Open OnDemand - Revision history

Lleung: /* Additional Apps */

2025-02-24T21:46:02Z

Additional Apps

← Older revision		Revision as of 21:46, 24 February 2025
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	==== Additional Apps ====		==== Additional Apps ====
	~~The~~ desktop ~~has additional software~~ available.		Please be aware that the desktop runs within an Apptainer environment. Certain features that require containerisation or Linux namespaces may not be available. This is particularly an issue with applications based on webkit/chromium and may require workarounds.

			The following are some applications that have been installed within the Desktop environment:

	===== Applications / Development =====		===== Applications / Development =====
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	* Citrix Workspace (Use Firefox or Chromium to connect to myappmf.ucalgary.ca)		* Citrix Workspace (Use Firefox or Chromium to connect to myappmf.ucalgary.ca)

	==== Applications / Office ====		===== Applications / Office =====
	* LibreOffice Suite		* LibreOffice Suite

	==== Applications / Other ====		===== Applications / Other =====
	* Visual Molecular Dynamics (VMD)		* Visual Molecular Dynamics (VMD)
	Please be aware that the desktop runs within an Apptainer environment. Certain features that require containerisation or Linux namespaces may not be available. This is particularly an issue with applications based on webkit/chromium and may require workarounds.

	=== Jupyter Notebooks ===		=== Jupyter Notebooks ===
	Open OnDemand offers Jupyter Notebooks via containers or environment modules. For most users, we recommend using the containers way to launch your Jupyter notebooks as it is the simplest. We also offer the environment module based method for users that already have a working workflow based on environment modules.		Open OnDemand offers Jupyter Notebooks via containers or environment modules. For most users, we recommend using the containers way to launch your Jupyter notebooks as it is the simplest. We also offer the environment module based method for users that already have a working workflow based on environment modules.

Lleung: /* Interactive Applications */

2025-02-24T21:44:13Z

Interactive Applications

← Older revision		Revision as of 21:44, 24 February 2025
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	==== Additional Apps ====		==== Additional Apps ====
	The desktop has additional software available~~, including:~~		The desktop has additional software available.

	* VMD		===== Applications / Development =====
	* Visual Studio Code		* Visual Studio Code
	* RStudio		* RStudio

			===== Applications / Internet =====
	* FileZilla		* FileZilla
	* RClone Browser		* RClone Browser
	* Chromium		* Chromium
	* Firefox		* Firefox
			* Citrix Workspace (Use Firefox or Chromium to connect to myappmf.ucalgary.ca)

			==== Applications / Office ====
			* LibreOffice Suite

	~~Because~~ the desktop runs within an Apptainer environment~~, certain~~ features that require containerisation or Linux namespaces may not be available.		==== Applications / Other ====
			* Visual Molecular Dynamics (VMD)
			Please be aware that the desktop runs within an Apptainer environment. Certain features that require containerisation or Linux namespaces may not be available. This is particularly an issue with applications based on webkit/chromium and may require workarounds.

	=== Jupyter Notebooks ===		=== Jupyter Notebooks ===

Lleung: /* Interactive Applications */

2025-02-24T21:35:35Z

Interactive Applications

Show changes

Lleung: Added support

2023-09-21T21:14:26Z

Added support

← Older revision		Revision as of 21:14, 21 September 2023
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	=== VNC session cannot reconnect ===		=== VNC session cannot reconnect ===
	If your VNC session closed, you may need to re-connect by going back to the Open OnDemand dashboard, listing your sessions under "My Interactive Sessions" page, then click on the blue "Launch Desktop" button.		If your VNC session closed, you may need to re-connect by going back to the Open OnDemand dashboard, listing your sessions under "My Interactive Sessions" page, then click on the blue "Launch Desktop" button.

			{{Support}}

	[[Category:ARC]]		[[Category:ARC]]
	{{Navbox ARC}}		{{Navbox ARC}}

Lleung: Added ARC navbox and category

2023-09-21T20:10:01Z

Added ARC navbox and category

← Older revision		Revision as of 20:10, 21 September 2023
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	=== VNC session cannot reconnect ===		=== VNC session cannot reconnect ===
	If your VNC session closed, you may need to re-connect by going back to the Open OnDemand dashboard, listing your sessions under "My Interactive Sessions" page, then click on the blue "Launch Desktop" button.		If your VNC session closed, you may need to re-connect by going back to the Open OnDemand dashboard, listing your sessions under "My Interactive Sessions" page, then click on the blue "Launch Desktop" button.

			[[Category:ARC]]
			{{Navbox ARC}}

Lleung: /* Create a custom Jupyter Notebook image */

2023-05-09T17:18:48Z

Create a custom Jupyter Notebook image

← Older revision		Revision as of 17:18, 9 May 2023
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	If additional packages are required in the notebook, you can create and use a customized container image and use it with Open OnDemand. As all the jupyter notebook images are based on Ubuntu with mamba, you may install additional packages using <code>apt-get</code>, <code>mamba</code>, and <code>pip</code>.		If additional packages are required in the notebook, you can create and use a customized container image and use it with Open OnDemand. As all the jupyter notebook images are based on Ubuntu with mamba, you may install additional packages using <code>apt-get</code>, <code>mamba</code>, and <code>pip</code>.

	To build a custom container image, create a Singularity build definition file that references the appropriate base jupyter notebook image. All custom Jupyter images should be based off of the base Jupyter notebook image for compatibility. In the following example, we will extend the <code>tensorflow-notebook</code> image with an additional pip package.		To build a custom container image, create a Singularity build definition file that references the appropriate base jupyter notebook image. All custom Jupyter images should be based off of the base Jupyter notebook image for compatibility. In the following example, we will extend the <code>tensorflow-notebook</code> image with a C++ compiler (g++) and an additional pip package (corels).

	Create a Singularity build file <code>custom-notebook.def</code> with the following contents:		Create a Singularity build file <code>custom-notebook.def</code> with the following contents:
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	apt-get autoremove; \		apt-get autoremove; \
	apt-get update --yes; \		apt-get update --yes; \
	apt-get install --yes --no-install-recommends g++; \		apt-get install --yes --no-install-recommends g++; \
	pip install corels\|lang=text}}		pip install corels\|lang=text}}
	To build <code>custom-notebook.def</code>, run: <code>singularity build custom-notebook.sif custom-notebook.def</code>. This will generate a <code>custom-notebook.sif</code> singularity image file.		To build <code>custom-notebook.def</code>, run: <code>singularity build custom-notebook.sif custom-notebook.def</code>. This will generate a <code>custom-notebook.sif</code> singularity image file.

	To use this custom image in Open OnDemand, move ~~this~~ file to <code>$HOME/ondemand/jupyter</code>. In Open OnDemand, when launching a new notebook, select 'Custom Singularity Image...' on the launch page.		To use this custom image in Open OnDemand, move the newly generated <code>.sif</code> file to <code>$HOME/ondemand/jupyter</code>. In Open OnDemand, when launching a new notebook, select 'Custom Singularity Image...' on the launch page and select the appropriate <code>.sif</code> file.

	==== Environment module based Jupyter notebooks ====		==== Environment module based Jupyter notebooks ====

Lleung: /* Create a custom Jupyter Notebook image */

2023-05-09T17:14:35Z

Create a custom Jupyter Notebook image

← Older revision		Revision as of 17:14, 9 May 2023
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	===== Create a custom Jupyter Notebook image =====		===== Create a custom Jupyter Notebook image =====
	~~To help facilitate~~ the ~~many different workflows~~ you ~~may have, we allow the~~ use of customized ~~Jupyter~~ notebook images~~. Simply place your custom Jupyter Singularity image at~~ <code>~~$HOME~~/~~ondemand~~/~~jupyter~~</code> ~~and select 'Custom Singularity Image...' on the launch page~~.		If additional packages are required in the notebook, you can create and use a customized container image and use it with Open OnDemand. As all the jupyter notebook images are based on Ubuntu with mamba, you may install additional packages using <code>apt-get</code>, <code>mamba</code>, and <code>pip</code>.

	All custom Jupyter images should be based off of the base Jupyter notebook image for compatibility. ~~Additional packages can then be installed via~~ <code>~~pip~~</code> ~~or <code>conda</code>. An example Dockerfile is given below~~.		To build a custom container image, create a Singularity build definition file that references the appropriate base jupyter notebook image. All custom Jupyter images should be based off of the base Jupyter notebook image for compatibility. In the following example, we will extend the <code>tensorflow-notebook</code> image with an additional pip package.
	~~{{Highlight\|lang=text\|code=FROM jupyter/base-notebook~~

	~~# Install any additional packages here~~		Create a Singularity build file <code>custom-notebook.def</code> with the following contents:
	~~RUN set~~ -~~ex; \~~		{{Highlight\|code=Bootstrap: docker
	~~conda install --yes \~~		From: jupyter/tensorflow-notebook
	~~-c conda-forge \~~
	~~ipywidgets ;\~~
	~~conda clean --all -f -y; \~~
	~~fix-permissions "$~~{~~CONDA_DIR}"; \~~
	~~fix~~-~~permissions "/home/${NB_USER}"~~

	~~USER $NB_UID~~		%post
			apt-get autoremove; \
			apt-get update --yes; \
			apt-get install --yes --no-install-recommends g++; \
			pip install corels\|lang=text}}
			To build <code>custom-notebook.def</code>, run: <code>singularity build custom-notebook.sif custom-notebook.def</code>. This will generate a <code>custom-notebook.sif</code> singularity image file.

	~~WORKDIR~~ $HOME		To use this custom image in Open OnDemand, move this file to <code>$HOME/ondemand/jupyter</code>. In Open OnDemand, when launching a new notebook, select 'Custom Singularity Image...' on the launch page.
	~~}}Build the docker image and convert it into~~ a Singularity ~~image~~.

	==== Environment module based Jupyter notebooks ====		==== Environment module based Jupyter notebooks ====

Dmitri: /* Connect to OnDemand */

2021-11-16T19:00:39Z

Connect to OnDemand

← Older revision		Revision as of 19:00, 16 November 2021
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	\|-		\|-
	\|[[ARC Cluster Guide\|ARC Cluster]]		\|[[ARC Cluster Guide\|ARC Cluster]]
	\|[https://ood-arc.rcs.ucalgary.ca \| ood-arc.rcs.ucalgary.ca]		\|[https://ood-arc.rcs.ucalgary.ca ood-arc.rcs.ucalgary.ca]
	\|}		\|}

Dmitri at 18:58, 16 November 2021

2021-11-16T18:58:27Z

← Older revision		Revision as of 18:58, 16 November 2021
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	\|-		\|-
	\|[[ARC Cluster Guide\|ARC Cluster]]		\|[[ARC Cluster Guide\|ARC Cluster]]
	\|ood-arc.rcs.ucalgary.ca		\|[https://ood-arc.rcs.ucalgary.ca \| ood-arc.rcs.ucalgary.ca]
	\|}		\|}

Lleung: /* Container-based Jupyter notebooks */

2021-08-16T21:48:50Z

Container-based Jupyter notebooks

← Older revision		Revision as of 21:48, 16 August 2021
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	==== Container-based Jupyter notebooks ====		==== Container-based Jupyter notebooks ====
	[[File:Open OnDemand Jupyter.jpg\|alt=Open OnDemand Jupyter Notebook\|thumb\|Open OnDemand Jupyter Notebook ]]		[[File:Open OnDemand Jupyter.jpg\|alt=Open OnDemand Jupyter Notebook\|thumb\|Open OnDemand Jupyter Notebook ]]
	We offer a selection of different Jupyter Notebooks derived from the official Jupyter Docker images. We ~~support the~~ following flavors of Jupyter notebooks:		We offer a selection of different Jupyter Notebooks derived from the [https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html. official Jupyter Stacks Docker images]. We will provide updated images with major ARC upgrades. The following flavors of Jupyter notebooks are currently available:
	{\| class="wikitable"		{\| class="wikitable"
			!
	!Image		!Image
	!Description		!Description
	\|-		\|-
	\|all-spark-~~notebook~~.sif		\|Spark Notebook
	\|Includes Python, R, and Scala support for Apache Spark.		\|all-spark-notebook_spark-#.#.#.sif
			\|Includes Python, R, and Scala support for Apache Spark.
			Spark version is listed in the filename.
	\|-		\|-
	\|datascience-~~notebook~~.sif		\|Julia Data Science Notebook
	\|Includes libraries for data analysis from the Julia, Python, and R communities.		\|datascience-notebook_julia-#.#.#.sif
			\|Includes libraries for data analysis from the Julia, Python, and R communities.
			Julia version is listed in the filename.
	\|-		\|-
	\|~~gpu~~-~~jupyter~~.sif		\|Python Scipy Notebook
	\|Includes ~~NVIDIA CUDA along with~~ the ~~datascience notebook. Based on https://github.com/iot-salzburg/gpu-jupyter/~~		\|scipy-notebook_python-#.#.#.sif
			\|Includes Python support for Apache Spark.
			Python version is listed in the filename
	\|-		\|-
	\|~~scipy~~-~~notebook~~.sif		\|Tensorflow Notebook
	\|~~Includes Python support for Apache Spark~~.		\|tensorflow-notebook_tensorflow-#.#.#.sif
			\|Based on the Scipy notebook but includes Tensorflow.
			Tensorflow version is listed in the filename.
	\|-		\|-
	\|~~tensorflow~~-~~notebook~~		\|
	\|Includes ~~Tensorflow in addition to~~ the ~~scipy~~ notebook.		\|gpu-jupyter.sif
			\|Includes NVIDIA CUDA along with the data science notebook.
			Based on https://github.com/iot-salzburg/gpu-jupyter/
	\|}		\|}
	~~Additional information on the jupyter-stacks images are available at https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html.~~		To select the flavour of your notebook, select the desired image in the drop-down menu in the launch page. You may optionally use a custom image as well by selecting 'Custom Singularity Image...' (see the next section below). You may also specify any additional arguments to Jupyter including whether to launch JupyterLab instead.

	On the ~~Jupyter Notebook launch page~~, select the desired image in the drop-down menu. You may optionally use a custom image as well by selecting 'Custom Singularity Image...' (see the next section below). You may also specify any additional arguments to Jupyter including whether to launch JupyterLab instead.

	===== Create a custom Jupyter Notebook image =====		===== Create a custom Jupyter Notebook image =====