On Advanced Scientific Understanding, Model Componentisation and Coupling in GENIE

1
On Advanced Scientific Understanding, Model
Componentisation and Coupling in GENIE

• Sofia Panagiotidi, Eleftheria Katsiri and John
  Darlington

2
Motivation

• Reverse engineer GENIE to inform research on
  component coupling frameworks
• Analysis of a monolithic piece of code such as
  GENIE.
• Extraction of interface and model coupling
  semantics.
• Development of methods for capturing such
  semantics and validating the development.
• Methods to express at higher-levels co-ordination
  structure.

1
3
Goals

• A flexible coupling framework where components
  can be individually developed and coupled
  together.
• The coupling needs to be correct, intelligent and
  without undue programming effort.
• In synch with existing efforts (GCF, Iceni I,
  Apples AMWAT, Reality Grid), but a system of the
  size and complexity of Genie requires a
  supporting semantic framework.

2
4
What is GENIE?

• Grid ENabled Integrated Earth system model.
• Investigate long term changes to the Earths
  climate (i.e. global warming) by integrating
  numerical models of the Earth system.
• e-Science aims
• Flexibly couple together state-of-the-art
  components to form unified Earth System Model
  (ESM).
• Execute resultant ESM on a Grid infrastructure.
• Share resultant data produced by simulation runs.
• Provide high-level open access to the system,
  creating and supporting virtual organisation of
  Earth System modellers.

3
5
GENIE model framework
4
6
Previous Work

• Separation of the code into pieces - Layered
  representation of the application.
• Wrapping GENIE as ICENI binary component.
• Delivery of Web-based System (portal) to allow a
  virtual organisation of environmental scientists
  to create and manage simulations at a high-level.
• Submission of multiple sweep experiments to the
  portal, exploiting multiple resources over a
  Condor pool.
• Implementation of database management system to
  allow scientists to share, access and visualise
  data produced by simulation runs.

5
7
Currently in GENIE

• genie.F is a glorified metafile containing
  if-then-else statements.
• Fortran routines act as wrappers, IN/OUT
  annotation.
• Life cycle phases scattered, i.e. igcm_adiab.F
  and initialise_atmos.F.
• Shared memory, file based I/O.
• Complex semantics (e.g. grid interpolations).
• Hard-coded time steps.

6
8
OLOGEN

• Ontology for GENIE
• Classes
• Relations

7
9
Entities (1)

• OLOGEN Class Hierarchy
• Abstractions - What is the abstraction
  granularity?
• Component
• Module (atmosphere, land, ocean etc)
• Model (IGCM, c-Goldstein, etc)
• Wrapper
• Routine
• Function ()
• Interface
• Data Flow Type (IN, OUT, INOUT, Control)
• Model Scope (Common, Model-Specific)
• Binding (Late, Current)
• Layer (Local, Wrapper)

is part of
8
10
Entities (2)
8
11
Relations
10
12
Higher-order Functions Co-ordination forms

• The Wrap Skeleton
• The Thread Coupler Skeleton
• Distribution Model
• Same-host
• Distributed
• Parallel

11
13
The Wrap Skeleton

• Wrap(c,list of wrapper input interfaces, list of
  wrapper output interfaces, list of local input
  interfaces, list of local output interfaces, list
  of control interfaces)C

12
14
The Thread Coupler SkeletonSCL, Darlington93

• IterFor koverall
• IterFor n step A
• IterFor m step B
• where
• step A threadA.execute
• threadB.notify(interfaceB)
• step B threadB.execute
• threadA.notify(interfaceA)

13
15
Nested Coupling
ocean_niter_tim
not
flag_land
not
flag_goldsteinocean and flag_goldsteinseaice
not
flag_checkfluxes_surf
land_niter_tim
katmos_int
14
16
Conclusions

• Use of reverse engineering approach to research
  on component coupling frameworks
• Analysis of a monolithic piece of code such as
  GENIE.
• Extraction of interface and model coupling
  semantics.
• Development of OLOGEN, an ontology for capturing
  such semantics and validating the development.
• Co-ordination via functional skeletons.

15
17
Acknowledgments
16