Differences

This shows you the differences between two versions of the page.

--- software:juypter:caviness [2026-03-26 16:34] – Add VALET package definition and activation mbotto
+++ software:juypter:caviness [2026-03-30 14:16] (current) – Delete obsolete copy (with misspelled path name) of Jupyter Notebook Caviness page mbotto
@@ Line 1: / Line 1: @@
-====== Jupyter Notebook Python Virtual Environment on Caviness======
-<note warning>
-This page is under construction.
-</note>
-The following steps will walk you through setting up a Conda virtual environment with Python 3 and Jupyter Notebook. It will also cover the steps of requesting a compute node 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.
-Before starting, make sure you set your workgroup. This example will demonstrate how to create a shared directory in your workgroup storage where you can create Conda environments that are accessible to everyone in your workgroup.
-<note warning>
-If you do not have a ''sw'' or ''sw/valet'' directory in your workgroup storage directory ''WORKDIR'', please consult with your PI (stakeholder of the workgroup) on how to setup for your workgroup software installs on Caviness before proceeding with these instructions (see [[abstract:caviness:install_software:workgroup-sw|Workgroup Software Installs on Caviness]] for more details).
-</note>
-Before creating the Jupyter Notebook environment, start by creating a directory in your workgroup storage for Conda environments. The ''%%--mode=2775%%'' option ensures that other people in your workgroup will also be able to create Conda environments in this directory:
-<code bash>
-[user@login00.caviness ~]$ workgroup -g my_workgroup
-[(my_workgroup:user)@login00.caviness ~]$ mkdir --mode=2775 ${WORKDIR_SW}/conda-envs
-</code>
-<note important>
-The environment variable ''WORKDIR_SW'' will only be set if the directory ''${WORKDIR}/sw'' already existed before you set your workgroup with ''workgroup -g''. You can check for existence of the directory ''${WORKDIR}/sw'' before setting your workgroup by running:
-<code bash>
-[user@login00.caviness ~]$ ls -d ${WORKDIR}/sw
-</code>
-</note>
-=====Create Jupyter Notebook Virtual Environment=====
-This example will use the Miniforge VALET package to enable usage of the Conda package manager. If you are new to Conda, make sure to review the documentation for [[software:miniforge:caviness|Miniforge on Caviness]].
-Start by loading the Miniforge VALET package (this command loads the default version, but you can specify a different version as needed):
-<code bash>
-[(my_workgroup:user)@login00.caviness ~]$ vpkg_require miniforge
-Adding package `miniforge/25.11.0-1` to your environment
-</code>
-After loading Miniforge, we can now use ''conda create'' to 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. We will specify a version directory by date ''20260326'' for the installation of the March 2026 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. Note that the list of packages to be installed is omitted from the output below.
-<code bash>
-[(my_workgroup:user)@login00.caviness ~]$ conda create --prefix=${WORKDIR_SW}/conda-envs/jupyter-notebook/20260326 python=3 jupyter
-Retrieving notices: done
-Channels:
- - conda-forge
-Platform: linux-64
-Collecting package metadata (repodata.json): done
-Solving environment: done
-  .
-  .
-  .
-## Package Plan ##
-  environment location: /work/my_workgroup/sw/conda-envs/jupyter-notebook/20260326
-  added / updated specs:
-    - jupyter
-    - python=3
-  .
-  .
-  .
-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/miniforge-testing/jupyter-notebook/20260326
-#
-# To deactivate an active environment, use
-#
-#     $ conda deactivate
-</code>
-=====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, and get the path to the parent directory of your Jupyter Notebook virtual environment:
-<code bash>
-[(my_workgroup:user)@login00.caviness ~]$ ls -d ${WORKDIR_SW}/valet
-[(my_workgroup:user)@login00.caviness ~]$ echo ${WORKDIR_SW}/conda-envs/jupyter-notebook
-/work/my_workgroup/sw/conda-envs/jupyter-notebook
-</code>
-Take note of the path echoed, then create a new file in ''${WORKDIR_SW}/valet'' named ''jupyter-notebook.vpkg_yaml'' and add the following text to it, **making sure to replace ''my_workgroup'' with the name of your workgroup**:
-<code yaml jupyter-notebook.vpkg_yaml>
-jupyter-notebook:
-    prefix: /work/my_workgroup/sw/conda-envs/jupyter-notebook
-    description: Jupyter Notebook virtual environments created with Conda
-    flags:
-        - no-standard-paths
-    actions:
-        - action: source
-          script:
-              sh: miniforge-activate.sh
-          order: failure-first
-          success: 0
-    versions:
-        "20260326":
-            description: environment built March 26, 2026
-            dependencies:
-                - miniforge
-</code>
-=====Activating the Jupyter Notebook Virtual Environment with VALET=====
-The versions of the virtual environment declared in the VALET package are listed using the ''vpkg_versions'' command:
-<code bash>
-[(my_workgroup:user)@login00.caviness ~]$ vpkg_versions jupyter-notebook
-Available versions in package (* = default version):
-[/work/my_workgroup/sw/valet/jupyter-notebook.vpkg_yaml]
-jupyter-notebook  Jupyter Notebook virtual environments created with Conda
-* 20260326        environment built March 26, 2026
-</code>
-Activating the virtual environment is accomplished using the ''vpkg_require'' command (in your login shell or inside job scripts). If you load the VALET package without having first loaded the ''miniforge'' package, ''miniforge'' will also be added as a dependency:
-<code>
-[(my_workgroup:user)@login00.caviness ~]$ vpkg_require jupyter-notebook/20260326
-Adding dependency `miniforge/25.11.0-1` to your environment
-Adding package `jupyter-notebook/20260326` to your environment
-(/work/my_workgroup/sw/conda-envs/jupyter-notebook/20260326) [(my_workgroup:user)@login00.caviness valet]$
-</code>