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doku:jupyterhub [2023/03/22 18:58] – [BYOI: Bring your own (Singularity) Image] katrin | doku:jupyterhub [2024/09/19 16:52] (current) – katrin | ||
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The VSC offers a JupyterHub service available for all VSC users at [[https:// | The VSC offers a JupyterHub service available for all VSC users at [[https:// | ||
- | Login works with any cluster user (both VSC3 and VSC4) and uses the OTP like on the cluster. A VPN connection is not needed. | + | Login works with any cluster user and uses the OTP like on the cluster. A VPN connection is not needed. |
Also make sure to checkout the [[doku: | Also make sure to checkout the [[doku: | ||
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* VSC-4 python venv | * VSC-4 python venv | ||
* VSC-4 conda python env | * VSC-4 conda python env | ||
- | * VSC-3 Singularity Image | + | * VSC-5 Singularity Image |
- | * VSC-3 GTX1080 | + | * VSC-5 A40 GPU Singularity Image |
- | * VSC-3 A40 GPU Singularity Image | + | * VSC-5 A100 GPU Singularity Image |
+ | * VSC-5 python venv | ||
+ | * VSC-5 conda python env | ||
+ | * VSC-5 A40 GPU conda python env | ||
+ | * VSC-5 A100 GPU Singularity Image | ||
* If you are participating in a training, there is most likely only a single fixed profile or special training profiles available | * If you are participating in a training, there is most likely only a single fixed profile or special training profiles available | ||
- | **Note:** You need a VSC4 user for the VSC4 profiles and a VSC3 user for the VSC3 profiles. You also need to have logged into the respective cluster via SSH at least once after getting a username. | + | **Note:** You need a VSC4 user for the VSC4 profiles and a VSC5 user for the VSC5 profiles. You also need to have logged into the respective cluster via SSH at least once after getting a username. |
In all profiles, you can choose the IDE, either Jupyter Notebook or the more modern Jupyter Lab (which is the default) | In all profiles, you can choose the IDE, either Jupyter Notebook or the more modern Jupyter Lab (which is the default) | ||
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To stop the server, click on ' | To stop the server, click on ' | ||
- | ===== BYOI: Bring your own (Singularity) Image ===== | + | ===== BYOI: Bring your own (Apptainer/Singularity) Image ===== |
- | It is possible to use a custom singularity image with our JupyterHub profiles. | + | It is possible to use a custom |
- | A good starting point is to have a look at the official JupyterHub Docker Stacks Images @ [[https:// | + | ==== Necessary Packages ==== |
- | In a nutshell it is only necessary | + | A good starting point for creating your own container |
+ | |||
+ | Apart from adding your own software the image also needs to have at least the following packages | ||
< | < | ||
- | jupyterhub==3.0.0 | + | # This package pulls in all the necessary dependencies to start a jupyter server |
- | git+https:// | + | # Make sure this always matches the current JupyterHub version used by VSC |
+ | jupyterhub==3.1.1 | ||
+ | |||
+ | # This package provides functionality needed to run in the slurm environment of VSC (e.g. `batchspawner-singleuser` script). | ||
+ | git+https:// | ||
+ | |||
+ | # June 2024: fix a dependency to an earlier version | ||
+ | nbclassic==0.3.7 | ||
</ | </ | ||
- | In addition we also install the following jupyterlab extensions in our images but they are not strictly necessary and just provide extended functionality like memory monitoring for the user: | + | In addition we usually |
* jupyterlab-system-monitor | * jupyterlab-system-monitor | ||
* jupyterlab-git | * jupyterlab-git | ||
- | * jupyterlab-widgets | + | * jupyterlab-widgets |
- | **An up 2 date list of packages can always be found in our repo: [[https:// | + | **An up 2 date list of packages can always be found in our repo: [[https:// |
- | In order to be able to use the image with JupyterHub you also have to make sure to convert it to a **singularity image** (or build it as a singularity image in the first place) and place it into a folder that is accessible from the VSC compute nodes. | + | === Run hooks from / |
- | + | ||
- | Building a singularity image from e.g. a docker container can easily be done with the `singularity build` command. See the singularity documentation for examples: [[https:// | + | |
- | + | ||
- | ==== Run hooks from / | + | |
If your image needs to run hooks before startup (e.g. the pyspark image depends on this [[https:// | If your image needs to run hooks before startup (e.g. the pyspark image depends on this [[https:// | ||
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Unfortunately the batchspawner package does not source them so we are using a custom startscript in our images called `vsc-singleuser.sh`. All it does is to run the hooks from `/ | Unfortunately the batchspawner package does not source them so we are using a custom startscript in our images called `vsc-singleuser.sh`. All it does is to run the hooks from `/ | ||
- | The script can be found at [[https:// | + | The script can be found at [[https:// |
Note: Contact us to get read rights to the repository. | Note: Contact us to get read rights to the repository. | ||
+ | ==== Build your own custom image from a docker image ==== | ||
+ | [[https:// | ||
+ | If you already have a docker image you want to start from or if you are more familiar with docker image creation you can just use that image and create it into a singularity image after you are finished. | ||
- | ===== FAQ ===== | + | Note: Make sure that you use the right versions for the current version of our JupyterHub (the version is displayed at the bottom of the [[http:// |
- | | + | After selecting / building the docker image all that needs to be done is to convert it into a **singularity image**. |
- | No this is a current limitation | + | You can do this by executing the following lines (assuming your docker image is named " |
+ | < | ||
+ | singularity build my_image.sif docker:// | ||
+ | </ | ||
+ | |||
+ | See the documentation for more examples: [[https:// | ||
+ | |||
+ | When the conversion process has finished make sure that the resulting " | ||
+ | |||
+ | Note: the conversion can be done on our cluster since we have singularity installed on our nodes. | ||
+ | |||
+ | ==== Directly build a singularity/ | ||
+ | |||
+ | Instead | ||
+ | |||
+ | For this you need to create a so called " | ||
+ | |||
+ | Here is a minimal example using the datascience docker stacks image as a basis: | ||
+ | < | ||
+ | BootStrap: docker | ||
+ | From: jupyter/ | ||
+ | |||
+ | %post | ||
+ | / | ||
+ | </ | ||
+ | |||
+ | If we save the file as " | ||
+ | |||
+ | Please | ||
+ | |||
+ | * VSC4: module load --auto apptainer/ | ||
+ | * VSC5: module load --auto apptainer/ | ||
+ | |||
+ | |||
+ | < | ||
+ | # load an apptainer module (see above) | ||
+ | module load --auto apptainer/< | ||
+ | |||
+ | # build the image | ||
+ | apptainer build my_image.sif my_image.def | ||
+ | </ | ||
+ | |||
+ | If you cannot use the versions provided on VSC you can of course also build the image on your own machine and upload it the VSC. | ||
+ | |||
+ | ===== FAQ ===== | ||
* **My Server instance is stuck and I get a timeout when I try to reload the window. Going to the VSC jupyterhub website also results in a timeout.** | * **My Server instance is stuck and I get a timeout when I try to reload the window. Going to the VSC jupyterhub website also results in a timeout.** |