Conda for teaching - Revision history

Haars0011: IA migration §11: fix malformed code block ( bug) → clean syntaxhighlight blocks (via update-page on MediaWiki MCP Server)

2026-06-19T07:30:06Z

IA migration §11: fix malformed code block (</source> bug) → clean syntaxhighlight blocks (via update-page on MediaWiki MCP Server)

← Older revision		Revision as of 07:30, 19 June 2026
Line 83:		Line 83:
	=== Python Kernel ===		=== Python Kernel ===

	<~~pre~~>		Create the <code>kernel.json</code>:

			<syntaxhighlight lang="bash">
	vim /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env/kernel.json		vim /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env/kernel.json
	</~~source~~>		</syntaxhighlight>
	<~~source~~ lang=~~'bash'~~>
			with this content:

			<syntaxhighlight lang="json">
	{		{
	"env": {		"env": {
	"PATH":		"PATH": "/cm/shared/apps/SHARED/my_conda_env/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin"
			},
	"/cm/shared/apps/SHARED/my_conda_env/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin"
	},
	"language": "python",		"language": "python",
	"argv": [		"argv": [
Line 103:		Line 106:
	"display_name": "my_conda_env"		"display_name": "my_conda_env"
	}		}
	</~~pre~~>		</syntaxhighlight>

	For Python, that's it. Ipykernel is installed automatically on conda initialisation.		For Python, that's it. Ipykernel is installed automatically on conda initialisation.

Haars0011: IA migration §11: strengthen staleness warning (old Bright /cm/shared paths), add modernization TODO (via update-page on MediaWiki MCP Server)

2026-06-19T07:29:56Z

IA migration §11: strengthen staleness warning (old Bright /cm/shared paths), add modernization TODO (via update-page on MediaWiki MCP Server)

← Older revision		Revision as of 07:29, 19 June 2026
Line 1:		Line 1:
	{{~~warning~~}} ~~While the technical information is~~ this page ~~is somewhat valid, some information may be outdated~~.		{{Warning\|This page describes the older cluster setup: the <code>/cm/shared/...</code> paths and the tcl modulefiles below are from the previous (Bright) cluster and do '''not''' match current Anunna, which uses the Lustre filesystem and EasyBuild buckets. The general approach — a shared conda environment registered as a Jupyter kernel — still applies, but the paths and commands need updating. For the current way to set up course kernels, see [[Steps for courses]] and [[Python]].}}

			<!-- TODO: modernise this page for current Anunna — replace the /cm/shared paths and tcl modulefile approach with a Miniforge environment on Lustre and the current course-kernel route (kernel registered at notebook.anunna.wur.nl; see Steps for courses). -->

	You are going to give a teaching course, and you need a specific code environment.		You are going to give a teaching course, and you need a specific code environment.

Honfi001 at 09:39, 12 March 2025

2025-03-12T09:39:27Z

← Older revision		Revision as of 09:39, 12 March 2025
Line 1:		Line 1:
	{{warning~~\|1=~~ While the technical information is this page is somewhat valid, some information is outdated.}}		{{warning}} While the technical information is this page is somewhat valid, some information may be outdated.

	You are going to give a teaching course, and you need a specific code environment.		You are going to give a teaching course, and you need a specific code environment.

Honfi001 at 09:36, 12 March 2025

2025-03-12T09:36:53Z

← Older revision		Revision as of 09:36, 12 March 2025
Line 1:		Line 1:
			{{warning\|1= While the technical information is this page is somewhat valid, some information is outdated.}}

	You are going to give a teaching course, and you need a specific code environment.		You are going to give a teaching course, and you need a specific code environment.

Haars0011 at 10:43, 25 January 2024

2024-01-25T10:43:39Z

← Older revision		Revision as of 10:43, 25 January 2024
Line 6:		Line 6:
	Next - create a folder for your environment:		Next - create a folder for your environment:

	<~~source lang='bash'~~>		<pre>
	mkdir /cm/shared/apps/SHARED/my_conda_env		mkdir /cm/shared/apps/SHARED/my_conda_env
	chmod +r /cm/shared/apps/SHARED/my_conda_env		chmod +r /cm/shared/apps/SHARED/my_conda_env
	</~~source~~>		</pre>
	You may want to manipulate the permissions for this folder if someone is going to set this up with you. Consider the commands in [[Shared folders]].		You may want to manipulate the permissions for this folder if someone is going to set this up with you. Consider the commands in [[Shared folders]].

Line 16:		Line 16:
	Also, note that you need to make the sh script executable before you can run it.		Also, note that you need to make the sh script executable before you can run it.

	<~~source lang='bash'~~>		<pre>
	wget https://repo.anaconda.com/archive/Anaconda3-YEAR.MONTH-Linux-x86_64.sh		wget https://repo.anaconda.com/archive/Anaconda3-YEAR.MONTH-Linux-x86_64.sh
	./Anaconda3-YEAR.MONTH-Linux-x86_64.sh -s -b -p /cm/shared/apps/SHARED/my_conda_env		./Anaconda3-YEAR.MONTH-Linux-x86_64.sh -s -b -p /cm/shared/apps/SHARED/my_conda_env
	</~~source~~>		</pre>

	Now you have a working conda environment in this folder. You can manipulate this here by running <code>/cm/shared/apps/SHARED/my_conda_env/bin/conda</code>, or, I would recommend creating a modulefile so that you can use it as default.		Now you have a working conda environment in this folder. You can manipulate this here by running <code>/cm/shared/apps/SHARED/my_conda_env/bin/conda</code>, or, I would recommend creating a modulefile so that you can use it as default.
Line 25:		Line 25:
	Create the following example modulefile in a matching <code>/cm/shared/modulefiles/SHARED/my_conda_env</code>:		Create the following example modulefile in a matching <code>/cm/shared/modulefiles/SHARED/my_conda_env</code>:

	<~~source lang='bash'~~>		<pre>
	#%Module -- tcl --		#%Module -- tcl --
	##		##
Line 56:		Line 56:
	prepend-path CPATH $root/include		prepend-path CPATH $root/include
	prepend-path MANPATH $root/share/man		prepend-path MANPATH $root/share/man
	</~~source~~>		</pre>

	This will allow you to <code>module load SHARED/my_conda_env</code> and thus have <code>conda</code> pathed to the currently active environment.		This will allow you to <code>module load SHARED/my_conda_env</code> and thus have <code>conda</code> pathed to the currently active environment.
Line 68:		Line 68:
	The setup for this is that you should create the following folder for their access:		The setup for this is that you should create the following folder for their access:

	<~~source lang='bash'~~>		<pre>
	mkdir -p /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env		mkdir -p /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env
	chmod +r /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env		chmod +r /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env
	</~~source~~>		</pre>

	This folder is something they will need to copy in place to their home directory, specifically <code>$HOME/.local/share/jupyter/kernels/</code>		This folder is something they will need to copy in place to their home directory, specifically <code>$HOME/.local/share/jupyter/kernels/</code>
Line 79:		Line 79:
	=== Python Kernel ===		=== Python Kernel ===

	<~~source lang='bash'~~>		<pre>
	vim /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env/kernel.json		vim /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env/kernel.json
	</source>		</source>
Line 99:		Line 99:
	"display_name": "my_conda_env"		"display_name": "my_conda_env"
	}		}
	</~~source~~>		</pre>

	For Python, that's it. Ipykernel is installed automatically on conda initialisation.		For Python, that's it. Ipykernel is installed automatically on conda initialisation.
Line 106:		Line 106:

	For an R kernel, you need to make sure that the IRkernel package is installed. This is the package that is used to communicate from Jupyter to your running R kernel.		For an R kernel, you need to make sure that the IRkernel package is installed. This is the package that is used to communicate from Jupyter to your running R kernel.
	<~~source lang='bash'~~>		<pre>
	#MISSING EXAMPLE CODE		#MISSING EXAMPLE CODE
	#PROBABLY /cm/shared/apps/SHARED/my_conda_env/bin/conda install R_irkernel		#PROBABLY /cm/shared/apps/SHARED/my_conda_env/bin/conda install R_irkernel
	</~~source~~>		</pre>

	You'll also need to create two files: <code>kernel.json</code> and <code>kernel.js</code>. the <code>kernel.js</code> is a helper script to allow jupyter to communicate to R effectively:		You'll also need to create two files: <code>kernel.json</code> and <code>kernel.js</code>. the <code>kernel.js</code> is a helper script to allow jupyter to communicate to R effectively:

	<~~source lang='bash'~~>		<pre>
	vim /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env/kernel.json		vim /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env/kernel.json
	</~~source~~>		</pre>
	<~~source lang='bash'~~>		<pre>
	{		{
	"env": {		"env": {
Line 126:		Line 126:
	"language": "R"		"language": "R"
	}		}
	</~~source~~>		</pre>

	<~~source lang='bash'~~>		<pre>
	vim /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env/kernel.js		vim /cm/shared/apps/SHARED/my_conda_env/kernel/my_conda_env/kernel.js
	</~~source~~>		</pre>
	<~~source lang='bash'~~>		<pre>
	const cmd_key = /Mac/.test(navigator.platform) ? 'Cmd' : 'Ctrl'		const cmd_key = /Mac/.test(navigator.platform) ? 'Cmd' : 'Ctrl'

Line 211:		Line 211:
	},		},
	}))		}))
	</~~source~~>		</pre>

	== Last Steps ==		== Last Steps ==
Line 217:		Line 217:
	In order to help your students get their kernel definitions into <code>$HOME/.local/share/jupyter/kernels/</code>, it's probably a good idea to write a small and simple notebook to do this when executed, or else instruct them to do:		In order to help your students get their kernel definitions into <code>$HOME/.local/share/jupyter/kernels/</code>, it's probably a good idea to write a small and simple notebook to do this when executed, or else instruct them to do:

	<~~source lang='bash'~~>		<pre>
	cp -rv /cm/shared/apps/SHARED/my_conda_env/kernel/* .local/share/jupyter/kernels/		cp -rv /cm/shared/apps/SHARED/my_conda_env/kernel/* .local/share/jupyter/kernels/
	</~~source~~>		</pre>

Maas036: /* Setup */

2020-05-27T10:01:46Z

Setup

← Older revision		Revision as of 10:01, 27 May 2020
Line 13:		Line 13:

	Then, install Anaconda into it (choose the year and month yourself!):		Then, install Anaconda into it (choose the year and month yourself!):

	Also, note that you need to make the sh script executable before you can run it.		Also, note that you need to make the sh script executable before you can run it.

Maas036: /* Setup */

2020-05-27T10:00:06Z

Setup

← Older revision		Revision as of 10:00, 27 May 2020
Line 13:		Line 13:

	Then, install Anaconda into it (choose the year and month yourself!):		Then, install Anaconda into it (choose the year and month yourself!):
			Also, note that you need to make the sh script executable before you can run it.

	<source lang='bash'>		<source lang='bash'>

Maas036: /* Setup */

2020-05-27T09:32:17Z

Setup

← Older revision		Revision as of 09:32, 27 May 2020
Line 12:		Line 12:
	You may want to manipulate the permissions for this folder if someone is going to set this up with you. Consider the commands in [[Shared folders]].		You may want to manipulate the permissions for this folder if someone is going to set this up with you. Consider the commands in [[Shared folders]].

	Then, install Anaconda into it:		Then, install Anaconda into it (choose the year and month yourself!):

	<source lang='bash'>		<source lang='bash'>

Dawes001 at 09:03, 27 May 2020

2020-05-27T09:03:03Z

← Older revision		Revision as of 09:03, 27 May 2020
Line 2:		Line 2:

	== Setup ==		== Setup ==
	First - find a good location that everyone can read (and not write). I'd suggest somewhere under /cm/shared/apps/SHARED/ as a starting point - this allows everyone to access this location. It's important not to put anything secret there - it's a public resource, so please bear that in mind.		First - find a good location that everyone can read (and not write). I'd suggest somewhere under <code>/cm/shared/apps/SHARED/</code> as a starting point - this allows everyone to access this location. It's important not to put anything secret there - it's a public resource, so please bear that in mind.

	Next - create a folder for your environment:		Next - create a folder for your environment:
Line 10:		Line 10:
	chmod +r /cm/shared/apps/SHARED/my_conda_env		chmod +r /cm/shared/apps/SHARED/my_conda_env
	</source>		</source>
	You may want to manipulate the permissions for this folder if someone is going to set this up with you. Consider the commands in [[Shared ~~Folders~~]].		You may want to manipulate the permissions for this folder if someone is going to set this up with you. Consider the commands in [[Shared folders]].

	Then, install Anaconda into it:		Then, install Anaconda into it:
Line 19:		Line 19:
	</source>		</source>

	Now you have a working conda environment in this folder. You can manipulate this here by running /cm/shared/apps/SHARED/my_conda_env/bin/conda , or, I would recommend creating a modulefile so that you can use it as default.		Now you have a working conda environment in this folder. You can manipulate this here by running <code>/cm/shared/apps/SHARED/my_conda_env/bin/conda</code>, or, I would recommend creating a modulefile so that you can use it as default.

	Create the following example modulefile in a matching /cm/shared/modulefiles/SHARED/my_conda_env :		Create the following example modulefile in a matching <code>/cm/shared/modulefiles/SHARED/my_conda_env</code>:

	<source lang='bash'>		<source lang='bash'>
Line 71:		Line 71:
	</source>		</source>

	This folder is something they will need to copy in place to their home directory, specifically $HOME/.local/share/jupyter/kernels/		This folder is something they will need to copy in place to their home directory, specifically <code>$HOME/.local/share/jupyter/kernels/</code>

	Inside this folder, create the following kernel.json file. Watch out that the paths will need to match the current environment path if you're using a different location!		Inside this folder, create the following <code>kernel.json</code> file. Watch out that the paths will need to match the current environment path if you're using a different location!

	=== Python Kernel ===		=== Python Kernel ===
Line 103:		Line 103:
	=== R Kernel ===		=== R Kernel ===

	For an R kernel, you need to make sure that the IRkernel package is installed. This is the package that is used to communicate from Jupyter to your running R kernel.<source lang='bash'>		For an R kernel, you need to make sure that the IRkernel package is installed. This is the package that is used to communicate from Jupyter to your running R kernel.
			<source lang='bash'>
	#MISSING EXAMPLE CODE		#MISSING EXAMPLE CODE
	#PROBABLY /cm/shared/apps/SHARED/my_conda_env/bin/conda install R_irkernel		#PROBABLY /cm/shared/apps/SHARED/my_conda_env/bin/conda install R_irkernel
	</source>		</source>

	You'll also need to create two files. the kernel.js is a helper script to allow jupyter to communicate to R effectively:		You'll also need to create two files: <code>kernel.json</code> and <code>kernel.js</code>. the <code>kernel.js</code> is a helper script to allow jupyter to communicate to R effectively:

	<source lang='bash'>		<source lang='bash'>
Line 212:		Line 213:
	== Last Steps ==		== Last Steps ==

	In order to help your students get their kernel definitions into $HOME/.local/share/jupyter/kernels/, it's probably a good idea to write a small and simple notebook to do this when executed, or else instruct them to do:		In order to help your students get their kernel definitions into <code>$HOME/.local/share/jupyter/kernels/</code>, it's probably a good idea to write a small and simple notebook to do this when executed, or else instruct them to do:

	<source lang='bash'>		<source lang='bash'>
	cp -rv /cm/shared/apps/SHARED/my_conda_env/kernel/* .local/share/jupyter/kernels/		cp -rv /cm/shared/apps/SHARED/my_conda_env/kernel/* .local/share/jupyter/kernels/
	</source>		</source>

Dawes001 at 09:01, 27 May 2020

2020-05-27T09:01:02Z

← Older revision		Revision as of 09:01, 27 May 2020
Line 56:		Line 56:
	</source>		</source>

	This will allow you to `module load SHARED/my_conda_env` and thus have `conda` pathed to the currently active environment.		This will allow you to <code>module load SHARED/my_conda_env</code> and thus have <code>conda</code> pathed to the currently active environment.

	== Jupyter Kernel ==		== Jupyter Kernel ==
Line 62:		Line 62:
	In order for students to be able to use this environment in jupyter, they will need a kernel definition.		In order for students to be able to use this environment in jupyter, they will need a kernel definition.

	Kernel definitions are usually a separate folder containing, in particular, a file called `kernel.json`, plus an icon that is displayed that represents this kernel, and other helper code.		Kernel definitions are usually a separate folder containing, in particular, a file called <code>kernel.json</code>, plus an icon that is displayed that represents this kernel, and other helper code.

	The setup for this is that you should create the following folder for their access:		The setup for this is that you should create the following folder for their access: