Conda for teaching - Revision history

Honfi001 at 09:39, 12 March 2025

2025-03-12T09:39:27Z

← Older revision		Revision as of 11:39, 12 March 2025
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	{{warning~~\|1=~~ While the technical information is this page is somewhat valid, some information is outdated.}}		{{warning}} While the technical information is this page is somewhat valid, some information may be outdated.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 11:36, 12 March 2025
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			{{warning\|1= While the technical information is this page is somewhat valid, some information is outdated.}}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 12:43, 25 January 2024
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	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]].

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	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.
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	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 --
	##		##
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	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.
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	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>
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	=== 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>
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	"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.
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	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": {
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	"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'

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	},		},
	}))		}))
	</~~source~~>		</pre>

	== Last Steps ==		== Last Steps ==
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	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 12:01, 27 May 2020
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	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 12:00, 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 11:32, 27 May 2020
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	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 11:03, 27 May 2020
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	== 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:
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	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:
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	</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'>
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	</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 ===
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	=== 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'>
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	== 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 11:01, 27 May 2020
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	</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 ==
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	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:

Dawes001: /* Jupyter Kernel */

2020-05-27T08:59:13Z

Jupyter Kernel

@@ Line 64: / Line 64: @@
 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.
-This is something they will need to copy in place to their home directory, specifically $HOME/.local/share/jupyter/kernels/
+<source lang='bash'>
 <source lang='bash'>
+{
@@ Line 86: / Line 99: @@
 </source>
-kernel.js
+For Python, that's it. Ipykernel is installed automatically on conda initialisation.
 <source lang='bash'>
 const cmd_key = /Mac/.test(navigator.platform) ? 'Cmd' : 'Ctrl'
@@ Line 167: / Line 208: @@
 	},
 }))
 </source>

Dawes001 at 08:45, 27 May 2020

2020-05-27T08:45:06Z

@@ Line 62: / Line 62: @@
 In order for students to be able to use this environment in jupyter, they will need a kernel definition.
+{
   "env": {
@@ Line 79: / Line 84: @@
   "display_name": "my_conda_env"
+}