segmentation fault - parallel running
I'm new in these things so i'm trying to do the tutorial "Green Water" as a introduction to VOF but when i try to do the parallel running i got a segmentation error as soon as i execute setFields in the Terminal
The message error is this: cristina@cristina-HP-Pavilion-g6-Notebook-PC:~/OpenFOAM/cristina-2.2.2/run/greenWater$ setFields /*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.2.2 | | \\ / A nd | Web: www.OpenFOAM.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 2.2.2-9240f8b967db Exec : setFields Date : Mar 23 2015 Time : 16:48:02 Host : "cristina-HP-Pavilion-g6-Notebook-PC" PID : 3973 Case : /home/cristina/OpenFOAM/cristina-2.2.2/run/greenWater nProcs : 1 sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 Reading setFieldsDict Setting field default values Setting internal values of volScalarField alpha1 #0 Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam222/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" #1 Foam::sigSegv::sigHandler(int) in "/opt/openfoam222/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" #2 in "/lib/x86_64-linux-gnu/libc.so.6" #3 Foam::tmp<Foam::Field<double> > Foam::fvPatch::patchInternalField<double>(Foam::UL ist<double> const&) const in "/opt/openfoam222/platforms/linux64GccDPOpt/bin/setFields" #4 Foam::zeroGradientFvPatchField<double>::zeroGradie ntFvPatchField(Foam::fvPatch const&, Foam::DimensionedField<double, Foam::volMesh> const&, Foam::dictionary const&) in "/opt/openfoam222/platforms/linux64GccDPOpt/lib/libfiniteVolume.so" #5 Foam::fvPatchField<double>::adddictionaryConstruct orToTable<Foam::zeroGradientFvPatchField<double> >::New(Foam::fvPatch const&, Foam::DimensionedField<double, Foam::volMesh> const&, Foam::dictionary const&) in "/opt/openfoam222/platforms/linux64GccDPOpt/lib/libfiniteVolume.so" #6 Foam::fvPatchField<double>::New(Foam::fvPatch const&, Foam::DimensionedField<double, Foam::volMesh> const&, Foam::dictionary const&) in "/opt/openfoam222/platforms/linux64GccDPOpt/bin/setFields" #7 Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::GeometricBoundaryField::readField( Foam::DimensionedField<double, Foam::volMesh> const&, Foam::dictionary const&) in "/opt/openfoam222/platforms/linux64GccDPOpt/bin/setFields" #8 Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::readFields(Foam::dictionary const&) in "/opt/openfoam222/platforms/linux64GccDPOpt/bin/setFields" #9 Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::readFields() in "/opt/openfoam222/platforms/linux64GccDPOpt/bin/setFields" #10 at setFields.C:0 #11 in "/opt/openfoam222/platforms/linux64GccDPOpt/bin/setFields" #12 in "/opt/openfoam222/platforms/linux64GccDPOpt/bin/setFields" #13 in "/opt/openfoam222/platforms/linux64GccDPOpt/bin/setFields" #14 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #15 in "/opt/openfoam222/platforms/linux64GccDPOpt/bin/setFields" Falha de segmentação (imagem do núcleo gravada) |
Hi Cristina,
tell us more because it is impossible to help you without knowing a little more about your parameters. You should make an archive with some of your directories like constant, system, mesh and 0. Best regards, Laurent |
Hi Laurent
Thank you for your reply, i think that now in the file "exercicio" is there all that is needed but if i'm missing something please let me know. https://www.dropbox.com/s/dk3jf4n0jo...cicio.tar?dl=0 Cristina |
Maybe a solution
Hi Cristina,
I have tried to run the application setFields using your directories and i have obtained a segmentation fault too. But when i run first the application blockMesh, and then setFields, it runs. So try this following command : blockMesh ; setFields and tell me if it works. Have a good day. Laurent |
Hi,
Just a small comment. Your mesh (the one in tar-file) definition is broken: Code:
... So regeneration of the mesh proposed by laurentD will fix the error. But it seems you performed additional steps like refineMesh and topoSet. |
Hi,
Thank your for your answer. I did run the blockMesh and the checkMesh before and everything was ok. Then i executed refineMesh and everything was also ok so i proceed to overwrite the mesh and did all the changes that were given in the tutorial but when i try setFields a segmentation fault appeared so i did as Laurent said and it did solve the setField problem but when i did the decomposePar command to do the parallel running (it did created some processor folders) appeared this error message: Code:
-> FOAM FATAL IO ERROR: |
Hi,
Can you post the sequence of commands you have used for the case (as a simple list)? If you utilize blockMesh after refineMesh, it cancels refineMesh mesh refinements. I guess alpha1.org in the tar file is from damBreak tutorial, while patches defined in blockMeshDict have names wall1, wall2 etc. So you should create alpha1.org with correct boundary names. |
Hi,
Sure, i'm using:
|
Hi,
There is no setRefin and setExtract files in the tar file. Not quite sure I got the meaning of Quote:
|
Sorry i forgot to put it in the list (edited now).
the files i miss are here. (i'm sorry!) https://www.dropbox.com/s/1m2gs1kcva...etExtract?dl=0 https://www.dropbox.com/s/e3w6e4lknud0ahk/setRefin?dl=0 Ok, i was doing that wrong because i thought that alpha1.org hadn't to be changed and was puting the code right in the alpha1. But now i have correct it. I have redone everything checking the mesh every change i made and discoverd that the problem appear after changing the oldInternalFaces to a wall (wall5), the error message said that the startFace number wasn't correct that sould be another. Code:
Checking topology... Code:
#0 Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam222/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" |
1 Attachment(s)
Hi,
I do not know what am I doing wrong but I was not able to reproduce the error. Maybe you mess-up boundary file during editing? As I am rather lazy, to skip entering commands every time, I have create Allprepare file: Code:
#!/bin/sh 1. I use sed to rename patch 2. It turns out that subsetMesh will create oldInternalFaces patch not only in boundary file but also in all files in 0 folder, so I rename the patch there also 3. I use changeDictionary for manipulation of the dictionaries (boundary file and boundaryField dictionaries in 0 folder) Attached archive is modified case. |
Thank you, with that code the solver run without problems and i learn something very useful. :)
Yes i don't know what i did wrong with the boundary file but definelly the problem was there. I will try to do it again in order to find the error. |
Same simulation but using foam-extend
Hey guys,
I'm trying to simulate something very similar with this problem presented by Cristina. When I run the steps to refine and extract mesh everything works fine at openFoam-2.3 but when I try to run the same steps at foam-extend-3.1, it presents an error during extract. Instead of extracting, it recreates the old mesh without the extract part. Could any help me, please? I think the problem is with subsetMesh at foam-extend-3.1. |
Hi Daniel,
I used OpenFoam 2.2.2 so i'm not familiar with the ones you specified. Are you using SHM to refine and extract according to an .stl file? If so the problem could be with the point you are using to select the part of the mesh you wanna keep. Or maybe something related with wanna keep the inside/outside cells of the contour defined by the .stl (check snappyHexMeshDict). I'm not a specialist but if i were you i would check this out. Best Regards Cristina |
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