intro story D-Flow FM

 

D-Flow Flexible Mesh

D-Flow Flexible Mesh (D-Flow FM) is the new software engine for hydrodynamical simulations on unstructured grids in 1D-2D-3D. Together with the familiar curvilinear meshes from Delft3D 4, the unstructured grid can consist of triangles, pentagons (etc.) and 1D channel networks, all in one single mesh. It combines proven technology from the hydrodynamic engines of Delft3D 4 and SOBEK 2 and adds flexible administration, resulting in:

  • Easier 1D-2D-3D model coupling, intuitive setup of boundary conditions and meteorological forcings (amongst others).
  • More flexible 2D gridding in delta regions, river junctions, harbours, intertidal flats and more.
  • High performance by smart use of multicore architectures, and grid computing clusters.
An overview of the current developments can be found here.
 
The D-Flow FM - team would be delighted if you would participate in discussions on the generation of meshes, the specification of boundary conditions, the running of computations, and all kinds of other relevant topics. Feel free to share your smart questions and/or brilliant solutions! 

 

=======================================================
We have launched a new website (still under construction so expect continuous improvements) and a new forum dedicated to Delft3D Flexible Mesh.

Please follow this link to the new forum: 
/web/delft3dfm/forum

Post your questions, issues, suggestions, difficulties related to our Delft3D Flexible Mesh Suite on the new forum.

=======================================================

** PLEASE TAG YOUR POST! **

 

 

Sub groups
D-Flow Flexible Mesh
DELWAQ
Cohesive sediments & muddy systems

 


Message Boards

Compilation on Ubuntu 18.10

CK
Clemens Klante, modified 1 Year ago.

Compilation on Ubuntu 18.10

Youngling Posts: 11 Join Date: 12/19/18 Recent Posts

When compiling under Ubuntu 18.10 I am getting this issue when running ./configure

checking for NETCDF... no
configure: error: Package requirements (netcdf) were not met:

No package 'netcdf' found

Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.

I could not find a package which is netcdf or any other related package. What package is needed to install Delft3D?

Adri Mourits, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Yoda Posts: 1224 Join Date: 1/3/11 Recent Posts

Hi Clemens,

You can download NetCDF from Unidata.

Use exactly the same C++ and Fortran compiler to build NetCDF and Delft3D. Please check in case of using a precompiled distribution. See also our prerequisites.

Regards,

Adri

CK
Clemens Klante, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Youngling Posts: 11 Join Date: 12/19/18 Recent Posts

Hi Adri,

 

thanks for your answer. First I tried to install Delft3D following this tutorial which lead me to the problem regarding NetCDF. Now I tried to install it using the build_ubuntu.16.04LT.readme file in the /src/ folder and get another error.

make: *** [Makefile:547: install-recursive] Error 1

Which I can not really understand.

It seemed quite strange to me to install the libraries under /home/user/Downloads/libraries/ and after a restart my system does not want to reboot again. Need to fix this first.

Is there maybe a detailed installation tutorial for Delft3D? Would like to use one for my next try, when my system is fixed again.

Thanks in advance

- Clemens

Adri Mourits, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Yoda Posts: 1224 Join Date: 1/3/11 Recent Posts

Hi Clemens,

Ubuntu is not our standard platform. But there is additional information available: Folder "https://svn.oss.deltares.nl/repos/delft3d/trunk/src" contains two text files with the name build_ubuntu*. They might be a bit outdated, but they still will be helpful. If you notice possible updates for these files, please post them here, then I will commit them.

Thanks.

Regards,

Adri

 

CK
Clemens Klante, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Youngling Posts: 11 Join Date: 12/19/18 Recent Posts

Hi again,

I will do so if I am able to. Just for me to know and to compare to, which distribution in the standard platform you support the most?

Regards,

Clemens

Adri Mourits, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Yoda Posts: 1224 Join Date: 1/3/11 Recent Posts

Hi Clemens,

CentOS. CentOS versions are basicly clones of Stable RedHat versions.

Regards,

Adri

CK
Clemens Klante, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Youngling Posts: 11 Join Date: 12/19/18 Recent Posts

Hi Adri,

thanks for the information. CentOS and Ubuntu are a bit different, but that should not be the problem. Could fix my computer and will start all over again.

A question regarding the SVN repository. If I see it correctly there is just the /trunk version available for download. Is this the stable version?

Regards,

Clemens

Adri Mourits, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Yoda Posts: 1224 Join Date: 1/3/11 Recent Posts

Hi Clemens,

Stable versions are in https://svn.oss.deltares.nl/repos/delft3d/tags/, see als download source code. The best way to start is by downloading the latest stable version, currently for Delft3D 4 (structured grid): https://svn.oss.deltares.nl/repos/delft3d/tags/delft3d4/62441/

and for Delft3D FM (Flexible mesh): https://svn.oss.deltares.nl/repos/delft3d/tags/delft3dfm/62800/

Regards,

Adri

Dmitry Kushnir, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Padawan Posts: 98 Join Date: 11/9/12 Recent Posts

Hi Clemens,

I had no problems compiling Delft3D version 7545 (https://svn.oss.deltares.nl/repos/delft3d/tags/delft3d4/7545) on Ubuntu 16.10 in the past. Since that revision many things have changed though, e.g. a D-FLOW-FM kernel was added (but no GUI for this model yet available), a new model launcher dimr was developed etc. Nevertheless, I suggest you to start from the tagged version 7545. Read this post (have a look at Installing_Delft3D.txt), the compilation procedure is explained step by step there. Also browse through the build_ubuntu-files in the src-folder as Adri suggested. I expect compiling Delft3D on Ubuntu 18.10 is pretty much similar to the compiling on Ubuntu 16.10.

Hope this will be a little help.

 

Regards,

Dmitry

CK
Clemens Klante, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Youngling Posts: 11 Join Date: 12/19/18 Recent Posts

Hi Dmitry,

first of all, all the best for 2019.

Thank you for the information, I will take a closer look at it as soon time allows.

As written the last time I tried the installation I destroyed my Ubuntu system. I assume this was caused due to the needed libraries I installed in /Documents according to the manual. The installation in /Documents seems not that appropriate to my taste as soon as it comes to standard libraries, which most likely come with Ubuntu in any case.

Do you maybe have any other tips or hints I should take care about while installing?

Regards,

Clemens

CK
Clemens Klante, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Youngling Posts: 11 Join Date: 12/19/18 Recent Posts

Hi Dmitry,

 

just wonder where you installed all the needed libraries? The last time I followed the instructions to install the libraries in my user folder the system has not been able to boot anymore. It seems that installations you suggested does not have this issue. Moreover, I would like to know if you tried to update to the newest revisions?

 

Regards,

Clemens

Dmitry Kushnir, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Padawan Posts: 98 Join Date: 11/9/12 Recent Posts

Hi Clemens,

If I remember correctly, I think I had installed all needed libraries to /usr/local/. Except for the HDF5, which I had compiled with flag --prefix=/opt/hdf5-[version of my hdf-5 source-code].

No, I have not tried to update my Delft3D installation yet. Maybe it will be worth trying when a flexible mesh version come to open-source.

Regards,

Dmitry

 

CK
Clemens Klante, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Youngling Posts: 11 Join Date: 12/19/18 Recent Posts

Hi Dmitry,

I had the time to work with the compilation. Since I had some problems with the library files last time, I decided to stick to the one which can be installed via apt-get, since all of them are available through apt-get as well.

Now I am still facing the problem to define the correct paths so that Delft3D can find them. Usually it quite easy to get the path with --link, but that does not work in all cases. Do you maybe know another command to get the install paths?

 

Thanks and regards,

Clemens

Dmitry Kushnir, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Padawan Posts: 98 Join Date: 11/9/12 Recent Posts

Hi Clemens,

I'm glad to read that your work is in progress.

Regarding installation of packages via apt-get: b oth mpich and netcdf must be compiled with exactly the same compiler as Delft3d. See prerequisites for building on Linux. In other words, these packages are being built manually from source instead of being downloaded from repo to avoid compiler version mismatch, which will cause the Delft3d compilation fail.

Regarding paths to dependencies: they all are defined in build.sh script, which is normally used for building Delft3D from source. Some manual modification of build.sh is needed though. You can also check Qinghua Ye's script on building the Delft3D on ubuntu, located in svn-repository: https://svn.oss.deltares.nl/repos/delft3d/trunk/src/build_ubuntu.16.04LT.readme.

 

Regards,

Dmitry

CK
Clemens Klante, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Youngling Posts: 11 Join Date: 12/19/18 Recent Posts

Hi Dmitry, 

that with the compiler sound reasonable, I will check on that. Right now I am working with the build.sh and the build_ubuntu16.04LT.sh script and try to fix them to my system. Have to check on the compilers, since I was not aware that Delft3D needs exactly the same one, but this should not be a problem. 

 

Best,

- Clemens

CK
Clemens Klante, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Youngling Posts: 11 Join Date: 12/19/18 Recent Posts

Hej at all,

I just edited my build.sh file (see attached) and wonder if that might work. I changed everything so that it should fit to my system. Now I just wonder if the "export" command in the console is temporary for the compilation or do I change this values globally?

When compiling right now I get this error.

Using GNU compilers in /usr/bin
Current settings:
export ACLOCAL=""
export AUTOMAKE=""
export AUTOHEADER=""
export AUTOCONF=""
export AUTORECONF_FLAGS=""
export LIBTOOLIZE=""
export LDFLAGS=""
export LDFLAGSMT_ADDITIONAL=" "
export LD_LIBRARY_PATH=":/usr/lib"
export MPIFC="mpif90"
export MPI_INCLUDE="/usr/include"
export MPILIBS_ADDITIONAL="-L/usr/lib -lfmpich -lmpich -lmpl -lcr"
export PKG_CONFIG_PATH="/usr/lib/pkgconfig:"
export PATH="/usr/bin:/home/clemens/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"

20190219.151516 :: Running ./autogen.sh --verbose &> /home/clemens/Delft3D/62441/src/logs/autogen.log in /home/clemens/Delft3D/62441/src
20190219.151544 :: Running ./autogen.sh --verbose &> /home/clemens/Delft3D/62441/src/logs/autogen.log in /home/clemens/Delft3D/62441/src/third_party_open/kdtree2
20190219.151550 :: Running CFLAGS='-O2 ' CXXFLAGS='-O2 ' AM_FFLAGS=' ' FFLAGS='-O2 ' AM_FCFLAGS=' ' FCFLAGS='-O2 ' AM_LDFLAGS=' ' ./configure --prefix=/home/clemens/Delft3D/62441/src &> logs/configure.log
20190219.151619 :: Running make ds-install &> logs/make.log
20190219.151709 :: Running make ds-install -C engines_gpl/dflowfm &> logs/make_dflowfm.log
20190219.151710 :: ERROR: Make fails!

Guess there is still something wrong with the prerequisites or with the compiler settings. Just wonder how to change it from gcc to icc, since I have intels compilers on my system.

Thanks a lot.

Attachments:

Adri Mourits, modified 1 Year ago.

RE: Compilation on Ubuntu 18.10

Yoda Posts: 1224 Join Date: 1/3/11 Recent Posts

Hi all,

There were some issues when compiling on Ubuntu. These are solved (with help of Mohammad Keshtpoor) in the trunk and in the following tagged version: 

https://svn.oss.deltares.nl/repos/delft3d/tags/delft3dfm/63172/

Regards,

Adri