Release Notes Delft3D-FLOW 5.00 / 5.01
Introduction of Delft3D-FLOW version 5.00.00
Delft3D open source is migrating from version 4.00.07 to 5.00.00. Here is an overview of the changes:
- The main binaries are:
- Executable deltares_hydro.exe (changed), using an INI-formatted input file (specified as command line argument). It converts the INI-formatted input file to an XML-formatted input file and starts d_hydro.exe. The XML-file is deleted after the calculation. The behaviour is the same as "deltares_hydro.exe" in previous versions.
- Executable d_hydro.exe (new), using an XML-formatted input file (specified as command line argument). It calls the constructor- and "Run"-methods of class "DeltaresHydro" in flow2d3d.
- Dynamic library flow2d3d.dll/libflow2d3d.so (changed interface), containing the kernel. "d_hydro.exe" can not use previous version "flow2d3d" libraries and previous "deltares_hydro.exe" can not use new "flow2d3d" libraries.
-
The directory structure of a Delft3D setup is going to change into:
<platform>/<package>/<module>/<binlib>
with:
<platform>: lnx32, lnx64, win32, win64
<package>: delft3d, deltares or empty
<module>: flow2d3d, wave, etc.
<binlib>: bin, lib, default, scripts
Remarks:
- All modules are portable: all needed scripts, libraries etc. are inside directory <module>
- A 64-bit installation may contain 32-bit binaries. Currently only Delft3D-FLOW, Delft3D-WAVE and SWAN are available as 64-bit.
- Compiling:
Windows:
Nothing changed
Linux:
a) Use newer versions of Gnu Automake:
- automake 1.11.1
- autoconf 2.68
- libtool 2.4.2
b) You can choose one of the following two ways to compile the code:
1) Execute:
./autogen.sh
./configure --prefix=`pwd`
make ds-install
2) Use build.sh. The compiler must always be specified when using the script "build.sh".
Example: build.sh -gnu
For 64-bit, add the option "-64bit" when executing "build.sh".
Example: build.sh -intel12 -64bit
Use method 1) when using a clean Linux distribution with properly installed tool.
Method 2) may be convenient when you need to specify explicitly the directories where used tools are installed.
c) Deltares aims on a fully tested version, created on CentOS 5.7, 64-bit, using Gnu C++ compiler version 4.1.2 and Gnu Fortran compiler version 4.6.2.
- Running a calculation:
The command to start a calculation is not changed: execute "deltares_hydro.exe" with the INI-formatted input file as command line argument.
When using the new directory structure, it is necessary to add the directory "<module>/lib" to the environment parameter used to find the dynamic libraries.
Windows script example:
set D3D_HOME=c:\Delft3D_win32
set exedir=%D3D_HOME%\flow2d3d\bin
set libdir=%D3D_HOME%\flow2d3d\lib
set PATH=%exedir%;%libdir%;%PATH%
%exedir%\deltares_hydro.exe config_flow2d3d.ini
Linux script example:
export D3D_HOME=/opt/delft3d_lnx64
exedir=$D3D_HOME/flow2d3d/bin
libdir=$D3D_HOME/flow2d3d/lib
export LD_LIBRARY_PATH=$exedir:$libdir:$LD_LIBRARY_PATH
$exedir/deltares_hydro.exe config_flow2d3d.ini
Delft3D-menu GUI:
- Use script "convert_xxx_to_old_directory_structure_xxx.xxx" to convert the binaries to the "old" directory structure. The script is placed in directory "<mycode>/bin" where <mycode> is the directory where the source code is checked out.
- Copy the newly created binaries into your Delft3D installation.
- The INI-formatted input file is automatically generated.
Remarks:
- The Gnu compiler is more strict than the Intel compiler. This may cause that models don't run using Gnu compiled binaries while they do run using Intel compiled binaries. Noticed
Gnu restrictions:
1) All input files must end with a "new line" character
2) A file may not be open for reading two times at the same time. This may occur with a meteo input file, to be read by several (DomainDecomposition) subdomains.
Workaround: let each subdomain read a separate copy of the meteo input file.
- The subdirectory "lib" is supposed to contain all compiler/platform specific dynamic libraries needed at runtime. On Windows this directory contains a lot of dll's. On Linux it is only filled when you receive a (precompiled) binary distribution, but it is empty when you compile the code yourself. You have to add the dynamic libraries from your system and your compiler.
- Some Linux platforms (including the Deltares h4 cluster) need the following line to be added to the run script:
export LD_PRELOAD="$libdir/libgfortran.so.3"
- Debugging (Windows):
- Execute "deltares_hydro.exe config_flow2d3d.ini -keepXML". This will store the XML-file with a name like "TMP_config_flow2d3d_11260.xml"
- Inside VisualStudio: start "d_hydro.exe" with commandline argument "TMP_config_flow2d3d_11260.xml"
- Remarks:
- The format of the new XML-file will change in the near future.
- Executable "deltares_hydro.exe" is based on a Tcl script. See "https://svn.oss.deltares.nl/repos/delft3d/trunk/src/third_party_open/tclkit".
- "deltares_hydro.exe" will be removed when the XML-file has it's final form and Delft3D-menu can start "d_hydro.exe" directly.
| Version |
flow2d3d, version 5.01.00.2163 (trunk, win32_intel/lnx64_intel) |
| Date |
01 Feb 2013 |
| Based On |
flow2d3d, version 5.00.10.1983, 16 Nov 2012 |
| Changed Functionality |
2083-2162: Delft3D-14744: Collect all current Z-model improvements in branches and merge them into the trunk
2030,2037: Delft3D-16060: Distribute discharge at 'Total Discharge' boundaries using the average water level along the open boundary (new) rather than the local water level (old) |
| New Functionality |
2068: Delft3D-16087: Use FLOW parallel output as input for WAQ
2060: Support different mpi implementations
2047-2049: Mormerge example added to the source code
|
| Fixed bugs |
2163: Delft3D-16137: Order of cross-sections in the output is wrong
2121: Delft3D-16108: Dry points get wet while they should not, and mess up Fourier results
2098,2107: Delft3D-16092: When sediment transport formula 5 (Bijker's formula) is used with Bailard-approach, the path of tabmom could not be found.
2074: On Linux, intall libDelftOnline.so.0 instead of libDelftOnline.so
2016: Delft3D-15196: Merge three Sediment Transport Formulas into the trunk, proposed and prepared by NIWA
1992: Delft3D-16030: Remove warnings related to the combination of DD with waves/morphology
|
| External Influence |
- The order of the output related to cross-sections is corrected (16137).
- Results will differ when using the Z-model layering (14744).
- Results will differ when using wave information in 3D models (WAVE online, offline and roller model) 14744).
- Minor differences may occur when using wave information in 2D models (14744).
- Minor differences may occur in the temperature in very shallow water (< secchi depth) (14744).
- A ddb file has to be created manually to be able to use FLOW parallel output as input for WAQ. Further testing, documentation and automatically generating the ddb file is required. (16087)
- MPI implementations other than MPICH2 are not tested, altough the source code allows others (2060).
- Results will differ when using a "Total Discharge" boundary. The old results can be obtained by adding the line "ZavgQt = #NO#" to the mdf file (16060).
|
| New Known Bugs / Change Requests |
- Delft3D-16161: Parallel run may crash when the model contains bedload sediments but no suspended sediments
- Delft3D-13751: The online visualisation (OLV) based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-15949: Output using mass balance polygons can cause crash when running parallel
- Delft3D-16066: 32 bit Linux version compiles with errors and aborts when running with the message "ERROR: d_hydro.exe: oc.c:159: create_nefis_files: Assertion `(BUInt8) -1 == (size_t)(BUInt8) -1' failed."
|
| Version |
flow2d3d, version 5.00.10.1983 (trunk, win32_intel/lnx64_intel) |
| Date |
16 Nov 2012 |
| Based On |
flow2d3d, version 5.00.09.1882, 18 Oct 2012 |
| Changed Functionality |
|
| New Functionality |
|
| Fixed bugs |
1983: Delft3D-15196: Merge three Sediment Transport Formulas into the trunk, proposed and prepared by NIWA
1980: Delft3D-16044: Support VisualStudio 2012
1960-1961: Delft3D-15779: Fourier output is wrong (Linux) or causes crash (Windows) when running parallel
1948: Delft3D-16029: HLES viscosity is not taken into account when roller model is switched on
1930-1933: VisualStudio 2010 solution file added for Intel13 Fortran compiler (Intel Composer 2013)
1909-1978: Delft3D-15920: Total discharge boundary / morphological simulation gives incorrect results in parallel mode
1903-1949: Delft3D-15700: Using Intel 11.0 compilers (Fortran and C), 64-bit, on Linux causes crashes
1890: Delft3D-15975: When running parallel, instantaneous discharge is wrong (and equals the cumulative discharge)
|
| External Influence |
|
| New Known Bugs / Change Requests |
- Delft3D-13751: The online visualisation (OLV) based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-15949: Output using mass balance polygons can cause crash when running parallel
|
| Version |
flow2d3d, version 5.00.09.1882 (trunk, win32_intel/lnx64_gnu) |
| Date |
18 Oct 2012 |
| Based On |
flow2d3d, version 5.00.08.1855, 21 Sept 2012 |
| Changed Functionality |
|
| New Functionality |
1877: Delft3D-15987: Different constituents may have different Thatcher-Harleman delay time.
|
| Fixed bugs |
1882: Delft3D-15992: dumping numbers for sandmining polygon is correctly initialized and the dredge-dumping structure is correctly read.
|
| External Influence |
|
| New Known Bugs / Change Requests |
- Delft3D-13751: The online visualisation (OLV) based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-15700: Using Intel 11.0 compilers (Fortran and C), 64-bit, on Linux causes crashes
- Delft3D-15779: Fourier output is wrong (Linux) or causes crash (Windows) when running parallel
- Delft3D-15949: Output using mass balance polygons can cause crash when running parallel
|
| Version |
flow2d3d, version 5.00.08.1855 (trunk, win32_intel/lnx64_gnu) |
| Date |
21 Sept 2012 |
| Based On |
flow2d3d, version 5.00.07.1698, 12 July 2012 |
| Changed Functionality |
|
| New Functionality |
1710: Delft3D-15886: Trigger dredging based on average depth rather than pointwise depth
|
| Fixed bugs |
1831: Delft3D-15936: When using stationairy roller model, enable setdown for shoaling waves
1730: Delft3D-15473: heat flux output of dry cells is set to be 0.
1799: Delft3D-15937: FLOW won't crash during initialization when specifying more than 20 output layers.
|
| External Influence |
|
| New Known Bugs / Change Requests |
- Delft3D-13751: The online visualisation (OLV) based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-15700: Using Intel 11.0 compilers (Fortran and C), 64-bit, on Linux causes crashes
- Delft3D-15779: Fourier output is wrong (Linux) or causes crash (Windows) when running parallel
- Delft3D-15949: Output using mass balance polygons can cause crash when running parallel
|
| Version |
flow2d3d, version 5.00.07.1698 (trunk, win32_intel/lnx64_gnu) |
| Date |
12 July 2012 |
| Based On |
flow2d3d, version 5.00.06.1677, 2 July 2012 |
| Changed Functionality |
|
| New Functionality |
1693,1694: Delft3D-15874: Add sediment sedimentation and resuspension fluxes to the set of output files intended as input for D-WAQ |
| Fixed bugs |
1684: Delft3D-15856: A warning should be generated when running with too large smoothing time
|
| External Influence |
- Models with a smoothing time larger than the total simulation time will not run anymore (15856)
|
| New Known Bugs / Change Requests |
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-13751: The online visualisation (OLV) based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
- Delft3D-15779: fourier output is wrong (Linux) or causes crash (Windows) when running parallel
- Delft3D-15700: Using Intel 11.0 compilers (Fortran and C), 64-bit, on Linux causes crashes
|
| Version |
flow2d3d, version 5.00.06.1677 (trunk, win32_intel/lnx64_gnu) |
| Date |
2 July 2012 |
| Based On |
flow2d3d, version 5.00.05.1576, 11 June 2012 |
| Changed Functionality |
|
| New Functionality |
|
| Fixed bugs |
1677: HdtOut = true: write output also halfway the time step
1676: Prevent dry cell erosion through thin dams and of cells with lower height
1663: Gather all needed dynamic libraries when installing on Linux
1654-1658: Delft3D-15854: Surfbeat/roller energy is building up at the outer side of drypoints/thin dams
1609: Delft3D-15838: time-varying bed level (and other sediment quantities) not written to history file if only bedload fractions are used
|
| External Influence |
- Results will differ when using the surfbeat/roller model (15854)
- Results may differ when using morphology (revision 1676)
|
| New Known Bugs / Change Requests |
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-13751: The online visualisation (OLV) based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
- Delft3D-15779: fourier output is wrong (Linux) or causes crash (Windows) when running parallel
- Delft3D-15700: Using Intel 11.0 compilers (Fortran and C), 64-bit, on Linux causes crashes
|
| Version |
flow2d3d, version 5.00.05.1576 (trunk, win32_intel/lnx64_gnu) |
| Date |
11 June 2012 |
| Based On |
flow2d3d, version 5.00.04.1520, 25 May 2012 |
| Changed Functionality |
|
| New Functionality |
|
| Fixed bugs |
1557: Delft3D-15801: Memory leak when using DomainDecomposition with dredging/dumping
|
| External Influence |
|
| New Known Bugs / Change Requests |
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-13751: The online visualisation (OLV) based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
- Delft3D-15779: fourier output is wrong (Linux) or causes crash (Windows) when running parallel
- Delft3D-15700: Using Intel 11.0 compilers (Fortran and C), 64-bit, on Linux causes crashes
|
| Version |
flow2d3d, version 5.00.04.1520 (trunk, win32_intel/lnx64_gnu) |
| Date |
25 May 2012 |
| Based On |
flow2d3d, version 5.00.03.1300, 5 March 2012 |
| Changed Functionality |
|
| New Functionality |
1432-1520: Delft3D-15557: Write output for specified layers only
1342-1408: Delft3D-15710: Add nesthd1 and nesthd2 to the open source repository |
| Fixed bugs |
1499: Delft3D-15804: restart single layer bed composition if no bedload or no suspended load fraction in simulation
1478: Delft3D-15775: "Smoothed peak wave period" is zero when running with WAVE online and using roller model
1470: Delft3D-15783: Produce an error message when the ddb-file contains errors
1427: Remove wrong order reorganisation causing crash when running parallel
1388-1391: Delft3D-15736: Coordinate units incorrectly represented on flow and wave output files
1363: fix error in writing current only bed roughness (z0ucur) to map file.
1358: Delft3D-15690: Velocity profile is wrong when using waves in 3D
1357,1401: Delft3D-15678: Open boundaries specified with time series are not handled correctly when running parallel using MPI
1357-1421: Delft3D-15667: Routine INCBC computes distances from (x,y)-coordinates that should be from array guu, gvv, etc
1332-1497: Delft3D-15693: Get FLOW compiled and optimised on the Lisa and the Huygens at SARA as part of PRACE project
1321-1323,1340, 1362, 1373: Updates for cygwin
1320: Delft3D-15680: A model using meteo data on a equidistant grid does not run in parallel mode
1318: Delft3D-15633: The new zuno model crashes in the first time step without any error message
1308: Directory "utils_flow" renamed into "deltares_common"
|
| External Influence |
- Results will differ when using waves in 3D (15690)
- Results will differ when using a wave component input file (15775)
- Minor differences may occur, initiated on water level boundaries (15667)
- QuickPlot may have visualisation problems when the output does not contain all the modelled layers (15557)
- See "Introduction of Delft3D-FLOW version 5.00.00" below
|
| New Known Bugs / Change Requests |
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-13751: The online visualisation based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
- Delft3D-15779: fourier output is wrong (Linux) or causes crash (Windows) when running parallel
- Delft3D-15700: Using Intel 11.0 compilers (Fortran and C), 64-bit, on Linux causes crashes
|
| Version |
flow2d3d, version 5.00.03.1300 (trunk, win32_intel/lnx64_gnu) |
| Date |
5 March 2012 |
| Based On |
flow2d3d, version 5.00.02.1289, 27 February 2012 |
| Changed Functionality |
|
| New Functionality |
1294-1300: Delft3D-15656: Merge Maarten van Ormondt improvements in the trunk:
- Spatially varying rain on regular equidistant grid added
- Spatially varying nett solar radiation on regular equidistant added to Ocean Heat model
- Keyword Anglon added to MDF file to specify longitude of grid
- Calibration parameter for flocculation (Van Rijn, 2007) added
- Calibration parameter for critical shear stress of fine sediments in Van Rijn (2007) added
- New formulation for avalanching added to prevent extreme slopes in morphological simulations
- Sediment tracers added
- When keyword Thresh in *mor file is set <= 0.0, the erosion flux of fine sediments (Partheniades-Krone) is limited by availability of sediment fraction (and not using FIXFAC approach)
|
| Fixed bugs |
|
| External Influence |
- See "Introduction of Delft3D-FLOW version 5.00.00" below
- Temperature results will differ when using heat flux model 5 (Ocean model) and when a time zone shift unequal to zero is defined (15656)
|
| New Known Bugs / Change Requests |
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-13751: The online visualisation based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
|
| Version |
flow2d3d, version 5.00.02.1289 (trunk, win32_intel/lnx64_gnu) |
| Date |
27 February 2012 |
| Based On |
flow2d3d, version 5.00.01.1252, 16 February 2012 |
| Changed Functionality |
|
| New Functionality |
1283: Delft3D-15633: The new zuno model crashes in the first time step without any error message
1281: Delft3D-15632: Accept a restart file one directory higher than the other input files
1279: Atmospheric pressure correction added for Riemann boundaries in combination with 3d-profile
1278-1284: Delft3D-15643: Factor "spw_merge_frac" added for merging spiderweb and background winds |
| Fixed bugs |
1282,1299: Delft3D-15616: Conversion of windspeed to windstress produces NaN when the windspeed pivot points coincide
1266: Delft3D-15635: Solved compile error on version_number.rc |
| External Influence |
- See "Introduction of Delft3D-FLOW version 5.00.00" below
|
| New Known Bugs / Change Requests |
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-13751: The online visualisation based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
|
| Version |
flow2d3d, version 5.00.01.1252 (trunk, win32_intel/lnx64_gnu) |
| Date |
16 February 2012 |
| Based On |
flow2d3d, version 5.00.00.1234, 03 February 2012 |
| Changed Functionality |
Delft3D-15611: The "opb" functionality (user created dynamic library) does not work when using the Gnu compiler (Linux)
Won't fix: workaround available. |
| New Functionality |
|
| Fixed bugs |
1249,1251: Delft3D-15617: Incorrect exchange of discharges between FLOW and culvert routine (plugin)
1250: Delft3D-15610: Parameter BALR1CONC contains NaNs |
| External Influence |
- See "Introduction of Delft3D-FLOW version 5.00.00" below
|
| New Known Bugs / Change Requests |
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-13751: The online visualisation based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
|
| Version |
flow2d3d, version 5.00.00.1234 (trunk, win32_intel/lnx64_gnu) |
| Date |
3 February 2012 |
| Based On |
flow2d3d, version 4.00.07.0892, 18 October 2011 |
| Changed Functionality |
902,903: Use Subversion client 1.7 for generation of version number information |
| New Functionality |
|
| Fixed bugs |
989-1234: Delft3D-15376: Merge OSX branch in trunk
1220: Changed balance (BalFil keyword) output fluxes from "flux per half time step" to actual "cumulative flux".
1218: Delft3D-15583: solve bed load transport disturbance at DD boundaries during transport in negative grid direction
1215: In vcxproj: use $(IFORT_COMPILER12) instead of $(IFORT_COMPILER11) when linking
1207: sedtyp stored in bedcomposition_module; don't modify dz_eros in gettoplyr
1200: support for "available mass of sediment" per layer in stratigraphy model (unit: kg/m^2)
1185,1193: Delft3D-15561: (x,y) coordinates does not correspond with (m,n) location on Delft3D-FLOW history file
1174,1188: Delft3D-15549: Running parallel does not work using version 4.00.07.0892
1186: Delft3D-15565: Delft3D-WAVE doesn't support relative path in grid file name
1176: Delft3D-14744: Use vertical dimension 0:kmax everywhere when writing rtur1
1166: Improved end-of-file error message for wave bathymetry file
1133: Delft3D-15530: Bed composition restart does not work if only bed load fractions are used
969-1131: Delft3D-15298: Remote OLV improvement: Replace top level Fortran with C++
1118: Delft3D-15512: Add an error message when run hangs
1117: Delft3D-15509: Version 4.00.06.834 produces wrong results on generating WAQ input files compared to version 4.00.03.565
1111: Delft3D-15496: FLOW model does not work combined with secondary flow
1103: Delft3D-15499: Meteo files are not read correctly by Delft3D-FLOW when the "TIME" line is too long
1099: Delft3D-15482: Incomplete cross-section in trih-file
1050: Enable distributed DD
1011: Fix various bugs associated with the combination of RTC and DD
950: Fixed problem with negative sediment amounts at open boundaries
|
| External Influence |
- See "Introduction of Delft3D-FLOW version 5.00.00" below
- Differences may occur on Linux due to usage of another compiler, platform and automake environment (15376)
- Minor differences may occur due to code reorganisation (15298)
- Online Visualisation is temporary disabled (13751)
|
| New Known Bugs / Change Requests |
- Delft3D-15610: Parameter BALR1CONC contains NaNs
- Delft3D-15611: The "opb" functionality (user created dynamic library) does not work when using the Gnu compiler (Linux)
- Delft3D-15612: When running a DomainDecomposition model distributed on the h4 cluster, the performance decreases dramatically
- Delft3D-13751: The online visualisation based on DataOnLine (DOL), without using Java, is ready to be merged in the main development stream
|
: give error message when using Non-Hydrostatic in 2D