Helix/bwVisu/JupyterLab - Revision history

H Schumacher: uv correction

2026-10-10T23:22:54Z

uv correction

← Older revision		Revision as of 01:22, 11 October 2026
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	<li>Create a new project and virtual environment:		<li>Create a new project and virtual environment:
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	uv init <env_parent_dir~~>/<env_name~~>		uv init <env_parent_dir>
	uv venv <env_parent_dir>/<env_name> --python <python version></syntaxhighlight>		uv venv <env_parent_dir>/<env_name> --python <python version></syntaxhighlight>
	* <code>env_parent_dir</code> is the path to the folder where the virtual environment shall be created. Relative paths can be used.		* <code>env_parent_dir</code> is the path to the folder where the virtual environment shall be created. Relative paths can be used.
	* The <code>--python <python_version></code> option can be omitted if the default Python version should be used.		* The <code>--python <python_version></code> option can be omitted if the default Python version should be used.
	* Caution: If you want to share the environment with others, make sure to		* Caution: If you want to share the environment with others, make sure to
	** Set your $HOME to the shared place before creating the environment: <code>HOME=<~~env_name~~></code>		** Set your $HOME to the shared place before creating the environment: <code>HOME=<env_parent_dir></code>
	** Create the environment directly in the shared place.		** Create the environment directly in the shared place.
	</li>		</li>
	<li>Install packages into the environment:		<li>Install packages into the environment:
	<syntaxhighlight lang="bash">uv ~~add <packagename></syntaxhighlight>~~<~~/li~~>		<syntaxhighlight lang="bash">cd <env_parent_dir>
			uv add <packagename></syntaxhighlight></li>
	<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>		<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>
	</ol>		</ol>

H Schumacher: Find the kernel section korrigiert

2026-10-08T17:58:47Z

Find the kernel section korrigiert

← Older revision		Revision as of 19:58, 8 October 2026
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	* If you are the only person using the environment:		* If you are the only person using the environment:
	<syntaxhighlight lang="bash">python3 -m ipykernel install --user --name=<kernel_name></syntaxhighlight>		<syntaxhighlight lang="bash">python3 -m ipykernel install --user --name=<kernel_name></syntaxhighlight>
⚫	The kernel can be found under <code>~/.local/share/jupyter/kernels/</code>.
	* If you installed the environment in a shared place and want to have the kernel there as well:		* If you installed the environment in a shared place and want to have the kernel there as well:
	<syntaxhighlight lang="bash">python3 -m ipykernel install --prefix <path_to_kernel_folder> --name=<kernel_name>		<syntaxhighlight lang="bash">python3 -m ipykernel install --prefix <path_to_kernel_folder> --name=<kernel_name>
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	* If you are the only person using the environment:		* If you are the only person using the environment:
	<syntaxhighlight lang="bash">uv run ipython kernel install --user --env VIRTUAL_ENV $(pwd)/.venv --name=<kernel_name></syntaxhighlight>		<syntaxhighlight lang="bash">uv run ipython kernel install --user --env VIRTUAL_ENV $(pwd)/.venv --name=<kernel_name></syntaxhighlight>
	The kernel can be found under <code>~/.local/share/jupyter/kernels/</code>.
	* If you installed the environment in a shared place and want to have the kernel there as well:		* If you installed the environment in a shared place and want to have the kernel there as well:
	<syntaxhighlight lang="bash">uv run ipython kernel install --prefix <path_to_kernel_folder> --env VIRTUAL_ENV $(pwd)/.venv --name=<kernel_name>		<syntaxhighlight lang="bash">uv run ipython kernel install --prefix <path_to_kernel_folder> --env VIRTUAL_ENV $(pwd)/.venv --name=<kernel_name>
Line 139:		Line 137:
	==== Step 2: Find the kernel ====		==== Step 2: Find the kernel ====

			* Private kernel:
⚫	The kernel can ~~then~~ be found under <code>path_to_kernel_folder/share/jupyter/kernels/<kernel_name></code>. As long as the same <code>path_to_kernel_folder</code> is used, all kernels will be saved next to each other in "kernels".
		⚫	*: The kernel can be found under <code>~/.local/share/jupyter/kernels/</code>.
			* Shared kernel:
		⚫	*: The kernel can be found under <code>path_to_kernel_folder/share/jupyter/kernels/<kernel_name></code>. As long as the same <code>path_to_kernel_folder</code> is used, all kernels will be saved next to each other in "kernels".

H Schumacher: falsche Zeilen gelöscht

2026-10-08T17:55:55Z

falsche Zeilen gelöscht

← Older revision		Revision as of 19:55, 8 October 2026
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	==== Step 1: Create the kernel ====		==== Step 1: Create the kernel ====
	'''Using venv or Conda'''		'''Using venv or Conda'''

	For a '''venv''' or '''Conda''' environment, the environment has to be activated before creating the kernel.

	<ol>		<ol>
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	<li>Install the ipykernel package:		<li>Install the ipykernel package:
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	# for venv or conda:
	pip install ipykernel		pip install ipykernel
		⚫	</syntaxhighlight>
	# for uv:
			</li>
⚫	~~uv add ipykernel~~</syntaxhighlight~~></li~~>
	<li>Register the virtual environment as custom kernel to Jupyter.		<li>Register the virtual environment as custom kernel to Jupyter.
	* If you are the only person using the environment:		* If you are the only person using the environment:

H Schumacher: Added uv instructions

2026-10-08T17:35:58Z

Added uv instructions

← Older revision		Revision as of 19:35, 8 October 2026
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	</li>		</li>
	<li>Activate your environment:		<li>Activate your environment:
	<syntaxhighlight lang="bash">conda activate <~~myenv~~></syntaxhighlight></li>		<syntaxhighlight lang="bash">conda activate <env_name></syntaxhighlight></li>
	<li>Install your packages:		<li>Install your packages:
	<syntaxhighlight lang="bash">conda install <~~mypackage~~></syntaxhighlight></li>		<syntaxhighlight lang="bash">conda install <packagename></syntaxhighlight></li>
	<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>		<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>
	</ol>		</ol>
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	Steps for creating a '''uv''' virtual environment:		Steps for creating a '''uv''' virtual environment:
	<ol style="list-style-type: decimal;">		<ol style="list-style-type: decimal;">
	<li>Open a terminal.</li>		<li>Open a terminal</li>
	<li>Create a new virtual environment:		<li>Create a new project and virtual environment:
	<syntaxhighlight lang="bash"~~>uv venv <env_parent_dir>/<env_name> --python <python version></syntaxhighlight~~>		<syntaxhighlight lang="bash">
			uv init <env_parent_dir>/<env_name>
			uv venv <env_parent_dir>/<env_name> --python <python version></syntaxhighlight>
	* <code>env_parent_dir</code> is the path to the folder where the virtual environment shall be created. Relative paths can be used.		* <code>env_parent_dir</code> is the path to the folder where the virtual environment shall be created. Relative paths can be used.
	* The <code>--python</code> option can be omitted if the default Python version should be used.		* The <code>--python <python_version></code> option can be omitted if the default Python version should be used.
	* Caution: If you want to share the environment with others, make sure to ~~already create it in the shared place.~~		* Caution: If you want to share the environment with others, make sure to
			** Set your $HOME to the shared place before creating the environment: <code>HOME=<env_name></code>
			** Create the environment directly in the shared place.
	</li>		</li>
	<li>Install packages into the environment:		<li>Install packages into the environment:
	<syntaxhighlight lang="bash">uv ~~pip install --python <env_parent_dir>/<env_name>/bin/python~~ <packagename></syntaxhighlight></li>		<syntaxhighlight lang="bash">uv add <packagename></syntaxhighlight></li>
	<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>		<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>
	</ol>		</ol>
Line 95:		Line 99:
	conda_kernels		conda_kernels

	=== Create a kernel from a ~~venv or Conda~~ virtual environment ===		=== Create a kernel from a virtual environment ===
			Please follow these instructions to create and find the kernel.

			==== Step 1: Create the kernel ====
			'''Using venv or Conda'''

	For a '''venv''' or '''Conda''' environment, the environment has to be activated before creating the kernel.		For a '''venv''' or '''Conda''' environment, the environment has to be activated before creating the kernel.
Line 102:		Line 110:
	<li>Activate the virtual environment.</li>		<li>Activate the virtual environment.</li>
	<li>Install the ipykernel package:		<li>Install the ipykernel package:
	<syntaxhighlight lang="bash"~~>pip install ipykernel</syntaxhighlight></li~~>		<syntaxhighlight lang="bash">
			# for venv or conda:
			pip install ipykernel
			# for uv:
			uv add ipykernel</syntaxhighlight></li>
	<li>Register the virtual environment as custom kernel to Jupyter.		<li>Register the virtual environment as custom kernel to Jupyter.
	* If you are the only person using the environment:		* If you are the only person using the environment:
Line 108:		Line 120:
	The kernel can be found under <code>~/.local/share/jupyter/kernels/</code>.		The kernel can be found under <code>~/.local/share/jupyter/kernels/</code>.
	* If you installed the environment in a shared place and want to have the kernel there as well:		* If you installed the environment in a shared place and want to have the kernel there as well:
	<syntaxhighlight lang="bash">python3 -m ipykernel install --prefix <path_to_kernel_folder> --name=<kernel_name~~></syntaxhighlight~~>		<syntaxhighlight lang="bash">python3 -m ipykernel install --prefix <path_to_kernel_folder> --name=<kernel_name>
			</syntaxhighlight>
⚫	The kernel can then be found under <code>path_to_kernel_folder/share/jupyter/kernels/<kernel_name></code>. As long as the same <code>path_to_kernel_folder</code> is used, all kernels will be saved next to each other in "kernels".
	</li>		</li>
	</ol>		</ol>

			'''Using uv'''
	=== Create a kernel from a uv virtual environment ===

	A kernel can also be created from a <code>uv</code> virtual environment. The environment does not have to be activated.

	<ol>		<ol>
	<li>Install the ~~<code>~~ipykernel~~</code>~~ package ~~into the <code>uv</code> environment~~:		<li>Install the ipykernel package:
	<syntaxhighlight lang="bash"~~>uv pip install --python <env_parent_dir>/<env_name>/bin/python ipykernel</syntaxhighlight></li~~>		<syntaxhighlight lang="bash">
			uv add ipykernel</syntaxhighlight></li>
	<li>Register the environment as a custom kernel ~~using <code>uv~~ ~~run</code>:~~		<li>Register the virtual environment as custom kernel to Jupyter.
	* If you are the only person using the environment:		* If you are the only person using the environment:
	<syntaxhighlight lang="bash">uv run ~~--directory~~ ~~<env_parent_dir>/<env_name>~~ ~~python~~ -m ~~ipykernel~~ ~~install~~ ~~--user~~ --name=<kernel_name></syntaxhighlight>		<syntaxhighlight lang="bash">uv run ipython kernel install --user --env VIRTUAL_ENV $(pwd)/.venv --name=<kernel_name></syntaxhighlight>
	The kernel can be found under <code>~/.local/share/jupyter/kernels/</code>.		The kernel can be found under <code>~/.local/share/jupyter/kernels/</code>.
	* If you installed the environment in a shared place and want to have the kernel there as well:		* If you installed the environment in a shared place and want to have the kernel there as well:
	<syntaxhighlight lang="bash">uv run ~~--directory <env_parent_dir>/<env_name> python -m~~ ~~ipykernel~~ install --prefix <path_to_kernel_folder> --name=<kernel_name~~></syntaxhighlight~~>		<syntaxhighlight lang="bash">uv run ipython kernel install --prefix <path_to_kernel_folder> --env VIRTUAL_ENV $(pwd)/.venv --name=<kernel_name>
			</syntaxhighlight>
	The kernel can then be found under <code>path_to_kernel_folder/share/jupyter/kernels/<kernel_name></code>. As long as the same <code>path_to_kernel_folder</code> is used, all kernels will be saved next to each other in "kernels".
	</li>		</li>
	</ol>		</ol>

			==== Step 2: Find the kernel ====

		⚫	The kernel can then be found under <code>path_to_kernel_folder/share/jupyter/kernels/<kernel_name></code>. As long as the same <code>path_to_kernel_folder</code> is used, all kernels will be saved next to each other in "kernels".


	=== Multi-Language Support ===		=== Multi-Language Support ===

I Tachakor: /* Create a kernel from a virtual environment */

2026-10-05T20:21:16Z

Create a kernel from a virtual environment

← Older revision		Revision as of 22:21, 5 October 2026
Line 95:		Line 95:
	conda_kernels		conda_kernels

	=== Create a kernel from a virtual environment ===		=== Create a kernel from a venv or Conda virtual environment ===

	For a '''venv''' or '''Conda''' environment, the environment has to be activated before creating the kernel.		For a '''venv''' or '''Conda''' environment, the environment has to be activated before creating the kernel.

I Tachakor: Helix/bwVisu/JupyterLab

2026-10-05T20:11:51Z

Helix/bwVisu/JupyterLab

Show changes

S Fischer: icons looks different now

2026-08-18T08:41:23Z

icons looks different now

← Older revision		Revision as of 10:41, 18 August 2026
Line 55:		Line 55:

	<ol style="list-style-type: decimal;">		<ol style="list-style-type: decimal;">
	<li>Load the miniforge module by clicking first on the ~~blue~~ hexagon icon on the left-hand side of Jupyter's start page and then on the "load" button right of the entry for miniforge in the software module menu.		<li>Load the miniforge module by clicking first on the double hexagon icon on the left-hand side of Jupyter's start page and then on the "load" button right of the entry for miniforge in the software module menu.
	<li>Open a terminal.</li>		<li>Open a terminal.</li>
	<li>Create a new virtual environment:		<li>Create a new virtual environment:
Line 140:		Line 140:

	<ol><li>'''How can I use bwForCluster Helix software modules?'''</br>		<ol><li>'''How can I use bwForCluster Helix software modules?'''</br>
	First click on the ~~blue~~ hexagon icon on the left-hand side of Jupyter's start page. Then load a module by clicking on the "load" button next to the corresponding module entry.</li>		First click on the double hexagon icon on the left-hand side of Jupyter's start page. Then load a module by clicking on the "load" button next to the corresponding module entry.</li>
	<li>'''My virtual environment works on Helix but not in the bwVisu JupyterLab job.'''</br>		<li>'''My virtual environment works on Helix but not in the bwVisu JupyterLab job.'''</br>
	If the environment uses Helix modules, you have to load the modules in the bwVisu job first. For example, when you used the python 3.13 module for creating the environment, the path to this python version is saved in the environment. When the module is not loadedin bwVisu, the path is not available and you might get an error like "''[...]/bin/python: error while loading shared libraries: libpython3.13.so.1.0: cannot open shared object file: No such file or directory''"</li>		If the environment uses Helix modules, you have to load the modules in the bwVisu job first. For example, when you used the python 3.13 module for creating the environment, the path to this python version is saved in the environment. When the module is not loadedin bwVisu, the path is not available and you might get an error like "''[...]/bin/python: error while loading shared libraries: libpython3.13.so.1.0: cannot open shared object file: No such file or directory''"</li>

S Fischer: Typo

2026-08-18T08:34:05Z

Typo

← Older revision		Revision as of 10:34, 18 August 2026
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	#*:[[File:BwVisu JuypterLab KernelPath.png\|In the JupyterLab job configuration form, a custom kernel path can be provided.\|right\|thumb\|x150px]]		#*:[[File:BwVisu JuypterLab KernelPath.png\|In the JupyterLab job configuration form, a custom kernel path can be provided.\|right\|thumb\|x150px]]
	#* If the kernel is saved somewhere else, the path can be provided in the "Kernel path" field when configuring the JupyterLab job (see image). For a kernel placed under <code>path_to_parent_dir/share/jupyter/kernels/my_kernel</code> the needed "Kernel path" would be <code>path_to_parent_dir/share/jupyter</code>.		#* If the kernel is saved somewhere else, the path can be provided in the "Kernel path" field when configuring the JupyterLab job (see image). For a kernel placed under <code>path_to_parent_dir/share/jupyter/kernels/my_kernel</code> the needed "Kernel path" would be <code>path_to_parent_dir/share/jupyter</code>.
	# When the kernel is used the first time, the file <code>notebook_secrets</code> is created automatically. It can be found under "Kernel path". For others to use the kernel, they must have read access to this file. The command <code>chmod 750 notebook_secrets</code> would for example allow the whole SDS@hd SV read access. For the access management in workspaces, please see [[Workspace#Setting_Permissions_for_Sharing_Files\| ~~Wokspace~~ Permissions]].		# When the kernel is used the first time, the file <code>notebook_secrets</code> is created automatically. It can be found under "Kernel path". For others to use the kernel, they must have read access to this file. The command <code>chmod 750 notebook_secrets</code> would for example allow the whole SDS@hd SV read access. For the access management in workspaces, please see [[Workspace#Setting_Permissions_for_Sharing_Files\| Workspace Permissions]].

	<u>Notes regarding the sharing of IPython kernels</u>		<u>Notes regarding the sharing of IPython kernels</u>

H Schumacher: Added hint to load modules first.

2026-05-07T14:32:03Z

Added hint to load modules first.

← Older revision		Revision as of 16:32, 7 May 2026
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	<ol><li>'''How can I use bwForCluster Helix software modules?'''</br>		<ol><li>'''How can I use bwForCluster Helix software modules?'''</br>
	First click on the blue hexagon icon on the left-hand side of Jupyter's start page. Then load a module by clicking on the "load" button next to the corresponding module entry.</li>		First click on the blue hexagon icon on the left-hand side of Jupyter's start page. Then load a module by clicking on the "load" button next to the corresponding module entry.</li>
			<li>'''My virtual environment works on Helix but not in the bwVisu JupyterLab job.'''</br>
			If the environment uses Helix modules, you have to load the modules in the bwVisu job first. For example, when you used the python 3.13 module for creating the environment, the path to this python version is saved in the environment. When the module is not loadedin bwVisu, the path is not available and you might get an error like "''[...]/bin/python: error while loading shared libraries: libpython3.13.so.1.0: cannot open shared object file: No such file or directory''"</li>
	<li>'''How can I navigate to my SDS@hd folder in the file browser?'''</br>		<li>'''How can I navigate to my SDS@hd folder in the file browser?'''</br>
			Please see the instructions at the [[Helix/bwVisu/Usage#Files \| Usage]] page.</li>
	Open a terminal and set a symbolic link to your SDS@hd folder in your home directory. For example:</li>
	<pre>cd $HOME
	mkdir sds-hd
	cd sds-hd
	ln -s /mnt/sds-hd/sd16a001 sd16a001</pre>
	<li>'''I prefer VSCode over JupyterLab. Can I start a JupyterLab job and then connect with it via VSCode?'''</br>		<li>'''I prefer VSCode over JupyterLab. Can I start a JupyterLab job and then connect with it via VSCode?'''</br>
	This is not possible. Please start the job directly on Helix instead. You can find the instructions at the [[Development/VS_Code#Connect_to_Remote_Jupyter_Kernel \| VSCode page]].</li>		This is not possible. Please start the job directly on Helix instead. You can find the instructions at the [[Development/VS_Code#Connect_to_Remote_Jupyter_Kernel \| VSCode page]].</li>

H Schumacher: Added instructions for using Helix modules

2026-05-05T11:24:22Z

Added instructions for using Helix modules

← Older revision		Revision as of 13:24, 5 May 2026
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	== FAQ ==		== FAQ ==

	<ol><li>'''My ~~conda~~ ~~commands~~ ~~are~~ ~~interrupted~~ ~~with~~ ~~message~~ ~~'Killed'.~~'''</br>		<ol><li>'''How can I use bwForCluster Helix software modules?'''</br>
			First click on the blue hexagon icon on the left-hand side of Jupyter's start page. Then load a module by clicking on the "load" button next to the corresponding module entry.</li>
⚫	Request more memory when starting Jupyter.</li>
	<li>'''How can I navigate to my SDS@hd folder in the file browser?'''</br>		<li>'''How can I navigate to my SDS@hd folder in the file browser?'''</br>
	Open a terminal and set a symbolic link to your SDS@hd folder in your home directory. For example:</li>		Open a terminal and set a symbolic link to your SDS@hd folder in your home directory. For example:</li>
Line 147:		Line 147:
	cd sds-hd		cd sds-hd
	ln -s /mnt/sds-hd/sd16a001 sd16a001</pre>		ln -s /mnt/sds-hd/sd16a001 sd16a001</pre>
⚫	<li>'''Jupyterlab doesn't let me in but asks for a password.'''</br>
⚫	Try using more memory for the job. If this doesn't help, try using the inkognito mode of your browser as the browser cache might be the problem.</li>
	<li>'''I prefer VSCode over JupyterLab. Can I start a JupyterLab job and then connect with it via VSCode?'''</br>		<li>'''I prefer VSCode over JupyterLab. Can I start a JupyterLab job and then connect with it via VSCode?'''</br>
	This is not possible. Please start the job directly on Helix instead. You can find the instructions at the [[Development/VS_Code#Connect_to_Remote_Jupyter_Kernel \| VSCode page]].</li>		This is not possible. Please start the job directly on Helix instead. You can find the instructions at the [[Development/VS_Code#Connect_to_Remote_Jupyter_Kernel \| VSCode page]].</li>
			<li>'''My conda commands are interrupted with message 'Killed'.'''</br>
		⚫	Request more memory when starting Jupyter.</li>
		⚫	<li>'''Jupyterlab doesn't let me in but asks for a password.'''</br>
		⚫	Try using more memory for the job. If this doesn't help, try using the inkognito mode of your browser as the browser cache might be the problem.</li>
	</ol>		</ol>