intro story Coast / Estuary

Coast / Estuary

Coastal systems are among the most dynamic physical systems on earth and are subject to a large variety of forces. The morphodynamic changes occurring to coastlines worldwide are of great interest and importance. These changes occur as a result of the erosion of sediments, its subsequent transport as bed load or suspended load, and eventual deposition. 
 
Estuaries are partly enclosed water bodies that have an open connection to the coast. Estuaries generally have one or more branching channels, intertidal mudflats and/or salt marshes. Intertidal areas are of high ecological importance and trap sediments (sands, silts, clays and organic matter).
Within the Delft3D modelling package a large variation of coastal and estuarine physical and chemical processes can be simulated. These include waves, tidal propagation, wind- or wave-induced water level setup, flow induced by salinity or temperature gradients, sand and mud transport, water quality and changing bathymetry (morphology). Delft3D can also be used operationally e.g. storm, surge and algal bloom forecasting. 
 
On this discussion page you can post questions, research discussions or just share your experience about modelling coastal and/or estuarine systems with Delft3D FM. 
 

** PLEASE TAG YOUR POST! **

 

 

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

 

 

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Problems in copying compiled binaries in Delt3D-GUI installation folder

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Pietro Mazzon, modified 3 Years ago.

Problems in copying compiled binaries in Delt3D-GUI installation folder

Youngling Posts: 11 Join Date: 12/26/17 Recent Posts
Hi everyone,

I have a problem in copying the compiled binaries in the Delf3D-GUI folder.

I followed the instructions in http://oss.deltares.nl/web/delft3d/source-code and I already checked in FAQ.

When I copy the folder win64 (from my compiled code folder) in the installation folder of Delft3D (substituting it) and then I check the file in the new win64 folder, I see that it didn't substitute some folders (such as flow2d3d, folders shown in picture_1), because they have different names (e.g. dflow2d3d and flow2d3d).

The problem is, when I try to run a simulation using the Delft3D-GUI, I get this message:
Executable "d_hydro.exe" not found on directory"C:/ProgramFiles/Deltares/Delf3D 4.03.01/win64/flow2d3d/bin"
(it is shown in picture_2, attached)

Obviously it searchs "d_hydro.exe" in "C:/ProgramFiles/Deltares/Delf3D 4.03.01/win64/flow2d3d/bin" and it doesn't find it since the compiled binaries are in folder "dflow2d3d" and not in folder "flow2d3d".

I tried to simply substitute the folder changing its name from "dflow2d3d" to "flow2d3d", but Delft3D didn't run and showed the window in picture_3 (attached).

Maybe it's a dumb thing, but following the instruction on the website I should just copy the folder "win64" and allow to substitute the file, but it doesn't work.

I tried to run also "substitute_delft3d_env.exe" but the command window opens and closes immediately.
May be this one the problem?

Does anyone have a solution for that?

//update: I compiled this trunk version, because I can't compile the last tag version (7545).


Thanks everyone,

Pietro
DG
David Gutiérrez, modified 3 Years ago.

RE: Problems in copying compiled binaries in Delt3D-GUI installation folder

Youngling Posts: 12 Join Date: 1/6/12 Recent Posts
Hi Pietro and all,

I have just found the same problem an after trying some possibilities regarding folder and script renaming with no luck I have found that the d_hydro.exe that I just built is not good (it doesn't run even from the command line).
However, using and old version (trunk from 2017-02-22) everything looks good.

After checking, I have realized that I had downloaded and built the trunk instead of the latest tagged version (which is the recommended at each moment).
I have checked tag 7545 out, rebuilt and tried the GUI again. Everything looks good (I have succesfully run some tutorial cases and they apparently run properly).

BTW, I have used VS2017 + IFORT 2018 to build. Which versions have you used?

So there are two issues here:
First, your d_hydro.exe is probably not good (as was not mine). My best guess is that the trunk is not in good "shape" to be built (at least with VS2017+ifort18)? Latest modifications are dated last friday.

Second, the trunk version includes some (not backwards compatible) modifications regarding the directory names. The avilable GUI doesn't support these modifications yet.

As mentioned, the current latest tag (7545) seems to be working fine, and has been my way to go.

Could someone from the development team could confirm these comments and that we are not missing anything else?

Thank you very much,
David
PM
Pietro Mazzon, modified 3 Years ago.

RE: Problems in copying compiled binaries in Delt3D-GUI installation folder

Youngling Posts: 11 Join Date: 12/26/17 Recent Posts
Hi David!

First of all, thanks for the reply.

I have the trunk version 8067. I suspected that the problem was with the trunk.
The problem is that is the only version that I could compile! I still have problems in compiling the tag version 7545 (system crashes at a certain point).

I tried to run the examples, and hydro.exe seems to work fine, but as I said I can't copy the binaries in the GUI folder, and I think you got the reason why it doesn't work!

I'm compiling the source code with VS2015 and IFORT16 because unfortunately I couldn't compile it with VS2017 and IFORT18 (I still don't understand why but I can't compile the tag version!)

Now I'm trying to checkout an older tag version (7426), hoping that I can compile this one!
I'll let you know if I'll solve it!

Thank you very much,

Pietro
DG
David Gutiérrez, modified 3 Years ago.

RE: Problems in copying compiled binaries in Delt3D-GUI installation folder

Youngling Posts: 12 Join Date: 1/6/12 Recent Posts
Hi Pietro,

at first, when trying to compile the trunk with VS17+IFORT18 it didn't work for me either. (When I tried 7545 after this steps it worked straight away).
What I had to do to make it work was:
- Modify the VS2017 installation to include:
+ the c++ MFC stuff. (Compatibility with MFC and ATL at the C++ section).
+ The VC++ tools (at the C++ section)
+ Windows 10 SDK (10.0.16299.0) (I use windows 7, but this is the SDK to be used).

After this modification (or including this items when installing Visual Studio), prepare the solution using prepare_sln.py.
If you want to use tag 7545 you will have to add the lines that reference VS2017 and IFORT 2018 from the prepare_sln.py file that came with the trunk into the prepare_sln.py that comes with 7545. Replacing the old one with the new one didn't work for me.

After preparing the solution, you have to open it in Visual Studio, right click the Solution and click "Retarget Solution". Then choose Windows 10 SDK v 10.0.16299.0).

After these steps, everything compiled fine for me. If you have already tried compiling and something went wrong, always use the Rebuild Solution command, instead of Build Solution.

Please let me know your findings to see if they work for you (so that these steps can be added to the manual).

Best,
David
PM
Pietro Mazzon, modified 3 Years ago.

RE: Problems in copying compiled binaries in Delt3D-GUI installation folder

Youngling Posts: 11 Join Date: 12/26/17 Recent Posts
Hi David!

Thanks again for the answer.

I'm using vs2015 and ifort16 (I tried with Vs 2017 and ifort18 but I couldn't compile).

I tried the two last tagged versions and with the last trunk version until now (in Vs I chose release, x64, as written in the instructions). But with all of them, the compilation stops when is has to compile the file flow2d3d_openda, saying that this package is not required to be installed in the x64 release. Then the compilation does not proceed and I have to shut down the system since it stops to work (I can't even run the task manager).

When I check in the folder both d_hydro.exe and flow2d3d are present, so I thought that it worked. But when I copy it in the GUI folder and I try to run it, it starts correctly but stops after a few seconds.

I don't really know why.

Do you have any suggestions?

And do you maybe know how to modify the batch_flow file created by delft dashboard in order to point to d_hydro.exe?
Maybe if I can run that bat file the program will work.

Thanks a lot!

Pietro
DG
David Gutiérrez, modified 3 Years ago.

RE: Problems in copying compiled binaries in Delt3D-GUI installation folder

Youngling Posts: 12 Join Date: 1/6/12 Recent Posts
Hi Pietro,

If the compilation process is not correctly finished, I would not trust the results. As you mention, d_hydro.exe might run, but who knows if what is happening behind is fine. So I would not go further without the compilation being correct.

I find it a bit odd that you have to shut your system down because the compilation "freezes". I have never seen that with Visual Studio.

regarding the compilation, in order to be able to solve the "problem" when getting through flow2d3d_openda I would need a bit more detailed description:
- SVN Checkout of tag (number?)
- Did you use the python script to generate the solution?
- Output from that script.
- Which solution do you open?
- You use x64, but Debug or Release?

- How long have you waited until shutting the system down?

That said, if you want to verify your existing exes:

When you say that the program stops after a few seconds, what model are you using to test if it runs?
A common reason for that behavior is bad model input.
Are you testing the exe with a model prepared by yourself?
What is the output of your run diagnostic files?
Have you tried running from the GUI the examples that come with the src?

Best,
David
PM
Pietro Mazzon, modified 3 Years ago.

RE: Problems in copying compiled binaries in Delt3D-GUI installation folder

Youngling Posts: 11 Join Date: 12/26/17 Recent Posts
Hi David,

Here the info that you asked:

-I tried with versions tag 7545 and 7426 and with the trunk version 8067

-Yes, I used the python script (selecting VS2015 Update 3 with .NET Framework 4.6 and IFORT2016: Intel Parallel Studio XE 2016 Update 4) and everything worked fine

-Outputs from that script: It created the .sln file "delft3d_open", "nefis" and "io_netcdf" and it modified some folders adding some file to them (folders: Tools_gpl, Scripts_lgpl, logs, utils_lgpl, engines_gpl, utlis_gpl, plugins_lgpl, third_party_open, tools_lgpl, m4)

-I run "delft3d_open.sln"

-I use x64, Release

-I tried to wait 20 minutes and 2 hours, but nothing changed. VS sais "ready" and the building doesn't proceed after skipping the compilation of "flow2d3d_openda"

-The examples from the respository folder run, but I'm not completely sure that the outputs are correct since I don't know what they have to produce!

-Yes, I prepared the model in Delft Dashboard following the instructions in the webinar about Delft Dashboard.

You were right! I tried to run the example standard_01 from Delft3D GUI (I ran FLOW and I selected the mdf file "f34.mdf") and the program worked!
I also tried to redo the file preparation using Dashboard and following the step-to-step instructions of the seminar, but I got the same error of the other time, attached at the post.

Let me know if you need more info.

Thanks!

Pietro
DG
David Gutiérrez, modified 3 Years ago.

RE: Problems in copying compiled binaries in Delt3D-GUI installation folder

Youngling Posts: 12 Join Date: 1/6/12 Recent Posts
Hi Pietro,

If f34 runs, now it's a matter of the model prepared with the dashboard.
As the error states, now it's time to check the diagnosis file. In the directory where your mdf file is, there should be some diagnostic files (they have "dia" in their names").
What are the contents of those files?

Best,
David
PM
Pietro Mazzon, modified 3 Years ago.

RE: Problems in copying compiled binaries in Delt3D-GUI installation folder

Youngling Posts: 11 Join Date: 12/26/17 Recent Posts
Hi David!

Don't know why, but after a few tests (just changing the boundary conditions in Delft Dashboard) my model ran.
Probably the source code compilation was complete, just VS freezed when it skipped the installation of "flow2d3d_openda", since everything is working (at least regarding what I'm using).

I really thank you for your help! I really appreciate it!


Just a feedback on the source code compilation to the developers: apparently my compilation freezed when it skipped the installation of "flow2d3dopenda", saying that for release x64, that installation was not needed. Then the system crushed.

So maybe you can try to fix this issue!

Thanks,

Pietro
DG
David Gutiérrez, modified 3 Years ago.

RE: Problems in copying compiled binaries in Delt3D-GUI installation folder (Answer)

Youngling Posts: 12 Join Date: 1/6/12 Recent Posts
Hi Pietro,

I am glad to hear that your simulation is running now.
To me, boundary conditions are normally the reason of the model complaining so it is not a surprise ;-)

Since your "Building software" combination is not the most recent and the chance of replicating the problem can be quite low, I don't know if someone will try to fix it...

Anyway, any further question, don't hesitate asking.

Best,
David