"Link to [install-singularity-jupyter-kernel.sh](https://docs.jupyter-jsc.fz-juelich.de/github/kreuzert/jupyter-jsc-notebooks/blob/documentation/03-HowTos/details/install-singularity-jupyter-kernel.sh)"
"Link to [install-singularity-jupyter-kernel.sh](https://gitlab.jsc.fz-juelich.de/jupyter4jsc/j4j_notebooks/-/raw/master/03-HowTos/details/install-singularity-jupyter-kernel.sh)"
<h1style="text-align: center">Install containerized Jupyter kernel at Jupyter-JSC</h1>
<h1style="text-align: center">Install containerized Jupyter kernel at Jupyter-JSC</h1>
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This Jupyter notebook will walk you through the installation of a containerized Jupyter kernel (for use at Jupyter-JSC, but it should actually work with any Jupyter server on a system where Singularity is installed). Considerable performance improvements (especially with respect to kernel start-up times) over e.g. conda-based Jupyter kernels on distributed filesystems, as are typically installed on HPC systems, might be experienced. In the example below, the `base-notebook` from the [Jupyter docker stacks](https://jupyter-docker-stacks.readthedocs.io/en/latest/) is used as an IPython kernel (already having the required `ipykernel` package installed), the approach presented here might be extended to any other [Jupyter kernel compatible programming language](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels), though.
This Jupyter notebook will walk you through the installation of a containerized Jupyter kernel (for use at Jupyter-JSC, but it should actually work with any Jupyter server on a system where Singularity is installed). Considerable performance improvements (especially with respect to kernel start-up times) over e.g. conda-based Jupyter kernels on distributed filesystems, as are typically installed on HPC systems, might be experienced. In the example below, the `base-notebook` from the [Jupyter docker stacks](https://jupyter-docker-stacks.readthedocs.io/en/latest/) is used as an IPython kernel (already having the required `ipykernel` package installed), the approach presented here might be extended to any other [Jupyter kernel compatible programming language](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels), though.
Requirements:
Requirements:
* Python environment with an installed `ipykernel` package in a Docker (or Singularity) container
* Python environment with an installed `ipykernel` package in a Docker (or Singularity) container
*`container` group access for the JSC systems as described [here](https://apps.fz-juelich.de/jsc/hps/juwels/container-runtime.html#getting-access) in the docs
*`container` group access for the JSC systems as described [here](https://apps.fz-juelich.de/jsc/hps/juwels/container-runtime.html#getting-access) in the docs
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Check that the Singularity container runtime is available via the JupyterLab environment,
Check that the Singularity container runtime is available via the JupyterLab environment,
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``` bash
``` bash
singularity --version
singularity --version
```
```
%% Output
%% Output
singularity version 3.6.4-1.el8
singularity version 3.6.4-1.el8
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Specify the filesystem location that stores the Singularity container image,
Specify the filesystem location that stores the Singularity container image,
Optional, if you already have a Singularity container image available at the above location: Convert a containerized Python environment (e.g. the Jupyter `base-notebook` that is [available via Dockerhub](https://hub.docker.com/r/jupyter/base-notebook)) into a Singularity container image to be used as an example here,
Optional, if you already have a Singularity container image available at the above location: Convert a containerized Python environment (e.g. the Jupyter `base-notebook` that is [available via Dockerhub](https://hub.docker.com/r/jupyter/base-notebook)) into a Singularity container image to be used as an example here,
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``` bash
``` bash
mkdir-p${IMAGE_TARGET_DIR}
mkdir-p${IMAGE_TARGET_DIR}
```
```
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Note that pulling and converting the Dockerhub image will take a bit of time,
Note that pulling and converting the Dockerhub image will take a bit of time,
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INFO: Creating SIF file...
INFO: Creating SIF file...
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Check that the Singularity image is available,
Check that the Singularity image is available,
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``` bash
``` bash
ls-lah${IMAGE_TARGET_DIR}
ls-lah${IMAGE_TARGET_DIR}
```
```
%% Output
%% Output
total 177M
total 177M
drwxr-sr-x 2 hoeflich1 cesmtst 4.0K Jan 19 11:59 .
drwxr-sr-x 2 hoeflich1 cesmtst 4.0K Jan 19 11:59 .
drwxr-sr-x 5 hoeflich1 cesmtst 4.0K Jan 19 11:59 ..
drwxr-sr-x 5 hoeflich1 cesmtst 4.0K Jan 19 11:59 ..
-rwxr-xr-x 1 hoeflich1 cesmtst 183M Jan 19 11:59 jupyter-base-notebook.sif
-rwxr-xr-x 1 hoeflich1 cesmtst 183M Jan 19 11:59 jupyter-base-notebook.sif
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Now, setup a Jupyter kernel specification with the `install-jupyter-kernel.sh` script from this repository (which basically writes a `kernel.json` file to the home directory location that Jupyter expects for user-specific kernels),
Now, setup a Jupyter kernel specification with the `install-jupyter-kernel.sh` script from this repository (which basically writes a `kernel.json` file to the home directory location that Jupyter expects for user-specific kernels),
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``` bash
``` bash
KERNEL_DISPLAY_NAME=Singularity-Python # don't use whitespaces here!
KERNEL_DISPLAY_NAME=Singularity-Python # don't use whitespaces here!
Link to [install-singularity-jupyter-kernel.sh](https://docs.jupyter-jsc.fz-juelich.de/github/kreuzert/jupyter-jsc-notebooks/blob/documentation/03-HowTos/details/install-singularity-jupyter-kernel.sh)
Link to [install-singularity-jupyter-kernel.sh](https://gitlab.jsc.fz-juelich.de/jupyter4jsc/j4j_notebooks/-/raw/master/03-HowTos/details/install-singularity-jupyter-kernel.sh)
If so, you should be able to choose and connect to the containerized Python kernel from the drop down menu and/or the kernel launcher tab (a reload of the JupyterLab web page might be necessary).
If so, you should be able to choose and connect to the containerized Python kernel from the drop down menu and/or the kernel launcher tab (a reload of the JupyterLab web page might be necessary).
