Francesco Serafin Second year admission

C R E A T I N G A N E W I N F R A S T R U C T U R E F O R G E O T O P 3 . 0

D O C T O R A L S C H O O L O F C I V I L ,

E N V I R O N M E N T A L A N D M E C H A N I C A L E N G I N E E R I N G

X X X I C Y C L E

Admission to the second year

S U P E R V I S O R : P R . P H D R I C C A R D O R I G O N C O - A D V I S O R : P H D O L A F D A V I D

P H D S T U D E N T : F R A N C E S C O S E R A F I N

24/10/16

TOPICS

During this year, I started to dig into mainly three topics: •  Graphs •  PDEs •  Reproducible research

…all related to Hydrology

24/10/16 Serafin F. Admission to the second year

GRAPHS

A graph is a set of vertices and a collection of edges that each connect a pair of vertices.

Algorithms 4th ed. – Sedgewick & Wayne

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

1819

2021

22

2324

25

26

27

28

29

30

31

32

33

34

35

36

37

38

3940

41

4243

4445

46

47

48

49

50

51

52

53

54

55

5657

58

59

60


GRAPHS

A graph is a set of vertices and a collection of edges that each connect a pair of vertices.

Algorithms 4th ed. – Sedgewick & Wayne

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

1819

2021

22

2324

25

26

27

28

29

30

31

32

33

34

35

36

37

38

3940

41

4243

4445

46

47

48

49

50

51

52

53

54

55

5657

58

59

60

?

What they got to do with Hydrology?


GRAPHS •  Hydrological System

http://www.revision.co.zw/the-hydrological-water-cycle/



http://www.revision.co.zw/the-hydrological-water-cycle/

NODES: physical processes EDGES: processes interactions



Rigon, Serafin, Bancheri – Hydrological cycle as a dynamical system

MASS BUDGET



•  Environmental Model

http://teeic.indianaffairs.gov/er/lhhydro/restech/desc/index.htm




http://teeic.indianaffairs.gov/er/lhhydro/restech/desc/index.htm

NODES: HRUs or subbasins EDGES: water flow




•  Mesh

http://www.innovationresearchfocus.org.uk/Issues/85/IRF85_HR2.html




•  Mesh

http://www.innovationresearchfocus.org.uk/Issues/85/IRF85_HR2.html

NODES: cell EDGES: interaction between cells


1

2

3

4

GRAPHS

They allow to enable IMPLICIT PARALLELIZATION. This is the reason why the implementation of a graph data structure for environmental modelling is the right answer to the request of computational speed.


Classes Research

�  Discrete Maths - DISI �  Complex Networks –

Summer School �  Algorithms & Data

Structures – DISI �  Geostatistics - DICAM

�  Ne3: parallel binary tree – multithreading version of a binary tree totally designed around PATTERNS

�  OMS v3: Tree Data Structure – beta version of the tree data structure which supports the running of different component in each node

GRAPHS


PDEs

Environmental models should be easier to implement, to read and to maintain.


PDEs

Environmental models should be easier to implement, to read and to maintain.

API: expansion of the existing library DSL: development of a built-in DSL in OMS v3


DSL

A DSL (Domain-Specific Language) is a computer language specialized to a particular application domain. This is in contrast to a GPL (General-Purpose Language), which is broadly applicable across domains.

https://en.wikipedia.org/wiki/Domain-specific_language

DSML model

Idea/Concept

Product

MANUAL

AUTOMATIC GENERATION

Source code

MANUAL

COMPILE

amou

nt o

f tim

e an

d ef

fort

http://www.slideshare.net/chanchaljayaraj/web-based-tool-for-domain-specific-modeling


Classes Research

�  Advanced Numerical Methods – Winter School

�  API based Boussinesq Groundwater Equation

�  Bachelor thesis co-tutor: A. Iemma – Richards equation 1D

�  Master thesis co-tutor: N. Tubini – Freezing Thawing processes study with numerical model

PDEs


PDEs

The Boussinesq Groundwater Equation


Giulio Supino 2016 – Master of Science Award

Acknowledgment to the two best master thesis in Water Engineering which graduations were held in the biennial July 1st, 2014 - April 30th, 2016. “Patterns for the application of modern informatics to the integration of PDEs: the case of Boussinesq Equation” The award ceremony was held during the XXXV National Conference of Hydraulics and Hydraulic Constructions in Bologna.

PDEs


Software, Hardware … Vaporware

I have been frustrated often with statisticians and computer scientists who write papers where they develop new methods and seem to demonstrate that those methods blow away all their competitors. But then no software is available to actually test and see if that is true. … In my mind, new methods/analyses without software are just vaporware … If there is no code, there is no paper. By Jeff Leek* http://simplystatistics.org/2013/01/23/statisticians-and-computer-scientists-if-there-is-no-code-there-is-no-paper/

REPRODUCIBLE RESEARCH


TOOLS •  Git – GitHub



•  Gradle



•  Gradle

•  Travis



•  Gradle

•  Travis

•  GEOframe



•  Gradle

•  Travis

•  GEOframe

http://github.com/geoframecomponents

https://github.com/GEOframeOMSProjects



•  Gradle

•  Travis

•  GEOframe

•  Documentation



•  Gradle

•  Travis

•  GEOframe

•  Documentation •  Online doc



•  Gradle

•  Travis

•  GEOframe




•  Gradle

•  Travis

•  GEOframe


•  BMI - OMS

�  BMI (Basic Modelling Interface) is a simple interface that model developers are asked to implement in order to simplify conversion of an existing model to a reusable, plug-and-play model component. In this way a modeling framework will be able to: �  Determine if a set of components

provide a complete model �  Connect each component that requires

a certain input variable to another component in the set that provides that variable as output



•  Gradle

•  Travis

•  GEOframe


•  BMI - OMS

�  BMI-OMS provide wrapper for loading BMI models into OMS compliant modeling frameworks and vice-versa.



•  Gradle

•  Travis

•  GEOframe


•  BMI - OMS


Target Journals

GMD – Geoscientific

Model Development

Computer Geosciences

EMS – Environmental

Modeling & Software


Scientific Output

Papers: -  Bancheri M., Serafin F., Abera W. , Formetta G. & Rigon R. - A well engineered

implementation of Kriging tools in the Object Modelling System v.3 – in preparation -  Rigon R., Serafin F., Bancheri M, A tools deployment for replicable and reproducible

research – Invited - OGRS 2016 Conferences proceedings – in preparation Conferences: -  M.Bancheri , W. Abera, G. Formetta, R.Rigon & F. Serafin , Implementing a Travel

Time Model for the Entire River Adige: the Case on JGrass-NewAGE, American Geophysical Union, Fall Meeting 2015, abstract \#H11K-03.

-  Serafin F., Bancheri M., Rigon R. & David O., A binary tree data structure for environmental modelling, International Congress on Environmental Modelling and Software, 2016, presentation

-  Bancheri, M, Formetta G., Serafin, F., Rigon R , Green T.R & David O. , Replicability of a modelling solution using NewAGE-Jgrass., International Congress on Environmental Modelling and Software, 2016, presentation

-  Bancheri M., Formetta G., Serafin, F., and Rigon R., Research reproduciblity and replicability: the case of JGrass-NewAge, XXXV Convegno nazionale di Idraulica e Costruzioni Idrauliche, 2016, poster


THANK YOU FOR YOUR

ATTENTION!


Francesco Serafin Second year admission

Education