3 MB
wheel-0.43.0 | py311h06a4308_0 146 KB
------------------------------------------------------------
Total: 37.7 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
bzip2 pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6
ca-certificates pkgs/main/linux-64::ca-certificates-2024.7.2-h06a4308_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
libffi pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
libuuid pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0
ncurses pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
openssl pkgs/main/linux-64::openssl-3.0.14-h5eee18b_0
pip pkgs/main/linux-64::pip-24.0-py311h06a4308_0
python pkgs/main/linux-64::python-3.11.7-h955ad1f_0
readline pkgs/main/linux-64::readline-8.2-h5eee18b_0
setuptools pkgs/main/linux-64::setuptools-69.5.1-py311h06a4308_0
sqlite pkgs/main/linux-64::sqlite-3.45.3-h5eee18b_0
tk pkgs/main/linux-64::tk-8.6.14-h39e8969_0
tzdata pkgs/main/noarch::tzdata-2024a-h04d1e81_0
wheel pkgs/main/linux-64::wheel-0.43.0-py311h06a4308_0
xz pkgs/main/linux-64::xz-5.4.6-h5eee18b_1
zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1
Proceed ([y]/n)? y
Downloading and Extracting Packages
...
...
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > conda activate /work/it_css/sw/anaconda-envs/jupyter-notebook/20240801
#
# To deactivate an active environment, use:
# > conda deactivate
#
$
==== VALET Package Definition ====
The new virtual environment can easily be added to your login shell and job runtime environments using VALET. Ensure you have a workgroup VALET package definition directory present:
[(it_css:traine)@login00 ~]$ ls -lad ${WORKDIR}/sw/valet
[(it_css:traine)@login00 ~]$ echo ${WORKDIR}/sw/anaconda-envs/jupyter-notebook
/work/it_css/sw/anaconda-envs/jupyter-notebook
Take note of the path echoed, then create a new file named ''${WORKDIR}/sw/valet/jupyter-notebook.vpkg_yaml'' and add the following text to it:
jupyter-notebook:
prefix: /work/it_css/sw/anaconda-envs/jupyter-notebook
description: Jupyter notebook in Python
flags:
- no-standard-paths
actions:
- action: source
script:
sh: anaconda-activate.sh
order: failure-first
success: 0
versions:
"20240801":
description: environment built August 1, 2024
dependencies:
- anaconda/2024.02
The ''prefix'' show here ''/work/it_css/sw/anaconda-envs/jupyter-notebook'' will need to be changed based on your workgroup and directory names.
===== Using Jupyter Notebook Virtual Environment =====
The versions of the virtual environment declared in the VALET package are listed using the ''vpkg_versions'' command:
[(it_css:traine)@login00 ~]$ vpkg_versions jupyter-notebook
Available versions in package (* = default version):
[/work/it_css/sw/valet/jupyter-notebook.vpkg_yaml]
jupyter-notebook Jupyter notebook in Python
* 20240801 environment built August 1, 2024
Activating the virtual environment is accomplished using the ''vpkg_require'' command (in your login shell or inside job scripts):
[(it_css:traine)@login00 ~]$ vpkg_require jupyter-notebook/20240801
Adding dependency `anaconda/2024.02` to your environment
Adding package `jupyter-notebook/20240801` to your environment
(/work/it_css/sw/anaconda-envs/jupyter-notebook/20240801) [(it_css:traine)@login00 valet]$
===== Running Jupyter Notebook on the Caviness Cluster =====
Running Jupyter Notebook on Caviness, or any HPC cluster for that matter, takes some extra steps. You can simply install Jupyter Notebook on your personal laptop and start it up. On Caviness, you need to run the Jupyter Notebook on a compute node. The steps below will show you how to request an interactive compute node and use VALET to load the Jupyter Notebook virtual environment. After starting the virtual environment, we will run Jupyter Notebook with arguments that will allow for the session to be accessed via a tunnel connection on your local system.
On Caviness you're **required** to run Jupyter notebook on a **compute node**. If you run it on the login node, you could cause slowness or other issues with the login node, and IT might kill your Jupyter Notebook session without warning.
==== Requesting an interactive job ====
In this example we will request an interactive job to connect us to a compute node with 2GB of memory for 1 hour on the ''it_css'' workgroup partition. Also it is important to pass the ''SLURM_EXPORT_ENV=NONE'' when requesting the interactive compute node. It will prevent issues with setting up a clean environment on the compute node.
[(it_css:traine)@login00 ~]$ SLURM_EXPORT_ENV=NONE salloc --mem=2G --time=1:00:00 --partition=it_css
==== Loading the Jupyter Notebook virtual environment ====
After the interactive job has been established, it is time to load the Jupyter Notebook virtual environment with ''VALET''. Even though we did this earlier, it needs to be done again since we are now on a compute node.
[[traine@r00n50 1201]$ vpkg_require jupyter-notebook/20240801
Adding dependency `anaconda/2024.02` to your environment
Adding package `jupyter-notebook/20240801` to your environment
(/work/it_css/sw/anaconda_envs/jupyter-notebook/20240801) [traine@r00n50 1201]$
Once the Jupyter Notebook virtual environment has been loaded on the interactive compute node session, your prompt should look something like this:
''(/work/it_css/sw/anaconda_envs/jupyter-notebook/20240801) [traine@r00n50 1201]$''
==== Starting Jupyter Notebook session ====
When starting the Jupyter Notebook session, specific options are passed, which are used to set up the tunnel connection.
[traine@r04n68 1201]$ jupyter notebook --no-browser --ip=$(hostname -s)
...
...
...
[I 2024-08-01 15:16:27.747 LabApp] JupyterLab extension loaded from /opt/shared/anaconda/2024.02/lib/python3.11/site-packages/jupyterlab
[I 2024-08-01 15:16:27.747 LabApp] JupyterLab application directory is /opt/shared/anaconda/2024.02/share/jupyter/lab
[I 2024-08-01 15:16:27.748 LabApp] Extension Manager is 'pypi'.
[I 2024-08-01 15:16:27.751 ServerApp] jupyterlab | extension was successfully loaded.
[I 2024-08-01 15:16:27.756 ServerApp] notebook | extension was successfully loaded.
[I 2024-08-01 15:16:27.757 ServerApp] panel.io.jupyter_server_extension | extension was successfully loaded.
[I 2024-08-01 15:16:27.760 ServerApp] Serving notebooks from local directory: /home/3347
[I 2024-08-01 15:16:27.760 ServerApp] Jupyter Server 2.10.0 is running at:
[I 2024-08-01 15:16:27.761 ServerApp] http://r00n50:8888/tree?token=8a17fdf02d91c23270f796620adc9d15fb4c4d47dc705cd2
[I 2024-08-01 15:16:27.761 ServerApp] http://127.0.0.1:8888/tree?token=8a17fdf02d91c23270f796620adc9d15fb4c4d47dc705cd2
[I 2024-08-01 15:16:27.761 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2024-08-01 15:16:27.765 ServerApp]
To access the server, open this file in a browser:
file:///home/1201/.local/share/jupyter/runtime/jpserver-20300-open.html
Or copy and paste one of these URLs:
http://r00n50:8888/tree?token=8a17fdf02d91c23270f796620adc9d15fb4c4d47dc705cd2
http://127.0.0.1:8888/tree?token=8a17fdf02d91c23270f796620adc9d15fb4c4d47dc705cd2
The Jupyter Notebook server is running and there is no prompt. **Make sure you copy the line noted above and it will be used later by changing the compute node to ''localhost''**
http://localhost:8888/tree?token=8a17fdf02d91c23270f796620adc9d15fb4c4d47dc705cd2
==== Setting up SSH tunnel to connect to Jupyter Notebook server ====
With the Jupyter Notebook server running on a compute node on Caviness, an SSH tunnel is needed to be able to make a connection and access the Jupyter Notebook server from a web browser on your local machine. This is done by opening a **second** SSH connection to Caviness. Follow the appropriate section below for Windows (PuTTY) or Terminal on a Linux/Mac laptop.
Your compute node name will likely be different than ''r00n50'', please make sure to change that accordingly. This SSH tunnel connection will have to remain open while you are using Jupyter Notebook. If it is closed or internet connectivity is lost, then your connection to Jupyter Notebook will also be lost.
==Windows (PuTTY)==
Once you open the PuTTY, it will show the //Session// window. For the //Host Name(or IP Address)//, you will need to enter the ''@caviness.hpc.udel.edu''.
In addition to your standard connection PuTTY settings, you will need to set up the tunnel setting. This is easily done by loading an existing session you have saved for Caviness and then adding the tunnel settings based on the image below. The tunnel setting is found under the Category //Connection -> SSH -> Tunnels//
{{:technical:recipes:putty-1.png?400|}}
Add the **Source port** as ''8888'' and **Destination** as ''r00n50:8888'' as shown in the image above, then click on **Add**. The //Tunnel// settings are now available to your session, so click **Open** to connect. You may need to enter the password for the Caviness/DARWIN account in the prompted window if you do not have an existing session. These settings are not saved. However, it is likely the necessary information to set up the tunnel the next time will change anyway. Remember, this SSH tunnel connection will have to remain open the entire time while you are using Jupyter Notebook.
{{ :technical:recipes:jupyter-notebook-1.png?nolink&400 |}}
==Linux/Mac==
Open a new terminal session on your local machine. Set up a SSH Tunnel using the below ''ssh'' command.
$ ssh -L 8888:r00n50:8888 traine@caviness.hpc.udel.edu
......................................................................
Caviness cluster (caviness.hpc.udel.edu)
This computer system is maintained by University of Delaware
IT. Links to documentation and other online resources can be
found at:
http://docs.hpc.udel.edu/abstract/caviness/
For support, please contact consult@udel.edu
......................................................................
Last login: Thu Aug 1 12:28:19 2024
[traine@login00 ~]$
==== Using your local browser to access Jupyter Notebook server ====
If everything this far has been set up correctly the final step is as easy as opening a web browser of choice on your local machine and entering the correct URL. If you followed the directions exactly, you can now use the URL from above changing the compute node to ''localhost'' in your local browser to connect to Jupyter Notebook server running on the compute node on Caviness.
**Example URL:**
''http://localhost:8888/tree?token=8a17fdf02d91c23270f796620adc9d15fb4c4d47dc705cd2''
If you are not able to connect to the Jupyter Notebook session at this point, then you will need to review the prior steps and make sure that you have added and configured the SSH tunnel properly based on your compute node. Remember, the SSH tunnel connection will have to remain open the entire time while you are using Jupyter Notebook.