1
Introduction to RETINA
2
The architecture of the RETINA project
2.1
Main pieces of CODE that make up the RETINA project
3
Where the code and data live
3.1
Overall structure
3.2
The HPC (Gruffalo)
3.3
The Retina VM (and getting there from gruffalo)
3.4
Overview of Docker container
3.5
The RETINA app Docker container
3.5.1
php code
3.5.2
API
3.6
The RETINA app user database Docker container
3.7
The PEcAn Docker container
3.7.1
PEcAn
3.8
The RStudio server Docker container
3.9
The BETY database Docker container
3.10
The model Docker containers
3.10.1
DNDC
3.10.2
BASGRA
3.10.3
ECOSSE
4
The scary diagram.
5
PEcAn
5.1
What is PEcAn?
5.2
Version of PEcAn that we are using
5.3
Packages
6
The RETINA Package
6.1
Functions
6.1.1
Database connections
6.1.2
Soil API related
6.1.3
Site/coordinate related
7
Walkthrough running a model
7.1
Initializing a run
7.2
Via a web browser
7.3
Visualizations for app:
7.4
More about outputs
7.4.1
Server Side Scripts
7.4.2
Retina side scripts
8
Restarting Docker
9
Logs and Errors
10
Rebuilding pecan API
11
The DNDC Model
11.1
Versions of DNDC
11.2
DNDC Parameters
11.2.1
The DNDC interface
11.2.2
Library Parameter Files
11.2.3
The DNDC Source file
11.3
The dnd file
11.3.1
Role of the file
11.3.2
How to create a dnd file
12
Info in Google Drive
12.1
Documents
12.2
Spreadsheets
13
Meeting Notes
14
Plotting Visualizations
15
Notes on ongoing DNDC solutions and the HPC
RETINA Documentation
4
The scary diagram.
This file was lost and needs to be redone …
