We use [Apptainer](https://apptainer.org/docs/user/main/index.html) to build/run containers on our HPC systems.
You will need a Linux system to run Apptainer natively on your machine, and it’s easiest to [install](https://apptainer.org/docs/user/main/quick_start.html) if you have root access.
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For a nice introduction to Apptainer on our HPC systems, have a look at the awesome [presentation by Michele](https://datashare.mpcdf.mpg.de/s/df4p3bMuWCF53Y3).
You can also browse [our documentation](https://docs.mpcdf.mpg.de/doc/computing/software/containers.html#apptainer).
### Building containers
## Building containers
Containers are built via a [definition file](https://apptainer.org/docs/user/latest/definition_files.html) and the `apptainer build` command.
In each folder of this repo you will find a definition `.def` file and a `README.md` that describes the exact build command.
### Pull from Dokcer Hub
## Pull from Dokcer Hub
You can easily [pull containers](https://apptainer.org/docs/user/latest/docker_and_oci.html#containers-from-docker-hub)
from the [Docker Hub](https://hub.docker.com/) or other OCI registries:
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### Convert from Docker Daemon or Docker Archive files
## Convert from Docker Daemon or Docker Archive files
You can also [convert images/containers](https://apptainer.org/docs/user/latest/docker_and_oci.html#containers-from-docker-hub) running in your Docker Daemon:
```shell
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- mention important flags, like `--nv` for example
- how to run the containers on our SLURM cluster
### Patching containers
## Patching containers
If you want to permanently modify files in your container, you can use persistent "overlays". These are writable file system images that sit on top of your immutable SIF container.
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You can apply overlays with the `run`, `exec`, `shell` and `instance start` commands.
### Using containers with RVS
## Using containers with RVS
The [Remote Visualisation Service (RVS)](https://docs.mpcdf.mpg.de/doc/visualization/index.html) allows you to run Jupyter sessions on the HPC systems.
You can use your container as a kernel within such a session by providing a `kernel.json` spec file.
#### 1. Setting up the container
### 1. Setting up the container
Make sure you install ipython and ipykernel in your container:
```
pip install ipython ipykernel
```
#### 2. Setting up RVS
### 2. Setting up RVS
Load apptainer module when initializing your RVS session.
#### 3. Creating the kernel
### 3. Creating the kernel
Create a kernel spec file
```bash
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If you want to access files outside your home directory, you have to bind them explicitly in the kernel spec file when calling the apptainer command.
For example, in the kernel spec file above we bind your `ptmp` folder.
### Local-to-HPC Workflow
## Local-to-HPC Workflow
**TODO: The sandbox option does not work 100% correctly for VSCode or PyCharm, use docker images instead! Need to update this guide!**
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We are still investigating if something similar is possible with `Docker` (please let us know if you find a way :) ).
#### 1. Create a definition file
### 1. Create a definition file
In the root directory of your library (repository) create a *definition*`*.def` file.
This definition file should reflect your environment in which you want your library to develop and use.
You can leverage base environments, such as docker images on DockerHub, or existing apptainers.
#### 2. Build the sandbox
### 2. Build the sandbox
Build the sandbox (container in a directory) instead of the default SIF format:
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Now we can add our library that we develop to the sandbox environment and install it in [`editable`](https://setuptools.pypa.io/en/latest/userguide/development_mode.html) mode:
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#### 4. Point your IDE's interpreter to the sandbox
### 4. Point your IDE's interpreter to the sandbox
You should be able to point the interpreter of your IDE (VSC, PyCharm, etc.) to the python executable inside the sandbox folder.
#### 5. Add your developed library to the my_container.def file
### 5. Add your developed library to the my_container.def file
While in principle you could build a SIF container directly from your sandbox, it is better to modify your *definition*`*.def` file to include your library/package.
In this way, your container is fully reproducible using only the definition file.
#### 6. Build your *.sif apptainer, deploy on our HPC systems
### 6. Build your *.sif apptainer, deploy on our HPC systems
Once you built the SIF container, you can copy it to our HPC systems and use it there.