surfaceElevation not found under OF1712
 

Hello all,

I am trying to use surfaceElevation under OF1712 (waves2Foam svn revision 2123) for postprocessing during the run. Unfortunately I run into errors. I saw this kind of problem before, but with regard to another OF version.

This is the error:

Surprisingly, the utility "surfaceElevation" is not on the system, though everything else seems to run fine. When I try to build it in OpenFOAM-v1712/applications/utilities/waves2Foam/applications/utilities/postProcessing/surfaceElevation I get this error:

The file "IOOutputFilter.H" does not exist on the system as well, so the compiler can't find it.

What am I doing wrong here? I read Niels post about setting some softlinks to get over this, but I cannot seem to figure out where, and the link to some release notes for OF1712 does not bring me to a post that I can relate to the problem.

Thank you!

Best regards,

Pascal.
--

Dear Pascal,


Make sure that recent changes to bin/bashrc (from bin/bashrc.org) are updated. I believe that I had to update some settings, because of changes to naming convention (e.g. make a diff on the two files).



Kind regards,


Niels

Dear Niels,

thank you for your reply. I did as you said, but did not find any settings related to the above problem. But I found a detail in the bin/bashrc script of waves2Foam (perhaps this might be related to the above problem...).
Beginning on line 98 in bashrc.org (OF v1712) it reads:

Unfortunately, this does not do what it is obviously meant to do, as line 98 always returns at least the string "v1712" (at least on my CentOS 6.4 machine). So OFPLUSBRANCH is always set to true, and WAVES_SOL is set accordingly to solvers1712_PLUS.
If the grep command only greps for '+', then the decision for the right branch is done correctly.
But: There is no such OF version/branch like 1712+ (as far as I could find out. There is just the v1712 of ESI, which is the PLUS branch in my understanding, correct?). In the solvers directory there is originally only a solver directory "solvers1712_PLUS", no "solvers1712".
Originally I copied the whole solvers1712_PLUS directory to solvers1712 and worked on this. Now I soft-linked solvers1712_PLUS to solvers1712, changed the grep command in bashrc, and compilation in the waves2Foam directory runs fine.

Nevertheless the surfaceElevation tool is NOT created, as the Allwmake script does not go into the respective directory! This seems deliberately, as indicated in the comment on line 164. Correct?
Delving thoroughly into the Allwmake script in waves2Foam, from line 164 it reads:

With OF version 1712 (without +) we end up in line 181. If there were a OF v1712+, we would end up in line 174. Both lines are identical. So no wonder surfaceElevation does not get created! :-)

Sorry for the verbosity, it reflects my learning curve during this investigation...

So how can I get the surface elevation at the defined probes? As far as I understand things, postProcessWaves2Foam needs the sampled probe data, which will not be sampled due to the lack of a working surfaceElevation tool and the respective library. Correct?

Thank you very much for your patience and input!

Best regards,

Pascal.

Hi Pascal,


ESI changed naming (removed '+'), which is why the grep command searches for both '+' and 'v[0-9]'. Therefore, both are considered PLUS and the scripting should be correct (at least it works on my Ubuntu 1604LTS). In summary: v1712 is a PLUS-branch in the compilation terminology.



I understand that you have changed the definition of OFPLUSBRANCH, so if you revert, it should work.


Kind regards,


Niels

Hello Niels,

ok, good to have the naming scheme change confirmed.
I don't understand where I changed the definition of OFPLUSBRANCH?

Nevertheless, the problem with the missing "IOOutputFilter.H" file will exists further, because this file simply does not exist in v1712. Could you give me a hint on how to compile surfaceElevation?

Thank you again!

Best wishes,

Pascal.

Hi Pascal,

Try to delete bin/bashrc (not! bin/bashrc.org) and compile again. If you had an old version of waves2Foam, you will face issues with compilation setting due to the name change. This is sorted by deleting bin/bashrc, which is not in the repository, but copied on first (and only first) compilation.

I hope that you will succeed.

Kind regards

Niels

Hi Niels,

I did as you said:
- deleted my adapted bin/bashrc
- reverted the solver directory back to the original state (only solver1712_PLUS existant)
- started Allwmake, which of course stopped because of the wrong path settings in the newly generated bin/bashrc.
- adapted new bin/bashrc paths to my systems configuration

I still got some errors:
- When there is no OceanWave3D-Fortran90 directory, libwaves2Foam.so is not generated, which causes more errors later on
- I put a copy of OceanWave3D-Fortran90 from a slightly earlier try into the ThirdParty directory, and things run farther now
- At some point there was the files scalarSquareMatrix.H and scalarSquareMatrixTemplates.C missing, which I copied for a try from /usr/local/foam/foam-extend-4.0/src/foam/matrices/scalarMatrices (yes, from an extend-4.0 installation!). That solved the compilation problem for now.

But still: Compilation of surfaceElevation is not done by the Allwmake script, and it fails when I do it "manually" in the $WAVE_POST directory.

Any ideas?

Thank you for your patience!

Cheers,
Pascal.
--

Hi Pascal,

Any of your many changes could have broken the installation. So:

1. Remove waves2Foam entirely.
2. Make sure that all dependencies are installed (refer to manual)
3. Make a fresh checkout
4. Compile without changing settings, etc (I recommend to try default installation directory).

This should work.

Kind regards

Niels

Hi Niels,

alright, I did exactly as you said above:
I removed every trace of waves2Foam on the system. All dependencies are installed (gfortran, git, svn). GSL is installed:
- in /usr/local/lib[64]/libgsl.so.0.16.0
- in /usr/lib[64]/libgsl.so.0.14.0 (which is the system install, but not available for distributed parallel)
Fresh checkout (revision 2124)

Then I did 4 runs of Allwmake:
0. No changes at all, even not created or touched bin/bashrc. Lots of output from compilation. For the sake of brevity and clarity, I did the second run with same settings, which leaves out the compiling messages.
1. As said above, no changes at all. Results see in attached file ..._01..., which shows many errors, mainly related to missing libOcean3D library, as far as I understand it.
2. Adapted GSL path settings to to /usr/local. Results see file ..._02.... No exciting changes though, as far as I can see.
3. Added OceanWave3D-Fortran90 directory. Results see file ...03.... This seemingly solve all problems, at least when looking at the compiler output.

BUT:
I am really sorry to bother you with this so insistently... the surfaceElevation directory in the postProcessing directory is NOT being processed by the Allwmake script.

On line 173 the script correctly branches out to process the postProcessing directory, but it does not do the same with the surfaceElevation directory:

When I add the line as indicated above in the code, compilation fails with:

The file is actually here:
/home/ofuser/OpenFOAM/ofuser-v1712/applications/utilities/waves2Foam/src/waves2FoamSampling/surfaceElevation/sampledSurfaceElevation/IOsampledSurfaceElevation.H

Where should it be located? In the SamplingNew path somewhere?

I hope this time I met your demands regarding the proper execution of the installation process...

Any more hints how to solve the surfaceElevation problem?

Thank you very much again!

Cheers, Pascal.

Hi Pascal,

Your git command does not work for some reason, which is evident from the first two log files. No compilation of OceanWave3D makes the entire compilation fail. I cannot reproduce the git-issue on Ubuntu.

Secondly, you are fine, since the runtime sampling of surface elevation tool is compiled (see compilation of libraries). Therefore you can sample runtime. I never use the postprocessing tool, which is the reason that it is not prioritised to port.

Kind regards

Niels

Hi Niels,

everything seems to be working correctly now. Actually, it seems that I somehow tricked myself into these problems... ;-)

Thank you again for your patience and advice! I hope to hear again from you on the inevitably upcoming next questions!

Best wishes,

Pascal.

Hi Pascal,

I also get problems running surfaceElevation with OpenFOAM v1712 as it seems that it does not exist on most recent versions. Did you find a solution or implement a new function to extract and integrate alpha field?

Thanks a lot,

Constance

Hi,

The surface elevation tool does work on 1712. I suppose that you face issues with an outdated bin/bash file in waves2Foam.

Kind regards

Niels

Hii Pascal,
How did you add OceanWave3D-Fortran90 directory? I've been experiencing the same issues.

Good winds, Lannes.

Latest working OF version for surfaceElavation??
 

Hi Niels

I'd like to know what is the latest version of OpenFoam in which the waves2Foam utility "surfaceElevation" can be compiled correctly? Is it OFv1712 as you mentioned earlier? I know it is not working on v1912 yet as I have tried it, but want to know the latest version I am able to use. Thank you.

Best regards
Ahmad

Latest working OF version for surfaceElavation??
 

Hi Niels

I am providing more details here on my problem. To begin, I noticed that you have updated the waves2Foam toolbox to work with OpenFOAM-v1912 on the source code history "2020-02-22 17:20:43: (r2137)". So, I installed OpenFOAM-v1912 on my Ubuntu 18.04.4 LTS. Here is the result of the foamInstallationTest command at the end of installation:



Executing /home/aeba402/OpenFOAM/OpenFOAM-v1912/bin/foamInstallationTest:


Basic setup :
-------------------------------------------------------------------------------

FATAL ERROR: OpenFOAM environment not configured.

Please follow the download and installation link in README.html:
<OpenFOAM installation dir>/OpenFOAM-v1912/README.html
for information on setting-up the OpenFOAM environment.



However, I searched on the forum and found out that it may be a negligible error. I also tested to see if OpenFOAM-v1912 is installed on my system. Here is the result of the command "blockMesh -help":



Usage: blockMesh [OPTIONS]
Options:
-blockTopology Write block edges and centres as obj files and exit
-case <dir> Specify case directory to use (instead of the cwd)
-dict <file> Alternative dictionary for the blockMesh description
-noClean Do not remove any existing polyMesh/ directory or files
-region <name> Specify alternative mesh region
-sets Write cellZones as cellSets too (for processing purposes)
-time <time> Specify a time to write mesh to (default: constant)
-doc Display documentation in browser
-help Display short help and exit
-help-compat Display compatibility options and exit
-help-full Display full help and exit

Block mesh generator.
The ordering of vertex and face labels within a block as shown below.
For the local vertex numbering in the sequence 0 to 7:
Faces 0, 1 (x-direction) are left, right.
Faces 2, 3 (y-direction) are front, back.
Faces 4, 5 (z-direction) are bottom, top.
7 ---- 6
f5 |\ |\ f3
| | 4 ---- 5 \
| 3 |--- 2 | \
| \| \| f2
f4 0 ---- 1
Y Z
\ | f0 ------ f1
\|
O--- X

Using: OpenFOAM-v1912 (1912) - visit www.openfoam.com
Build: _f3950763fe-20191219
Arch: LSB;label=32;scalar=64



So, I can say that regardless of the error, OpenFOAM is installed on my system now. Then I started installing the waves2Foam toolbox. As OpenFOAM was installed on ~/OpenFOAM/OpenFOAM-v1912 in my system, I followed the following procedure. This is similar to what I found online with some modifications.



cd $FOAM_UTILITIES

svn co http://svn.code.sf.net/p/openfoam-ex...her/waves2Foam

cd waves2Foam

rc=bin/bashrc

cp -p bin/bashrc.org $rc

sed -i 's|$WM_PROJECT_USER_DIR|$WM_PROJECT_DIR|' $rc

sed -i 's|FOAM_USER_APPBIN|FOAM_APPBIN|' $rc

sed -i 's|FOAM_USER_LIBBIN|FOAM_LIBBIN|' $rc

sed -i 's|lib64|lib|' $rc

./Allwmake > log.waves2foam

tail -f log.waves2foam

Ctrl+C at the end when I saw "Compilation Done" on my screen.



I have also attached the log.waves2foam file for your reference. In the log file, I noticed that there is nothing on the "surfaceElevation" compilation under COMPILE POST-PROCESSING section though there is already a directory named "$FOAM_UTILITIES/waves2Foam/applications/utilities/postProcessing" for that.

Following the waves2Foam installation, I can work with the toolbox but I have noticed that some commands are not detected at all and cannot be used. For example, "porousWaveFoam" and "surfaceElevation". I don't need to work with "porousWaveFoam" at the moment, but need to use "surfaceElevation". I mentioned them together as I thought they may give you a clue on where the problem is.

I installed older versions of OpenFOAM one by one from v1912 to v1606+ and Terminal could detect the "surfaceElevation" command on OpenFOAM-v1606+ after installing waves2Foam toolbox on it.

I hope this is enough information. Can you please detect where the problem lies by this information? Thank you very much for your help in advance.

Cheers
Ahmad

It is correct that the postprocessing tool surfaceElevation is not compiled for 1912. In any case, I will always recommend to use the runTime surface elevation tool, which is compiled and does work.


Kind regards


Niels

Hi Niels

Thanks very much for your reply. I got it. So, not having surfaceElevation command compiled in the toolbox is normal and I don't need to worry about it. I need to only go for the run time surface elevation and use the "postProcessingProperties" file in constant folder and then use "postProcessWaves2Foam" utility command which is compiled to get the required data.

I found a "postProcessingProperties" file in your waveFlume tutorial to use it for my case. Now, I have some questions regarding the input in the file. This is how the text inside the "postProcessingProperties" file looks like:



deleteParentOutputDirectory false;

regularSpectrum
{
callName surfaceElevation;

removeDuplicate true;
inputDir surfaceElevationAnyName;

deltaT 0.01;
tMin 10.0; // Default: minimum time
//tMax 11.0; // Default: maximum time

// The action list is a set of processes on the data
actionList ( interpolateSurfaceElevation powerSpectraLS write2Ascii removeData );

nFreq 4;
period 2.0;
allDataSets true;
}



Sorry it is clear for you but I want to make sure I also understand what you meant exactly by these and be able to tailor them for my case, so can you please explain the following?

- I saw in your porousDamBreak case that instead of "regularSpectrum" you have used "data" in the "postProcessingProperties" file. Should I always use them or can I, say, use irregularSpectrum for the post-processing of irregular waves? What is the difference between data and regularSpectrum as the names?

- What are deltaT, tMin, tMax here?

- actionList items are clear, but I don't know what "allDataSets" means. Can you please explain it? Also, "nFreq" and "period" should be related to the "power spectrum analysis based on a least-squares technique" you mentioned in the manual. I haven't used the technique, can you please let me know where was your reference for learning about the technique. I assume the one you have used should be useful as I can find all the inputs needed in the toolbox properly.

Sorry for writing too long. Thank you in advance for your help.

Best regards
Ahmad

Good that it works.

I recommend that you look into the code to answer your questions, since I have not really worked with this tool for a very long time. I do recall, however, that allDataSets allows you to specify all wave gauges without explicitly mentioning gauge indices. My general experience is that it is helpful to code some of the data processing steps yourself, so this might be a good learning experience.

The least-squares approach on the reflection decomposition is described in the appendix of our article (Jacobsen et al., 2012).

Kind regards

Niels

Hi Niels

Thanks for your reply. That was helpful. I will take a deep dive into the code and will try to code some of my data processing.

Best regards
Ahmad