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This is CPlantBox with the installation script for BonnaHPC

This is a stabled forked version of CPlantBox/master Aug-2024

• https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/tree/1089fe0421e24e834f69720598b0789cc7079148

To install in BonnaHPC navigate to the desired installation folder (e.g. ~/workspace) and use the shell script below:

#!/bin/bash
wget https://raw.githubusercontent.com/Murilodsv/CPlantBox/master/installCPlantBoxBonna.py

module purge
module load Python/3.8.2-GCCcore-9.3.0
module load VTK/8.2.0-foss-2020a-Python-3.8.2
module load CMake/3.16.4-GCCcore-9.3.0

python3 installCPlantBoxBonna.py

Examples are provided in "CPlantBox/tutorial/examples/". For instance:

cd tutorial/examples/python
python3 example1a.py

The dependecies are listed in the requirements.txt file.

Installation on the JSC agrocluster

Refer to the wiki:
https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/wiki/CPlantBox-on-the-J%C3%BClich-Supercomputer-cluster

Folder sructure

/modelparameter Plant parameter files
/src CPlantBox C++ codes
/test Python tests for all CPlantBox classes
/tutorial learn to use CPlantBox
/experimental Specific applications (in sub-folders). contrary to scripts in /tutorial, might not be kept up to date

Code documentation

Create the documentation by running doxygen in the folder $ doxygen doxy_config

The documentation will be located in the folder /doc. Compile doc/latex/refman.tex to generate the full doxygen documentation in doc/latex/refman.pdf.

Collaboration diagrams give an overview of the code in folder /docs.

Examples

Simulation videos availabe in Youtube Channel https://www.youtube.com/channel/UCPK-pFfpK94jiamgwHxX32Q