Python - Revision history

Honfi001 at 15:56, 23 October 2025

2025-10-23T15:56:43Z

← Older revision		Revision as of 17:56, 23 October 2025
Line 127:		Line 127:
	</pre>		</pre>

	The ~~code above initializes lmod by sourcing~~ <code>/~~etc~~/bash.~~bashrc~~</code>, ~~then it loaded~~ the modules ~~required by the environment~~. Finally, it executes ipykernel_launcher from the virtual environment created. In this example, the code above is saved in <code>/home/WUR/user001/wrap.sh</code> . Make sure the wrapper script is executable.		The wrapper script uses <code>#!/bin/bash -l</code> as the interpreter of the script. The <code>-l</code> flag tell bash to start as a login shell, which loads lmod by default. The modules are reset and the desired buckets and modules are loads.

			Finally, the wrapper script executes the module '''ipykernel_launcher''' from the virtual environment we just created. In this example, the code above is saved in <code>/home/WUR/user001/wrap.sh</code> . Make sure the wrapper script is executable.

	The last thing to do now is to modify the kernel.json file of the jupyter kernel created above. It should be located at <code>~/.local/share/jupyter/kernels/my_env_kernel_name/kernel.json</code>		The last thing to do now is to modify the kernel.json file of the jupyter kernel created above. It should be located at <code>~/.local/share/jupyter/kernels/my_env_kernel_name/kernel.json</code>

2025-10-22T13:14:48Z

← Older revision		Revision as of 15:14, 22 October 2025
Line 116:		Line 116:

	<pre>		<pre>
	#!/bin/bash		#!/bin/bash -l
	~~source /shared/apps/lmod/current/init/bash~~
	~~#Set the modulepath~~
	~~export MODULEPATH=/shared/modulefiles~~
	~~# Set Default Modules~~
	~~export LMOD_SYSTEM_DEFAULT_MODULES="slurm"~~
	~~# Load Default Modules~~
	~~if [ -z "$__Init_Default_Modules" ]; then~~
	~~export __Init_Default_Modules=1;~~
	~~module --initial_load restore~~
	~~else~~
	~~module refresh~~
	fi
	~~## Edit lines below this~~
	~~#------------------------------------------------------------------~~-

	#modules to load		module reset
			# modules to load
	module load 2024		module load 2024
	module load Python/3.12.3		module load Python/3.12.3

2025-05-15T12:25:42Z

← Older revision		Revision as of 14:25, 15 May 2025
Line 116:		Line 116:

	<pre>		<pre>
	~~## Do not edit~~
	#!/bin/bash		#!/bin/bash
	source /shared/apps/lmod/current/init/bash		source /shared/apps/lmod/current/init/bash
Line 131:		Line 130:
	fi		fi
	## Edit lines below this		## Edit lines below this
			#-------------------------------------------------------------------

	#modules to load		#modules to load

2025-05-15T12:24:20Z

2025-05-15T12:23:47Z

@@ Line 116: / Line 116: @@
 <pre>
 #!/bin/bash
-source /etc/bash.bashrc
+source /shared/apps/lmod/current/init/bash
 #modules to load
 module load 2024

2025-02-27T15:05:45Z

Creating Jupyter kernels from virtual environments

← Older revision		Revision as of 17:05, 27 February 2025
Line 126:		Line 126:
	</pre>		</pre>

	The code above initializes lmod by sourcing <code>/etc/bash.bashrc</code>, then it loaded the modules required by the environment. Finally, it executes ipykernel_launcher from the virtual environment created. In this example, the code above is saved ~~inside~~ <code>/home/WUR/user001/wrap.sh</code> Make sure the wrapper script is executable.		The code above initializes lmod by sourcing <code>/etc/bash.bashrc</code>, then it loaded the modules required by the environment. Finally, it executes ipykernel_launcher from the virtual environment created. In this example, the code above is saved in <code>/home/WUR/user001/wrap.sh</code> . Make sure the wrapper script is executable.

	The last thing to do now is to modify the kernel.json file of the jupyter kernel created above. It should be located at <code>~/.local/share/jupyter/kernels/my_env_kernel_name/kernel.json</code>		The last thing to do now is to modify the kernel.json file of the jupyter kernel created above. It should be located at <code>~/.local/share/jupyter/kernels/my_env_kernel_name/kernel.json</code>

2025-02-27T15:04:53Z

Creating Jupyter kernels from virtual environments

← Older revision		Revision as of 17:04, 27 February 2025
Line 126:		Line 126:
	</pre>		</pre>

	The code above initializes lmod by sourcing <code>/etc/bash.bashrc</code>, then it loaded the modules required by the environment. Finally, it executes ipykernel_launcher from the virtual environment created. Make sure the wrapper script is executable.		The code above initializes lmod by sourcing <code>/etc/bash.bashrc</code>, then it loaded the modules required by the environment. Finally, it executes ipykernel_launcher from the virtual environment created. In this example, the code above is saved inside <code>/home/WUR/user001/wrap.sh</code> Make sure the wrapper script is executable.

	The last thing to do now is to modify the kernel.json file of the jupyter kernel created above. It should be located at <code>~/.local/share/jupyter/kernels/my_env_kernel_name/kernel.json</code>		The last thing to do now is to modify the kernel.json file of the jupyter kernel created above. It should be located at <code>~/.local/share/jupyter/kernels/my_env_kernel_name/kernel.json</code>

2025-02-17T15:19:14Z

Creating Jupyter kernels from virtual environments

← Older revision		Revision as of 17:19, 17 February 2025
Line 78:		Line 78:
	* install the '''ipython''' package		* install the '''ipython''' package
	* generate the kernel		* generate the kernel
	* Write a wrapper		* Write a wrapper script
			* Make the wrapper script executable
	* Edit the kernel file		* Edit the kernel file

Line 125:		Line 126:
	</pre>		</pre>

	The code above initializes lmod by sourcing <code>/etc/bash.bashrc</code>, then it loaded the modules required by the environment. Finally, it executes ipykernel_launcher from the virtual ~~environemnt~~ created.		The code above initializes lmod by sourcing <code>/etc/bash.bashrc</code>, then it loaded the modules required by the environment. Finally, it executes ipykernel_launcher from the virtual environment created. Make sure the wrapper script is executable.

	The last thing to do now is to modify the kernel.json file of the jupyter kernel created above. It should be located at <code>~/.local/share/jupyter/kernels/my_env_kernel_name/kernel.json</code>		The last thing to do now is to modify the kernel.json file of the jupyter kernel created above. It should be located at <code>~/.local/share/jupyter/kernels/my_env_kernel_name/kernel.json</code>

2025-02-17T11:58:34Z

Modules

← Older revision		Revision as of 13:58, 17 February 2025
Line 8:		Line 8:

	== Modules ==		== Modules ==

			Each module year bucket comes with a version of Python installed

			* '''2023''': Python/3.11.3
			* '''2024''': Python/3.12.3

			Additionally, modules of bundles of python extensions are also installed

			* Python-bundle-PyPI

	== Mamba ==		== Mamba ==

2025-02-17T11:54:17Z

Creating Jupyter kernels from virtual environments

← Older revision		Revision as of 13:54, 17 February 2025
Line 113:		Line 113:
	# wrapper line		# wrapper line
	# exec <pathToVirtualEnvPythonExecutable> -m ipykernel_launcher "$@"		# exec <pathToVirtualEnvPythonExecutable> -m ipykernel_launcher "$@"
	exec /lustre/scratch/<AFFILIATION>/<GROUP>/PythonEnv/my_env/bin/bin/python -m ipykernel_launcher "$@"		exec /lustre/scratch/<AFFILIATION>/<GROUP>/user001/PythonEnv/my_env/bin/bin/python -m ipykernel_launcher "$@"
	</pre>		</pre>