Bolding & Bruggeman (BB)

GOTM/FABM workshop

What: A best practices workshop using GOTM/FABM

Where: Middelfart, Denmark

When: September 2-6 2019

Why: GOTM/FABM is a comprehensive open source modelling system for studying natural waters, used all over the world by master- and PhD-students as well as post-docs and scientists. It combines a state-of-the-art model for water column hydrodynamics and turbulence (GOTM) with a flexible, extensible system for modelling aquatic biogeochemistry and ecology (FABM). This workshop will provide an in-depth overview of the GOTM/FABM system, covering everyday use (compilation, set-up), advance tasks such as calibration and sensitivity analysis, and development of new functionality, including new biogeochemical models. The emphasis will lie on best practices for working with the modelling system - practices we have obtained during decades of active involvement in the development and application of GOTM/FABM. The workshop will adress both the new user as well as the more experienced modeller. The workshop will discuss both marine and limnological applications.

Format: The workshop will alternate between short presentations and hands-on sessions. It will go through all steps involved in creating a solid model set-up. Some work will be carried out in small groups.

Participants are expected to bring their own laptop and all information they intend to use for their location of interest (specifics to follow). It is the aim that participants will leave with a well-calibrated model setup ready for further use and analysis.

For the code development session, participants must have a working Fortran compiler installed to get the full benefit (evaluation versions of the Intel compiler can be installed on Windows - on Mac and Linux gcc is available). GOTM/FABM is platform-independent: users with Windows, Mac and Linux will have the same options.

Who: Jorn Bruggeman and Karsten Bolding will be responsible for the workshop.

Our aim: The major aim of the workshop is to enhance the GOTM/FABM workflow for the participants. An efficient work-flow is important in the simulate-compare-adjust modelling cycle. In addition we hope to create a network between the participants they can benefit from in their future work.

Important: Please register to the workshop by sending an email to karsten@bolding-bruggeman.com no later than February 1. 2019. In order to proceed with the planning of the workshop we want to be sure there is sufficient interest (20 participants is the minimum).

Speakers: Hans Burchard (HB), Jorn Bruggeman (JB), Karsten Bolding (KB)

Below a preliminary program is provided. Additional information will be provided if we reach the minimum number of 20 participants.

Program:

  • Monday - Theory and background
    • 09:00 to 12:00: Arrival and getting computers ready - KB, JB
    • 10:00 to 10:30: Coffee break
    • 12:00 to 13:00: Lunch
    • 13:00 to 13:30: Introduction to workshop - KB
    • 13:00 to 14:45: Theory behind GOTM - HB
    • 14:45 to 15:00: Social activity - KB
    • 15:00 to 15:30: Coffe break
    • 15:30 to 17:00: Theory behind FABM - JB
  • Tuesday - Basic model work-flow
    • 09:00 to 12:00: The GOTM/FABM model setup - KB
    • 10:00 to 10:30: Coffee break
    • 09:55 to 10:00: NNS Annual
    • 12:00 to 13:00: Lunch
    • 13:00 to 14:30: User case configurations - short demonstrations + group work
    • 14:30 to 15:00: Output specification - and PyNcview.
    • 15:00 to 15:30: Coffee break
    • 15:30 to 17:00: User case work continued
  • Wednesday - Sensitivity, auto-calibration and ensemble simulations + social activity
    • 09:00 to 09:30: Introduction to sensitivity and calibration - JB
    • 09:30 to 10:30: ACPy - gotm.yaml - KB
    • 10:30 to 11:00: Coffee break
    • 11:00 to 12:00: ACPy continued - KB
    • 12:00 to 17:00: Social activity - 3 hour sailing trip on Aventure.
  • Thursday - Becoming a developer - working on set-ups
    • 09:00 to 10:00: Git, Code overview and compilation (CMake) - JB
    • 10:00 to 10:30: Coffee break
    • 11:00 to 12:00: Implementing a simple model in FABM - JB
    • 12:00 to 13:00: Lunch
    • 13:00 to 15:00: Individual/group work
    • 15:00 to 15:30: Coffee break
    • 15:30 to 17:00: Individual/group work - continued
  • Friday - Becoming a developer
    • 09:00 to 10:00: Plenum discussion - elaboration on Workshop topics
    • 10:00 to 10:30: Coffee break
    • 10:30 to 12:00: Individual/group work
    • 12:00 to 13:00: Lunch
    • 13:00 to 14:00: Prepare short presentations - what does NOT work!!
    • 14:00 to 15:00: Presentations - max 10 min
    • 15:00 to 15:30: Coffee break
    • 15:30 to ??:??: Presentations - max 10 min
    • ??:?? : Departure
  • Saturday - optional - further develop/maintain your network
    • 09:00 to 15:00: If sufficient interest we will arrange a network activity

Price: The workshop fee is Euro 800,-. In case of sufficient interest a deposit of Euro 200,- will be requested by March 1. 2019. Final payment will be August 1. 2019.

Accommodation: Information to be provided - but we intend to have the workshop and accomodation at the same place. Expected price app. Euro 120/night.

Contact: