[mwaqas]

Hi everyone

I am using snappyHexMesh for my geometry (simple cylinder). when I run my program in parallel, I get meshed geometry. but when I try to use simple (not parallel), I get only background mesh (not cylinder). It means my case is ok, may be I am writing wrong command in terminal widows. I write following commands.

1) blockMesh
2) surfaceFeatureExtract
3) snappyHexMesh

Can you please tell me, all these commands are fine or not. Thank you

[matejfor]

all these commands are OK. Can you post the output of the commands which do not work? which version of OF are you using? More info = better chance to get answer which helps you.

matej

[mwaqas]

OF is 2.3.0 Ubuntu 13.10
All these commands are working properly, I dont get any error. But when I open Paraview I get only background Mesh (cube). I dont get my geometry (cylinder).
But for some case (without any change in snappyHexMeshdict, blockMeschdict and stl.), when I run in parallel I get my geometry (cylinder)

[matejfor]

Hmmm... I'm just wondering. Running the case in paralel means, you do the snappyHexMesh with mpirun and then do the reconstrutParMesh ?

Are you writting intermediate mesh (you set it in snappyHexMesh) or you overwrite the mesh into 0 direcotory?

Your new mesh is where? in constant directory, in 0 direcotry or in 1 or 2 direcotry?
Still hard to say where the problem is.

Matej

[mwaqas]

Yes I am running snappyHexMesh with mpirun and then do the reconstrutParMesh.
I am not writing any intermediate Mesh.
And my new mesh is constant directory.

[matejfor]

hmmmm... and if you would write some intermediate meshes, would you have them in serial as well as in parallel case?

It is just very strange problem or I am missing something.

[chegdan]

@Mwaqas

Post your case somewhere and let some people debug the setup. This will be the quickest way possible.

[pbachant]

Sounds like you want to run

snappyHexMesh -overwrite

[Bachduong]

Hi guys.
My OF is 2.3.0 and Ubuntu 14.04.
I try to run tutorial https://www.hpc.ntnu.no/display/hpc/...l+Calculations (2d airfoil), but i have a problem when i write command "surfaceFeatureExtract",

bachduong@bachduong-desktop:~/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh$ surfaceFeatureExtract
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.3.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.3.0-f5222ca19ce6
Exec : surfaceFeatureExtract
Date : Sep 04 2014
Time : 22:36:56
Host : "bachduong-desktop"
PID : 11333
Case : /home/bachduong/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh
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

Reading surfaceFeatureExtractDict



--> FOAM FATAL IO ERROR:
cannot open file

file: /home/bachduong/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh/system/surfaceFeatureExtractDict at line 0.

From function regIOobject::readStream()
in file db/regIOobject/regIOobjectRead.C at line 87.

FOAM exiting

What's wrong?
Thanks!

[matejfor]

Hi,
there is nothing wrong, only oportunity for you start reading the error messages the FOAM is spitting out. For example in your case, it writes:

cannot open file

file: /home/bachduong/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh/system/surfaceFeatureExtractDict at line 0.

meaning it needs the file surfaceFeatureExtractDict, where you specify the parameters (which surface and what angle of triangles it should read as feature and which to ignore)
you will find plenty examples among tutorials.

good luck
matej

[Bachduong]

Originally Posted by matejfor

Hi,
there is nothing wrong, only oportunity for you start reading the error messages the FOAM is spitting out. For example in your case, it writes:

cannot open file

file: /home/bachduong/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh/system/surfaceFeatureExtractDict at line 0.

meaning it needs the file surfaceFeatureExtractDict, where you specify the parameters (which surface and what angle of triangles it should read as feature and which to ignore)
you will find plenty examples among tutorials.

good luck
matej

Thank you for fast reply, i add file surfaceFeatureExtractDict. Do you have some files (i.e constant, system..) for this case? Perhaps i used incorrect files because while i type "mpirun -np 2 snappyHexMesh -overwrite -parallel", i get some errors

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.3.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.3.0-f5222ca19ce6
Exec : snappyHexMesh -overwrite -parallel
Date : Sep 05 2014
Time : 14:36:33
Host : "bachduong-desktop"
PID : 3989
Case : /home/bachduong/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh
nProcs : 2
Slaves : 1("bachduong-desktop.3990")
Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
polling iterations : 0
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

Read mesh in = 0.01 s

Overall mesh bounding box : (-1.2 -2.2 -0.1) (5 2.2 0.1)
Relative tolerance : 1e-06
Absolute matching distance : 7.60526e-06

Reading refinement surfaces.
Read refinement surfaces in = 0.01 s

Reading refinement shells.
Refinement level 2 for all cells inside refinementBox
Read refinement shells in = 0 s

Setting refinement level of surface to be consistent with shells.
Checked shell refinement in = 0 s

Reading features.
Read features in = 0 s


Determining initial surface intersections
-----------------------------------------

[1] hexRef8 : Dumping cell as obj to "/home/bachduong/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh/processor1/cell_7.obj"
[0] hexRef8 : Dumping cell as obj to "/home/bachduong/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh/processor0/cell_372.obj"
[1] hexRef8 : Dumping cell as obj to "/home/bachduong/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh/processor1/cell_43.obj"
[0] hexRef8 : Dumping cell as obj to "/home/bachduong/OpenFOAM/bachduong-2.3.0/run/tutorials/incompressible/pimpleDyMFoam/airfoil/airfoil_snappyHexMesh/processor0/cell_408.obj"
[1]
[1]
[1] --> FOAM FATAL ERROR:
[1] Celllevel does not satisfy 2:1 constraint.
On face 15 owner cell 7 has refinement 4 neighbour cell 43 has refinement 2
[1]
[1] From function [0]
[0]
[0] --> FOAM FATAL ERROR:
[0] Celllevel does not satisfy 2:1 constraint.
On face 735 owner cell 372 has refinement 2 neighbour cell 408 has refinement 4
[0]
[0] From function hexRef8::checkRefinementLevels(const label)
[0] in file polyTopoChange/polyTopoChange/hexRef8.C at line 4908.
[0]
FOAM parallel run aborting
[0]
hexRef8::checkRefinementLevels(const label)
[1] in file polyTopoChange/polyTopoChange/hexRef8.C at line 4908.
[1]
FOAM parallel run aborting
[1]
[1] [0] #0 #0 Foam::error:rintStack(Foam::Ostream&)Foam::error :rintStack(Foam::Ostream&) at ??:?
[1] #1 Foam::error::abort() at ??:?
[0] #1 Foam::error::abort() at ??:?
[0] #2 Foam::hexRef8::checkRefinementLevels(int, Foam::List<int> const&) const at ??:?
[1] #2 Foam::hexRef8::checkRefinementLevels(int, Foam::List<int> const&) const at ??:?
[1] #3 Foam::hexRef8::hexRef8(Foam:olyMesh const&, bool) at ??:?
[0] #3 Foam::hexRef8::hexRef8(Foam:olyMesh const&, bool) at ??:?
[0] #4 Foam::meshRefinement::meshRefinement(Foam::fvMesh& , double, bool, Foam::refinementSurfaces const&, Foam::refinementFeatures const&, Foam::shellSurfaces const&) at ??:?
[1] #4 Foam::meshRefinement::meshRefinement(Foam::fvMesh& , double, bool, Foam::refinementSurfaces const&, Foam::refinementFeatures const&, Foam::shellSurfaces const&) at ??:?
[0] #5
at ??:?
[1] #5 [0] at ??:?
[0] #6 __libc_start_main
in "/lib/x86_64-linux-gnu/libc.so.6"
[0] #7
[1] at ??:?
[1] #6 __libc_start_main--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[0] at ??:?
in "/lib/x86_64-linux-gnu/libc.so.6"
[1] #7 --------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 3989 on
node bachduong-desktop exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

[himanshu28]

Originally Posted by Bachduong

Thank you for fast reply, i add file surfaceFeatureExtractDict. Do you have some files (i.e constant, system..) for this case? Perhaps i used incorrect files because while i type "mpirun -np 2 snappyHexMesh -overwrite -parallel", i get some errors

Hi,

I am getting the same error were you able to resolve your issue.

Thank you

Regards

[enginpower]

@Bachduong,
you should check your snappyHexMeshDict file because it seems the cell zone refinements are not well defined.
Based on my small experience, I can say only this.

[himanshu28]

Originally Posted by enginpower

@Bachduong,
you should check your snappyHexMeshDict file because it seems the cell zone refinements are not well defined.
Based on my small experience, I can say only this.

Hi,
Thanks for the reply.

I Figured out the problem, the issue was that I had an old mesh "Point" file copied to my poly mesh folder and I was running the snappyHexMesh with that file, Hence the error.