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Add gprc4bmi dockerfile, instructions/docs.
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‎Dockerfile‎

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FROM ghcr.io/ecoextreml/stemmus_scope:1.5.0
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LABEL maintainer="Bart Schilperoort <b.schilperoort@esciencecenter.nl>"
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LABEL org.opencontainers.image.source = "https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing"
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# Requirements for building Python 3.10
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RUN apt-get update && apt-get -y upgrade
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RUN apt-get install -y build-essential zlib1g-dev libncurses5-dev libgdbm-dev \
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libnss3-dev libssl-dev libreadline-dev libffi-dev libsqlite3-dev wget libbz2-dev
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RUN apt-get install -y libhdf5-serial-dev
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# Get Python source and compile
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WORKDIR /python
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RUN pip3.10 install /opt/PyStemmusScope/[docker]
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RUN pip3.10 install grpc4bmi==0.5.0
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# Set the STEMMUS_SCOPE environmental variable, so the BMI can find the executable
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# # Set the STEMMUS_SCOPE environmental variable, so the BMI can find the executable
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WORKDIR /
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ENV STEMMUS_SCOPE ./STEMMUS_SCOPE
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ENV STEMMUS_SCOPE /STEMMUS_SCOPE
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EXPOSE 55555
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# Start grpc4bmi server
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CMD run-bmi-server --name "PyStemmusScope.bmi.implementation.StemmusScopeBmi" --port 55555 --debug

‎docs/bmi.md‎

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## Using the BMI
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A [notebook demonstration the use of the Basic Model Interface](../notebooks/BMI_demo/) is available.
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A [notebook demonstration the use of the Basic Model Interface](notebooks/BMI_demo.ipynb) is available.
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For more information on using BMI, see the [CSDMS website](https://csdms.colorado.edu/wiki/BMI).
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If you need access to other model variables that are not yet available in the BMI, please raise an issue on the [STEMMUS_SCOPE repository](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues), or leave a comment if an issue is open already.
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## grpc4bmi
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A [Docker image is available](https://ghcr.io/ecoextreml/stemmus_scope-gprc4bmi) in which the model as well as the Python BMI have been wrapped in a container.
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This allows communication with a STEMMUS_SCOPE BMI through [gprc4bmi](https://grpc4bmi.readthedocs.io/en/latest/).
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Doing so avoids the needs to install PyStemmusScope yourself, only Docker/apptainer and a python environment with gprc4bmi are required.
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A demonstration is available [here](notebooks/gprc4bmi_demo.ipynb)
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## Developer instructions
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The Python BMI implemented in this package communicates with the Matlab code through STDIN/STDOUT, or via a socket to the Docker container.

‎docs/notebooks/gprc4bmi_demo.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# grpc4bmi demonstration\n",
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"\n",
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"If you want to run the model plus BMI in a container, this is possible with the `stemmus_scope_grpc4bmi` docker image.\n",
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"\n",
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"The image contains both the STEMMUS_SCOPE model and the Python BMI. The interface uses [`grpc4bmi`](https://grpc4bmi.readthedocs.io/) for communication with the running container.\n",
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"\n",
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"To run this notebook you need to have grpc4bmi installed in your python environment."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"from grpc4bmi.bmi_client_docker import BmiClientDocker\n",
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"\n",
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"model = BmiClientDocker(\n",
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" image='ghcr.io/ecoextreml/stemmus_scope-gprc4bmi:1.5.0', \n",
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" image_port=55555,\n",
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" work_dir=\"/home/bart/tmp/stemmus_scope\",\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"We can ensure that the model is named STEMMUS_SCOPE:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'STEMMUS_SCOPE'"
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]
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},
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"execution_count": 2,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"model.get_component_name()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Initialization works like normal. Note that you do not want to have the `DockerImage` or `ExeFilePath` entries in your configuration file (!):"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": []
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},
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"execution_count": 3,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"model.initialize(\"/home/bart/tmp/stemmus_scope/config_grpc4bmi.txt\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [],
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"source": [
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"model.update()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"We can succesfully request values from the model:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"array([3.6085965])"
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]
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},
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"execution_count": 5,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"import numpy as np\n",
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"model.get_value(\"respiration\", dest=np.zeros(1))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "PyStemmusScope",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.12"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎mkdocs.yml‎

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- BMI:
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- "BMI instructions": bmi.md
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- "BMI demonstration": notebooks/BMI_demo.ipynb
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- "grpc4bmi demonstration": notebooks/gprc4bmi_demo.ipynb
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- Contributing guide: CONTRIBUTING.md
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- API reference: reference.md
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