pritha55 / do3se-photosynthesis-model

This is a temporary repository for experimenting with photosynthesis model. Do not use this for developing the model!

fortran_environment

A base setup for a fortran environment with compiler, testing etc

Info

WAF Build Tool

The Fortran code is built using the Waf_ build tool. This requires Python 2.5 or newer (including 3.x) to be available. If any errors with waf check if update needed (See troubleshooting at bottom).

Environment Setup (DOCKER)

You will need docker in order to create a virtual environment to run the fortran model

Windows

https://docs.docker.com/docker-for-windows/

Ubuntu

https://docs.docker.com/install/linux/docker-ce/ubuntu/

Build and Run

Build

Replace 'fortran_environment' with the name of your model

docker build . -t fortran_environment

Run

Note can add args like 'abc' in example below

docker run -it fortran_environment ./build/run_model abc

Environment Setup (MANUAL)

This is the instructions for running without docker on windows

Dependencies

• MinGW - http://www.mingw.org/wiki/Getting_Started
  • Needs specific compilers?
  • assuming your directory for MinGW is the default "C:\MinGW", setup your PATH environment variable to include "C:\MinGW\bin" && "C:\MinGW\msys\1.0\bin"
  • Check this is working by opening cmd or powershell and typing "make -h". This should give you some options for the make command
• Git For windows - https://git-scm.com/download/win
  • This provides access to git bash
• Python 2.7 - https://www.python.org/downloads/release/python-2717/
  • Add python to your environment variables "C:/Python27". Make sure to rename python.exe to python2.exe
  • Add pip to your environment variables "C:/Python27/Scripts"
• Python Virtual Env - Install python2 virtual env python2 -m pip install --user virtualenv

Note: Ensure you reopen command panels after editing PATH Vars

Setup

1. From git bash Create the python virtual environment python2 -m virtualenv venv and activate . ./venv/scripts/activate. When Activated you should now have (venv) at the start of the current path in the command line

Test run

1. With the environment activated run python waf configure followed by python waf build
2. You should now have a run_model.exe file in the build folder. Run this in bash/cmd and you should see hello world as a response