Delft3D 4 open source workshop

1. Delft3D 4 Open Source Workshop
Before we start:
1.Are you registered at oss.deltares.nl?
2.Use TortoiseSVN to download:
https://svn.oss.deltares.nl/repos/delft3d/branches/research/Deltares/201
51106_workshop
(~ 5 seconds)
3.Use TortoiseSVN to download:
https://svn.oss.deltares.nl/repos/delft3d/tags/5425/
(~ 5 minutes)
4.If you are using VisualStudio 2010: check that “Service Pack 1” is
installed:
Menu -> Help -> About Microsoft Visual Studio:
Microsoft Visual Studio 2010 Professional - ENU Service Pack 1 (KB983509)
KB983509
If not: execute “…workshopsourcecodeVS10sp1-KB983509.exe”
(~ 50 minutes)

2. Delft3D 4 Open Source
Workshop
Delft, Nov. 06, 2015
Adri Mourits
Qinghua Ye

3. Overview
• Introduction
• Code management
• Development environment
Exercises
• General code structure Delft3D-FLOW, -MOR, -WAVE
• Ongoing developments
• Short topics
Exercises
Central hall:
Coffee: 10:30 – 11:00
Lunch: 12:30 – 14:00
Coffee: 15:30 – 16:00
Drinks: 17:30 – 18:30

4. Overview
Organization of this workshop
• All information is at
https://svn.oss.deltares.nl/repos/delft3d/branches/research/Deltare
s/20151106_workshop
• You do the work
• Adri and Qinghua give information when needed
• Work on exercises/your own stuff whenever you want
• Switch to other workshops whenever you want
• For the rest:

5. Introduction

6. Introduction
• Assumed knowledge
• What is Delft3D?
http://www.deltaressystems.com/hydro/product/621497/delft3d-suite
• Delft3D 4 versus Delft3D Flexible Mesh
• NOT in this workshop
• GUI usage
http://oss.deltares.nl/web/delft3d/screen-casts
• Creating a model
http://oss.deltares.nl/web/delft3d/modelling-guidelines
http://oss.deltares.nl/web/delft3d/training-courses
Adri Mourits Qinghua Ye

7. Introduction
Open Source Software site: www.oss.deltares.nl

8. Introduction
Open Source Software site: www.oss.deltares.nl -> Delft3D:
• Getting started, download source code
• Screen casts
• Webinars
• Modelling Guidelines
• FAQ, release notes
• Forum/discussion groups

9. Code management

10. Code management
Overview:
• SVN
• Setups
• FLA
• Future Open Source plans

11. Code management - SVN
SVN
• Trunk, main line:
• Fixing bugs
• New developments being merged in
• Run on testbench
=> Possibly not stable
• Tags:
• Copies of stable, fully tested Trunk-revisions
=> Use the latest. Currently
https://svn.oss.deltares.nl/repos/delft3d/tags/5425
• Branches:
• Separate develop versions
• “Your own private version”

12. Code management - SVN
SVN
• New branch:
• For “big” changes
• When stability is harmed too much
• Private developments

13. Code management – Setups
Receiving from Deltares:
Setups (Windows):
• Open source installation (“Install-Shield.exe”):
All User Interfaces but not the FLOW/WAQ/WAVE executables
• Services installation:
All user interfaces and also FLOW/WAQ/WAVE executables
(Delft3D service package needed, see
http://oss.deltares.nl/web/delft3d/service-packages)
Setups (Linux):
• GUIS currently not available
• Services installation: FLOW/WAQ/WAVE executables
(Delft3D service package needed)
License File needed when using UserInterfaces / Delft3D-menu.

14. Code management – from Deltares
Receiving from Deltares:
GUI
• QuickPlot source code:
https://svn.oss.deltares.nl/repos/delft3d/trunk/src/tools_lgpl/matlab/
quickplot
MatLab needed.

15. Code management - FLA
FLA
When delivering source code changes, an FLA agreement must be
signed.

16. Code management – future plans
Future Open Source plans
• Flexible Mesh: currently in a restricted community, later fully open
• Delta Shell (Framework, partly): 2016

17. Development environment

18. Development environment
Overview:
• Windows
• VisualStudio 2010/2012/2013
• Linux
• Automake, valgrind
• Resulting files
• Version numbers
See file “….srcREADME “

19. Windows
• Execute “prepare_sln.py”
• Select VS- and Intel-version
=> delft3d_open.sln
• Build configuration “Release” (default) or “Debug” (only for
tracing/solving bugs)
• Platform x64 (default) or Win32
Development environment

20. Development environment
Linux
• GNU Autotools/Libtools
• 2 build methods:
1. If all tools are installed on default location:
./autogen.sh
./configure --prefix=`pwd`
make ds-install
2. If some tools are not on default location:
Check paths/settings in script “build.sh” and execute
build.sh –intel11.1 -64bit
• Debug:
Add flag –debug when executing build.sh
valgrind $exedir/deltares_hydro.exe $argfile
TotalView
Write statements

21. Development environment
Resulting release files (Windows)
• FLOW:
….binwin64flow2d3dbin:
d_hydro.exe
flow2d3d.dll
mormerge, plugins, datsel, kubint, lint
delftonline.dll
MPICH dll’s
more dll’s (OpenDA, compiler, xml etc.)
• Wave with SWAN:
….binwin64wavebin:
wave.exe
….binwin64swanbin:
swan_4072ABCDE_del_w64_i11_omp.exe
Resulting files FLOW, debug (Windows)
….srcengines_gpld_hydrobinx64Debug
To be started
Small executable
XML input file
Big dll containing
Delft3D-FLOW
Remote Online Visualisation
Parallel calculations

22. Development environment
Resulting release files (Linux)
• FLOW:
….binlnx64flow2d3dbin:
d_hydro.exe
libflow2d3d.so
mormerge, plugins, datsel, kubint, lint
libDelftOnline so
more so’s (OpenDA, compiler, xml etc.)
• Wave with SWAN:
….binlnx64wavebin:
wave.exe
….binlnx64swanbin:
swan_4072ABCDE_del_l64_i11_omp.exe
Install script called via “post build event (Win)”/ “ds-install rule (Lin)”
To be started
Small executable
XML input file
Big dll containing
Delft3D-FLOW
Remote Online Visualisation
Parallel calculations
Assumption:
Installed centrally

23. Development environment
Version number
6.02.01.5425
Update_version_tools:
• Windows: pre-build commands in projects
• Linux: make rule “BUILT_SOURCES = ./always”
Every module has it’s own version number!
Increased
when not
backwards
compatible
New major
functionality
Minor
changes,
used to
distinct stable
versions
SVN,
Automatically
generated
revision
number
Delft3D
FLOW
WAQ
WAVE
PART
Deltares_COMMON
DELFTIO
NEFIS
ESMFSM
D_HYDRO

24. Development environment
Update_version_tools:
• On every compile action, version number, date and time are
generated
• Tri-diag file:
• “c:Program Files (x86)DeltaresDelft3D 4.01.00
win32libwhat.exe flow2d3d.dll”:
Deltares, DELFTIO Version 1.09.00.5541, Oct 30 2015, 11:33:15
Deltares, DELTARES_COMMON Version 1.00.00.5541, Oct 30 2015, 11:33:00
Intel Fortran RTL Message Catalog V12.1-110 Apr 04 2012
$HeadURL:
https://svn.oss.deltares.nl/repos/delft3d/tags/5425/src/utils_lgpl/delta
res_common/packages/deltares_common/src/deltares_common_version.F90.svn
$
Deltares, NEFIS Version 5.08.01.5541 (Win64), Oct 30 2015, 13:49:44
Deltares, ESMFSM Version 4.06.00.5541, Oct 30 2015, 11:32:56
Deltares, FLOW2D3D Version 6.02.01.5541M, Oct 30 2015, 13:49:50
*** Deltares, FLOW2D3D Version 6.02.01.5541M, Oct 30 2015, 11:39:09
*** built from : https://svn.oss.deltares.nl/repos/delft3d/tags/5425

25. Exercises

26. General code structure

27. General code structure
• Directory structure / VS projects
• FLOW
• Main (DD/OLV)
• Trisim (gdp)
• Tricom (time loop)
• Trisol (ADI)
• MOR
• Erosed
• Bott3d
• WAVE
• SWAN
• Doxygen
• NaN check

28. General code structure
FLOW Directory structure
From
top-level
To
…srcengines_gplflow2d3dpackageskernelsrccomputeadi.f90

29. General code structure
Directory structure

30. General code structure
Directory structure
• Bin: resulting executables
• Examples: Ready-to-run testcases (after compiling release version)
• Src: source code
• Engines_gpl: source code per kernel
• Third_party_open: source code/binaries from outside this source
tree (mainly from outside Deltares)
• Tools: additional programs, Post processing
• Utils: Generic libraries, used by more than one kernel

31. General code structure
Directory structure
Engines:
• d_hydro: Executable starting FLOW dynamic lib
• flow2d3d: Delft3D-FLOW kernel
• Packages: source code, separated from binaries, doc, scripts, etc.
• Part, waq, wave

32. General code structure
Directory structure
Generic
package names
Package dependencies:
data
manager
kernel
io
plugin
flow2d3d
main

33. General code structure
Directory structure
Each package:
Separate src
(,include) and
binaries

34. General code structure
Directory structure
Kernel/src: Traditional
Functional splitting Trisim structure

35. General code structure
Directory structure
Files!

36. General code structure
Directory structure
Linux:
• Binaries next to source code (*.o, *.lo, *.la) default
• Libraries/executables copied to “src/lib” and “src/bin” default
• Install script copies to “bin/lnx64” Deltares

37. General code structure
Visual Studio
2010

38. General code structure
FLOW - Main
…srcengines_gpld_hydropackagesd_hydrosrcd_hydro.cpp
main (argc, argv, envp)
…
DeltaresHydro * DH = new DeltaresHydro (argc, argv, envp);
DH->Run ();
DeltaresHydro::DeltaresHydro (argc, argv, envp)
…
dllhandle = LoadLibrary (“flow2d3d”);
entryPoint = GetProcAddress (dllhandle, “DeltaresHydroEntry”);
DeltaresHydro::~DeltaresHydro (void)
DeltaresHydro::Run (void)
…
this->startComponent->Run ();
exe

39. General code structure
FLOW - Main
…srcengines_gplflow2d3dpackagesflow2d3dsrcflow2d3d.cpp
DeltaresHydroEntry (DeltaresHydro * DH)
DH->startComponent = new Flow2D3D (DH);
Flow2D3D::Flow2D3D (DeltaresHydro * DH)
Flow2D3D::~Flow2D3D (void)
Flow2D3D::Run (void)
if (this->dd != NULL)
this->dd->Run ();
else {
TRISIM (ndom, nmap, id, flags, runid);
}
dll

40. General code structure
FLOW - Fortran entry for each subdomain:
…srcengines_gplflow2d3dpackagesmanagersrctrisim.F90
subroutine trisim
…
allocate(gdp)
…
retval = trisim_init
…
retval = trisim_step
…
retval = trisim_finish
gdp: GlobalDataPointer
Structure containing
(pointers to) all
arrays/parameters being
global inside one subdomain.
gdp must be passed through
“everywhere” inside one
subdomain for thread safety.
Fortran

41. General code structure
FLOW - Subdomain initialization:
…srcengines_gplflow2d3dpackagesmanagersrctrisim_mod.F90
function trisim_init
…
call gdp_alloc(gdp)
…
call tdatmain
…
call tripoi
…
call tricom_init
Scan input, write time
dependent data to TMP-files
Allocate arrays
Read complete input
Check input
Initialization

42. General code structure
FLOW - Subdomain step:
…srcengines_gplflow2d3dpackagesmanagersrctrisim_mod.F90
function trisim_step
call tricom_step
…srcengines_gplflow2d3dpackagesmanagersrctricom_step.F90
subroutine tricom_step
…
do nst = itstrt, itstop - 1, 1
…
call postpr
… update wave info
call trisol (/z_trisol/z_trisol_nhfull)
enddo
Time loop
Post processing
Solver

43. General code structure
FLOW - Subdomain solver:
…srcengines_gplflow2d3dpackageskernelsrcmaintrisol.f90
subroutine trisol
…
call f0isf1
timnow = timnow + 0.5_fp
call incbc
call adi(…stage1)
… susp. transport solvers
call f0isf1
timnow = timnow + 0.5_fp
call incbc
call adi(…stage2)
… susp. transport solvers
First half timestep:
v implicit, u explicit
Second half timestep:
u implicit, v explicit

44. General code structure
Morphology
…srcengines_gplflow2d3dpackageskernelsrcmaintrisol.f90
subroutine trisol
…
call adi(…stage1)
… susp. transport solvers
call erosed
…
call bott3d
…
call adi(…stage2)
… susp. transport solvers
call erosed
…
call bott3d
Sediment fluxes at bed
Bathymetry update

45. General code structure
WAVE - main
…srcengines_gplwavepackageswavesrcwave.f90
program waves_main
…
if (not stand_alone)
do while perform_step
wait for FLOW signal
call swan_tot
enddo
else
call swan_tot
endif

46. General code structure
WAVE – swan_tot
…srcengines_gplwavepackagesmanagersrcswan_tot.f90
subroutine swan_tot
…
do itide = 1, swan_run%nttide
do i_swan = 1, n_swan_grids
… get input (from FLOW)
… write swan input
call run_swan
call read_swan_output
enddo
… write wave output (to FLOW)
enddo

47. General code structure
Code documentation using Doxygen:
www.oss.deltares.nl -> download -> manuals
Link to preprocessed Doxygen output:
http://apidocs.oss.deltares.nl/delft3d
Or generate it yourself:
• Download and install Doxygen from
• http://www.stack.nl/~dimitri/doxygen/
• Download and install Graphviz from
• http://www.graphviz.org/
• In src directory give command:
doxygen doxyfile_delft3d
• Open the generated “delft3d-apidochtmlindex.html”
• Search for top level flow routines as a starting point: trisim, tricom,
trisol, or specifically for morphology erosed.

48. General code structure
Code documentation using Doxygen

49. General code structure
Not a Number (NaN) check
By default, FLOW continues calculation with NaNs:
• Full check is too time consuming
• Input is scanned on NaNs
• Waterlevel is scanned on NaNs every half time step
Debugging with full NaN check (Intel compiler):
• Activate 4 lines of code in trisim.f90 (see next slide)
• Recompile

50. General code structure
NaN check
…srcengines_gplflow2d3dpackagesmanagersrctrisim.F90
subroutine trisim
…
use ifcore
…
INTEGER*4 OLD_FPE_FLAGS, NEW_FPE_FLAGS
…
NEW_FPE_FLAGS = FPE_M_TRAP_OVF + FPE_M_TRAP_DIV0 +
FPE_M_TRAP_INV
OLD_FPE_FLAGS = FOR_SET_FPE (NEW_FPE_FLAGS)

51. Ongoing developments

52. Ongoing developments
Overview of developments on next 3 slides (for completeness)
• OSS site:
http://oss.deltares.nl/web/delft3d/publications
• Open source branches
• Closed source branches

53. Ongoing developments – OSS site

54. Ongoing developments – Open source branches
20140104_Delwaq_Special_KRWV_UNOPS
20140128_12924_ice_coverage
20140203_QP_for_VOF_bankEROSION
20140319_back_temp
20140322_nefis_variable_cell_dimension
20140402_quasi_3d_bend_flow
20140416_ShinHanul
20140429_moerman
20140512_Irv
20140716_Delwaq_parallel_testing
20140911_broekema_sed_transport_analysis
20140925-Salt_Intrusion
20141001-Delwaq-EWACS
20141014-New_solver_24_by_Leo
20141118_EC-only_unstruc_multibc
20141128_consolidation_v2
20150217_delwaq_netcdf
20150310_tangential_boundary_conditions
20150317_Sinbad_sediment_transport
20150414-Delwaq_new_solver_24
20150421_33933_vs2013
20150429_unst-807_d-hydro
20150501_UNST-
812_morphology_for_XBeach_in_DFlowFM
20150612_33986_wave_data_location_shifted
20150709_TU_Andres_veg
20150709_Zju_Sun_sed_tranport
20151106_workshop
https://svn.oss.deltares.nl/repos/delft3d/branches/research/Deltares/

55. Ongoing developments – Closed source branches FM
0.8
0.8.2_acceptance_testing
0.9
0.71
1.0
20131213_389_coupling_with_delft3d-wave
20131219_trachytopen_UNST-376
20140911_unstruc_profiling_vortech
20141017_unstruc_sedmor
20141114_selfattraction_lecoz
20141118_unstruc_multibc
20150120_secondary_flow_UNST-485
20150303_1d2d_sobek_dflowfm
20150501_dflowfm_integratedmodelling
20150726_dflowfm-tools_UNST-167
20151005_velocity_reconstruction
20151022_dflowfm_xbhyd
unstruc_xbeach

56. Short topics
• Linux
• Parallel
• Debugging
• Domain Decomposition
• Your suggestions
• …

57. Questions & answers / discussion
Questions or comments?