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institute_lorentz:institutelorentz_maris_slurm_jupyterhub [2017/09/21 08:17] – lenocil | institute_lorentz:institutelorentz_maris_slurm_jupyterhub [2018/07/19 15:19] – [Launching Notebooks] lenocil | ||
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Maris cluster provides a JupyterHub service which uses a dedicated '' | Maris cluster provides a JupyterHub service which uses a dedicated '' | ||
- | authorized users. Users should | + | authorized users. Users should |
- | JupyterHub spawns single-user notebooks by requesting consumable resources to '' | + | JupyterHub spawns single-user notebooks by requesting consumable resources to '' |
===== Access ===== | ===== Access ===== | ||
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{{ : | {{ : | ||
- | :!: Please note that maris' jupyterhub has **admin_access | + | :!: Maris' jupyterhub has the feature |
===== Launching Notebooks ===== | ===== 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 | 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 | ||
- | * NOTEBOOK1: NumNodes=1 NumCPUs=4 NumTasks=1 CPUs/Task=4 mem=16G | + | * NOTEBOOK1: NumNodes=1 NumCPUs=4 NumTasks=1 CPUs/Task=4 mem=16G |
- | * NOTEBOOK2: NumNodes=1 NumCPUs=2 NumTasks=1 CPUs/Task=2 mem=8G | + | * NOTEBOOK2: NumNodes=1 NumCPUs=2 NumTasks=1 CPUs/Task=2 mem=8G |
- | * NOTEBOOK3: NumNodes=1 NumCPUs=1 NumTasks=1 CPUs/Task=1 mem=4G | + | * NOTEBOOK3: NumNodes=1 NumCPUs=1 NumTasks=1 CPUs/Task=1 mem=4G |
- | * NOTEBOOK4: NumNodes=1 NumCPUs=16 NumTasks=1 CPUs/ | + | * NOTEBOOK4: NumNodes=1 NumCPUs=16 NumTasks=1 CPUs/ |
+ | * NOTEBOOK5: NumNodes=1 NumCPUs=16 NumTasks=1 CPUs/ | ||
Additions to the list above are possible and should be discussed with '' | 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. | If the resources requested are available a single-user notebook instance will be launched and you will be ready to run your code interactively. | ||
- | Jupyterhub will write output and error files relative to the spawning of each notebook instance using the filename scheme '' | + | Jupyterhub will write output and error files relative to the spawning of each notebook instance using the filename scheme '' |
:!: If launching a notebook fails, please **read these output files before contacting '' | :!: If launching a notebook fails, please **read these output files before contacting '' | ||
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==== `IPython Clusters' | ==== `IPython Clusters' | ||
- | JupyterHub users can distribute the load of their calculations to different maris' nodes using [[http:// | + | JupyterHub users can distribute the load of their calculations to different maris' nodes using [[http:// |
- | [[: | + | [[: |
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< | < | ||
- | export CONDA_ENVS_PATH=/ | + | / |
+ | ${HOME}/.conda/envs | ||
</ | </ | ||
- | :!: If the creation of a new conda environment through the web interface produces an `xsrf' error, then edit your jupyter configuration file usually | + | :!: 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 | c.NotebookApp.disable_check_xsrf = True | ||
</ | </ | ||
+ | ===== Matlab on maris jupyterhub ===== | ||
+ | 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' | ||
+ | |||
+ | < | ||
+ | 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 | ||
+ | </ | ||
+ | |||
+ | Then as usual log on to https:// | ||
+ | |||
+ | :!: Be aware that if there are NOT any matlab licenses available you will not be able to initiate the matlab kernel. | ||
+ | |||
+ | :!: license availability can be checked using | ||
+ | |||
+ | < | ||
+ | license matlab | ||
+ | </ | ||
+ | |||
+ | See also: https:// |