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- | ====== JupyterHub with Slurm on Maris ====== | ||
- | JupyterHub is a multi-user server for Jupyter (AKA IPython) notebooks. Though JupyterHub you can create and share documents that contain live code, equations, visualizations and text notes (comments). | ||
- | Maris cluster provides a JupyterHub service which uses a dedicated '' | ||
- | authorized users. Users should request access to the maris cluster as described | ||
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- | JupyterHub spawns single-user notebooks by requesting consumable resources to '' | ||
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- | ===== Access ===== | ||
- | Maris' JupyterHub can be reached via a web browser at | ||
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- | https:// | ||
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- | Please note that access to the page above is restricted to within the IL network. | ||
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- | {{ : | ||
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- | :!: Maris' jupyterhub has the feature **admin_access** enabled. This means admin users have the ability to take actions on users' behalf, such as stopping and restarting their servers. | ||
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- | ===== Launching Notebooks ===== | ||
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- | All users that have access to maris will also be able to use JupyterHub. Launching a notebook is as easy as selecting the resources needed from the dropdown menu that appears upon a successful login. Currently, the choices are | ||
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- | * NOTEBOOK1: NumNodes=1 NumCPUs=4 NumTasks=1 CPUs/Task=4 mem=16G 30 days | ||
- | * NOTEBOOK2: NumNodes=1 NumCPUs=2 NumTasks=1 CPUs/Task=2 mem=8G 30 days | ||
- | * NOTEBOOK3: NumNodes=1 NumCPUs=1 NumTasks=1 CPUs/Task=1 mem=4G 30 days | ||
- | * NOTEBOOK4: NumNodes=1 NumCPUs=16 NumTasks=1 CPUs/ | ||
- | * NOTEBOOK5: NumNodes=1 NumCPUs=16 NumTasks=1 CPUs/ | ||
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- | Additions to the list above are possible and should be discussed with '' | ||
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- | If the resources requested are available a single-user notebook instance will be launched and you will be ready to run your code interactively. | ||
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- | Jupyterhub will write output and error files relative to the spawning of each notebook instance using the filename scheme '' | ||
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- | :!: If launching a notebook fails, please **read these output files before contacting '' | ||
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- | :!: It has been observed that jupyterhub `forgets' | ||
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- | ===== Jupyterhub Enabled Extensions ===== | ||
- | |||
- | ==== `Files' | ||
- | The //Files// tab allows users to create, modify and remove files. Furthermore, | ||
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- | < | ||
- | # use system' | ||
- | ipython kernel install --name=my-python-kernel --user | ||
- | ls ${HOME}/ | ||
- | my-python-kernel | ||
- | # or more appropriately | ||
- | jupyter kernelspec list | ||
- | </ | ||
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- | Set the JUPYTER_PATH environment variable to provide extra directories for the kernels search path. JUPYTER_PATH should contain a series of directories, | ||
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- | :!: Users can install their custom python environments (see [[: | ||
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- | ==== `Running' | ||
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- | This tab shows and controls | ||
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- | ==== `IPython Clusters' | ||
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- | JupyterHub users can distribute the load of their calculations to different maris' nodes using [[http:// | ||
- | [[: | ||
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- | ==== JupyterHub `Conda' | ||
- | This tab allows users to list and manage conda environments using jupyter' | ||
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- | < | ||
- | / | ||
- | ${HOME}/ | ||
- | </ | ||
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- | :!: If the creation of a new conda environment through the web interface produces an `xsrf' error, then edit your jupyter configuration file located at '' | ||
- | < | ||
- | c.NotebookApp.disable_check_xsrf = True | ||
- | </ | ||
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- | ===== Matlab on maris jupyterhub ===== | ||
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- | The Leiden Institute of Physics (LION) provides a certain number of matlab licenses available to its users. Here follows a simple session that will enable your notebooks to use matlab' | ||
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- | < | ||
- | cd / | ||
- | python3 setup.py build --build-base="/ | ||
- | pip3 install imatlab --user | ||
- | python3 -m imatlab install --user | ||
- | # check that the matlab kernel was installed | ||
- | jupyter kernelspec list | ||
- | Available kernels: | ||
- | python3 | ||
- | imatlab | ||
- | </ | ||
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- | Then as usual log on to https:// | ||
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- | :!: Be aware that if there are NOT any matlab licenses available you will not be able to initiate the matlab kernel. | ||
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- | :!: license availability can be checked using | ||
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- | < | ||
- | license matlab | ||
- | </ | ||
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- | See also: https:// |