Modular System for Shelves and Coasts(MOSSCO)

Coupling biological processes to Earth System Models

C. Lemmen, R. Hofmeister, M.H. Nasermoaddeli, O. Kerimoglu, K.Klingbeil, F. Kosters, H. Burchard, K.W. Wirtz

Helmholtz-Zentrum Geesthacht, Bundesanstalt furWasserbau, and Institut fur Ostseeforschung Warnemunde

3rd Workshop on Coupling Technologies for Earth System Models, 20-22 April 2015, Manchester, UK

1/22

Research questions

Science questions to address

1. What are important feedbacks in coastal systems?2. What determines coastal nutrient gradients and variability?3. How to value the ecosystem service of nutrient retention

(WDF/MSRL) ?

2/22

Coasts are interfaces

→ Different domains and scales→ Different disciplines and communities→ Different tools and models =⇒ diversity

3/22

Model zooDisciplines, domains, scales

Ecology Algae,zooplankton,nutrients,detritus(NPZD)

BiogeochemistryCarbonatesystem, N, P,(Si) cycles

Physics Radiation,temperature,salinity,transport,turbulence

Atmosphere Wind + radiation +deposition

Ocean Currents, turbulence, waves,stratification

Suspended matter Aggregation, sinking,fragmentation

Surface Shear stress, biologicalmodification

Floor erosion, deposition, nutrient(im)mobilization

Plankton Nutrient cycle, growth,sinking, adaptation

4/22

Modular approach to the system

Modular

→ Create a system that is open todiverse process/domaindescriptions

→ External experts take care of theirspecific model parts, ensurecouplability

→ Reference implementationdemonstrates application potential

→ No central control→ “Externalization”

5/22

Couplings and opportunities

FABMFramework for AquaticBiogeochemical Modelssf.net/p/fabm/

ESMFEarth System ModelingFrameworkwww.earthsystemmodeling.org

Delft3DDeltares Delft3Doss.deltares.nl/web/delft3d

→ Address new researchquestions

→ Exchange models andsoftware/code

→ Open forextension/complementaryresearch

→ Stimulation of developments→ Model- und module

comparison→ Knowledge transfer

6/22

How to make modular?

Model

I/O

Meta

Time

CPU

I/O

Meta

Time

CPUexpose

allow

Communication

interface

General coupleability

→ Communication interface /Basic model interface

→ Independent of couplingframework

All models are created equal

→ (you know this is not true ...)

7/22

MOSSCO overview

Some

model

BM

IC

MI

ES

MF

Other

model

w/ ESMF

MOSSCO = concepts

- Coupleability

- Metadata

- Scheduling

MOSSCO = examples

- basic model interfaces

- component model interfaces

- applications

MOSSCO = communications

- fully ESMF compatible

- naming conventions

- interdisciplinary

MOSSCO

8/22

Model intercomparison

HAMSOM

DriverCom

ponentESM

F

Frame-workMOSSCO

GOTM, MITgcm, ROMS, ...

GETM

DriverCom

ponentESM

F

Frame-workMOSSCO

9/22

Cross-domain coupling

FABM(pclake, aed,

maecs)

DriverCom

ponentESM

F

Frame-workMOSSCO

Delft3Derosed

DriverCom

ponentESM

F

Frame-workMOSSCO

FABMsed(omexdia)

DriverCom

ponentESM

F

Frame-workMOSSCO

10/22

Use cases

Available bricks

SPMfabm

OCEANgotm

ATMOS

Geology

Ecologybenthos

WAVES

fabm

Ecologypelagial

OCEANgetm

NetCDFinfrastructure

BGCsoil

Bentic erosion app

SPMfabm

OCEANgotm

ATMOS

Geology

Ecologybenthos

WAVES

fabm

Ecologypelagial

OCEANgetm

NetCDFinfrastructure

BGCsoil

Benthic-pelagic ecosystem app

OCEANgetm

ATMOS

Geology

Biostabilityfabm

Ecologypelagial

OCEANgotm

NetCDFinfrastructure

BGCsoil

Riverload

Erosiondeposition

Waves

3D Dentrification app

11/22

Open development and software

mossco.de

mossco.de/doc

mossco.de/code

mossco.de/bugs

12/22

Benthic effect on erosion

20 [indv/m ]

2150 [indv/m ]

2350 [indv/m ]

0 [5 [mg/g]10 [m

mg/g]

g/g]

Tellina fabula

Microphytobenthos

Time [day]

Water level

Le

ven

[m

]S

PM

[m

g/l]

SP

M [m

g/l]

SPMfabm

OCEANgotm

ATMOS

Geology

Ecologybenthos

WAVES

fabm

Ecologypelagial

OCEANgetm

NetCDFinfrastructure

BGCsoil

13/22

Benthic-pelagic coupling

Jan Apr Jul Oct Jan Apr Jul Oct Jan

DIN in water column [mmol-N/m³]

PON in water column [mmol-N/m³], obs. [mg-chl/m³]

SPM in water column [mg/l]

denitrification[mmol-N/m²/d]

benthic respiration[mmol-O2/m²/d]

depth

in se

dimen

t [cm]

Jan Apr Jul Oct Jan Apr Jul Oct Jan

0510152025

Jan Apr Jul Oct Jan Apr Jul Oct Jan

05

10152025

Jan Apr Jul Oct Jan Apr Jul Oct Jan

4.05.57.08.510.0

Jan Apr Jul Oct Jan Apr Jul Oct Jan

0.20.4

Jan Apr Jul Oct Jan Apr Jul Oct Jan

12

24

Jan Apr Jul Oct Jan Apr Jul Oct Jan4 cm

3 cm

2 cm

1 cm

depthin

sediment

oxygen penetration depth [cm]

Nitrate in pore water [mmol-N/m³]

0 3 6 9 12 15 18 21 24

Jan Apr Jul Oct Jan Apr Jul Oct Jan2003, 2004

SPMfabm

OCEANgotm

ATMOS

Geology

Ecologybenthos

WAVES

fabm

Ecologypelagial

OCEANgetm

NetCDFinfrastructure

BGCsoil

14/22

Soil surface denitrification

OCEANgetm

ATMOS

Geology

Biostabilityfabm

Ecologypelagial

OCEANgotm

NetCDFinfrastructure

BGCsoil

Riverload

Erosiondeposition

Waves

15/22

Deployment

It should be this easy ...

16/22

Coupling specification

17/22

Sequential runs

0 50000 100000 150000Time since simulation start (ms)

allconstant

getmlink_connectorpelagic_soil_cosoil_pelagic_co

transport_connemossco_gffn

toplevelfabm_sediment

rename_connectofabm_pelagic

0.0 % ( 2 ms) 47.4 % ( 76 s ) 0.3 % (454 ms) 1.1 % ( 2 s ) 0.6 % (985 ms) 0.0 % ( 3 ms) 0.8 % ( 1 s )100.0 % (161 s ) 43.7 % ( 70 s ) 0.0 % ( 0 ms) 5.9 % ( 10 s )

18/22

Sequential runs

1000 2000 3000 4000Prozessoranzahl

500

1000

1500

2000

Geschwindigkeits-zuwachs

"per

fekt

e" S

kalie

rung

Gütegre

nze (5

0%)

Zielbereich fürSkalierung

"Sweet spot"Optimale Skalierung bei

4096 CPU. Pro Tag Rechenzeitwerden 2 Simulationsjahre eines

gekoppelten Systems mit1 Million Gitterzellen

berechnet.

19/22

Similar efforts

MOSSCO

German EnvironmentalHindcast and FrameworkEnabler

UKEP

Waves

(WaveWatchIII)

Land surface (JULES)

River flow

Inundation

Atmosphere (Unified Model)

UKV - 1.5km

Implicit coupling

Marine

Ecosystem

(ERSEM)

‘Coupled’

Input forcing

UK km-scale

ATMOSPHERE + SURFACE + MARINE + ECOSYSTEM

COUPLING

FRAMEWORK

OASIS

coupling

(3-way)

Global BCs

Coupled SST

Coastal Shelf

Sea (NEMO)UKCO

1.5km

Regional BCs

Coupled u,v, T….

- DRAFT -

WORK IN PROGRESS

Regional BCs

Coupled u,v, p….

Sediment

Global/regional scale boundary

conditions (forecasts/analyses)

‘Hydrological Modelling’

A prototype research system

Draft for Prototype UKEnvironmental Prediction,courtesy of Lucy Bricheno, NOC

20/22

Conclusions

What we’ve learned

1. a lot beyond FORTRAN (FABM+ESMF APIs)2. it takes 1 day to 6 months to build a component3. mismatch between computing + science4. dedicated bottom up works for now5. user acceptance challenging

21/22

Recommendations... to model developers

Making diversity work

1. Make your model coupleable, BMI-ify it2. Go open source, you might have to give up (read) control3. Ask funding orgs to support documentation and code

maintenance

22/22