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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RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc

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Compiling on Windows: flex.exe and byacc.exe was unable to start correctly
d_hydro.exe x64 visual studio 2013 ifort 15.0 windows 10 flex.exe byacc.exe win32
Answer (Unmark)
4/24/16 9:23 AM
Hi! To start, I am using:
Windows 10
Visual Studio Community 2013
Intel Parallel Studio XE 2015 Update 6 Fortran Composer
trunk files via Tortoise SVN (revision 6072)

I used the python script to generate the delft3d_open.sln. I initially ran the configuration Release win32. During compile, a window popped up saying that byacc.exe was unable to start correctly. Final Build output says: Build: 75 succeeded, 1 failed, 7 up-to-date, 0 skipped. The complete log is attached in this post. It tried to run all the examples using the run_all_examples.bat file, and some trial runs were looking for the x64 binaries, so I tried running that configuration too..

During compilation of the configuration Release x64, I was notified that flex.exe and byacc.exe was unable to start correctly on two different incidents during compile. Final Build output says: 67 succeeded, 2 failed, 4 up-to-date, 10 skipped. The complete log is also attached in this post. It tried to run all the examples again, and experienced the following:

flow_wave_parallel: Hydrodynamic simulation window said "Unknown option -d", and was taking too long so I Ctrl+Brk for that
fluidmud: d_hydro.exe stopped working

What can I do to fix these errors? For info, I intend to run FLOW and WAVE modules; how do these errors affect me?
Attachments: BuildLog_win32_20160424.txt (176.2k), BuildLog_x64_20160424.txt (158.5k)
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
4/29/16 11:43 AMas a reply to Marjorie Turiano.
Hi Marjorie,

Thank you for attaching the build log. That is very useful.

1. Don't use the 32bit version. The 64bit version is the standard one.
2. You have two compilation problems:
2.a. Related to flex/byacc: Most probably you try to compile the source code on your C-drive and you don't have permission to (have the compilation process) create directory "c:\tmp" (for you). Can you try creating that directory manually? If you have created it (possibly with help of an administrator of your system), this error will disappear. An alternative solution will be to compile the source code on your D-drive (assuming you do have the permission to create directory "d:\tmp"). flex/byacc is only used to build the tool named "vs". You will most probably not need it. So you can also ignore this error.
2.b. Related to compiling the library named delftio: The error message is (see line 660 in your build log):
"37>ifort: error #10036: unable to run 'C:\PROGRA~2\Intel\COMPOS~1\bin\intel64\fortcom'"
This error is generated by the Intel compiler itself. Googling did not give any solution, see for example this post. The only thing that might solve this is to re-install the Intel compiler.
But the funny thing is that all main programs seems to be build without errors. That surprises me, given the problems related to delftio. I suggest to ignore this error, as long as the resulting programs run normally.
3. flow_wave_parallel: You have to execute "smpd -install", as an administrator(!), on your system once, to start the mpich deamon (needed for parallel runs only). Please follow the instructions at the top of file "...\examples\01_standard\run_flow2d3d_parallel.bat" as precise as possible.
Before starting a coupled FLOW - WAVE calculation, you must remove all temporary/intermediate files from the run directory, created on previous trials.
4. Fluidmud: If you do not intent to use this functionality, you can ignore this testcase

Regards,

Adri
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
5/18/16 10:05 AMas a reply to Adri Mourits.
Hi! I'm sorry it took a while for me to give feedback. Thank you for your responses; they are very helpful. I have further comments though:

1. 64bit version as standard is noted. When I installed the Delft3D GUI, the default folder I found in the install directory (C:\Deltares\delft3d_ohmw_4.01.01.rc.03) is win32, so I initially thought I must copy win32 files. Also, the ohmw install guide said:
"Download the source code of Delft3D-FLOWand D-Water Quality form https://svn.oss.deltares.nl/repos/delft3d/trunk. Generated the executables of Delft3D-FLOW and D-Water Quality and copy the directory <...\bin\win32> (generated when compiling the open source) and his contents to the directory <c:\Deltares\Delft3D_4.01.01.rc.03\win32>. A more precise description is given on http://oss.deltares.nl/web/delft3d/source-code."

Do I copy the files from the win64 folder (in directory I use in compiling) into the win32 folder (in the directory of Delft installation), or do I create a win64 folder within the Delft installation directory?

2.a. I am using my personal laptop, so I really do not have administrator issues. I observed that the process was able to create the C:\tmp folder by itself. I was still bothered by the error notification that comes up during compile, so after more googling, I found this: http://www.techcrises.com/how-to/how-to-fix-error-code-0xc000007b-in-windows-7-8-8-1/

I followed the instructions for fixing compatibility issue between system and application. I noticed that when I compiled again, I am already prompted to allow flex.exe and byacc.exe to run. However, somewhere during the process of compile, flex.exe and byacc.exe fails to run again. I observed the memory consumed by my computer during compile, and noticed that the flex and byacc apps consumes a lot of memory, and when memory is very low, I am prompted to close Visual Studio (but I just ignore this). I think my computer force stops the flex and byacc applications due to low memory. But I have 8Gb RAM, which I thought is quite decent...

2.b. I reinstalled the Intel Parallel Studio Fortran Composer before, but the errors were still there. I tried to fix compatibility issues for fortcom.exe, as in what I did for the flex and byacc apps, and noticed that errors regarding this are not showing anymore.

3. Following the instructions in "...\examples\01_standard\run_flow2d3d_parallel.bat" solved it.

4. Fluidmud still does not work. But I don't think I need this because I'm dealing with morphology for non-cohesive sediments.

I am attaching the build logs of my latest compile session.

To summarize, I believe errors in during my compile are primarily due to compatibility issues, and possibly inadequate memory. But the example test cases for features I need are working, so I believe this is okay.

Thanks a lot!


Sincerely,
Marjorie
Attachments: BuildLog_win32_20160518.txt (50.3k), BuildLog_x64_20160518.txt (62.9k)
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
5/27/16 1:34 PMas a reply to Marjorie Turiano.
Hi Marjorie,

Thanks for your feedback. We will improve the text in the installation guide.

You should copy on top of win32, overwriting already existing files. Even if you compiled 64bit.

Looking at your build log, the problem is indeed not related to the "tmp" directory. But still something goes wrong related to flex/byacc. They are small programs and should not use a lot of memory/disc space/cpu. 8Gb should be more than enough. You better forget about this problem; you won't need the tool named "vs".

Regards,

Adri
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
2/21/17 2:41 AMas a reply to Marjorie Turiano.
I met the same error. But the error code was 0x0000142.
Have you solved the problem?


Thinkpad T440 windows10
VS2010
Intel Fortran 2012 update 1
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
2/25/17 9:39 AMas a reply to Adri Mourits.
Hi, could you help me to solve the problem?
I'm going to be crazy!

Firstly, I use a lenovo laptop to compile :
Windows 10, visual studio 2010, Intel Fortran compiler 2013 update 4. The Delft 3D source code version tag is 6906.I found there were hundreds of processes named flex.exe, and these processes use up all the 8GB memory.Then a dialog shown that flex.exe was unable to start correctly. And so did the application of byacc.exe. Sometimes the memory using up led to blue screen.Blue screen code was WATCHDOG VIOLATION. And the blue screen never appeared after I use cmd.exe to complie. Such as:
"c:\Program Files (x86)\Microsoft Visual Studio 10.0\Common7\IDE\devenv.exe" /Build "Release|x64" "D:\software\delft3DSC\6906\src\delft3d_open.sln" /out "d:\software\buildlog2.log"
The result was "sucess 72,failed 1 ,skipped 9". And log shows "c1 : fatal error C1083: Cannot open the source file:“src\vs_l.c”: No such file or directory"


Secondly, I tried on another computer: win 10, 16GB Ram, vs 2015 community update 3, Intel parallel studio xe 2016, Delft source code tag 6906. I met the same dialogs. And system shown that the RAM was using up.
I don't know how to fix the problem.

Thank you!
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
3/15/17 5:56 PMas a reply to Nautilus Chan.
Hi Nautilus,

The easiest workaround is to remove the following map from the VS sln file:
tools_gpl -> vs

vs is the only project using Lex/Yacc and you probably will not use it.

Regards,

Adri
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
4/13/17 1:14 AMas a reply to Adri Mourits.
Hi Adri,

I started with VS 2015 and Intel Fortran 2017 compiler. Then tried VS2015 with Intel 2016. Now I am down to VS 2013 with Intel 2013 and I still had the flex.exe didn't start properly error. I followed your instructions to remove the vs mapping from the build which takes it further but then always comes up with these errors near the end of the build. I have attached the output and the errors. I manually tried copying the dlls to waq\bin folder from ia32 compiler, it still kept giving that error after trying to rebuild.

Any help is appreciated.

Thanks,
Ruban
Attachment

Attachments: Output-Build.txt (223.4k), errolist.PNG (70.7k)
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
flex.exe byacc.exe
Answer (Unmark)
4/13/17 8:44 AMas a reply to Nautilus Chan.
Hi,

Try to fix compatibility settings between your system and the flex and byacc applications; follow Method 4 from this link: how to fix compatibility issues. Also check the "Run this program as an administrator" so it will no longer need to prompt you in the middle of compile.

Reading through my older post above, I also did this fix with the intel fortcom.exe application. Make sure to keep copies of original application files, just in case.

Hope this helps.


Sincerely,
Marjorie
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
4/17/17 8:41 PMas a reply to Marjorie Turiano.
Hi Marjorie,

Thanks for the reply. I have done what you suggested but same errors. I am on a Windows 10 machine. Should I be setting the to in Windows 7 or older environment? Also any recommendation on which VS version and Fortran version to use?

Thanks,
Ruban
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
windows flex.exe byacc.exe
Answer (Unmark)
4/18/17 10:48 AMas a reply to Ruban Sivarasa.
Hi,

I cannot make recommendations on what tools are best. But when I compiled the Delft3D source code I used Visual Studio Community 2013 and Intel Parallel Studio XE 2015 Update 6 Fortran Composer.

Under compatibility tab, you may "Run compatibility troubleshooter" for your system to choose what setting may be compatible with your application. In my case, the flex and byacc apps were set to run in compatibility mode with Windows XP.


Regards,
Marjorie
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
4/18/17 8:13 PMas a reply to Marjorie Turiano.
OK great. I will give this another try with your setup. Do you know which revision you downloaded from Deltares? I was currently trying to build revision 6686.

Thanks for your help.

Regards,
Ruban
RE: Compiling on Windows: flex.exe and byacc.exe was unable to start correc
Answer (Unmark)
4/21/17 4:34 PMas a reply to Ruban Sivarasa.
Hi,

I suggest you try to compile the current latest tag. I compiled the source files from the trunk at the time. It was version 6072.


Regards,
Marjorie