CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > OpenFOAM Native Meshers: snappyHexMesh and Others

Parallel snappyHexMesh

Register Blogs Members List Search Today's Posts Mark Forums Read

Like Tree2Likes
  • 1 Post By chegdan
  • 1 Post By pbachant

Reply
 
LinkBack Thread Tools Display Modes
Old   July 14, 2014, 08:06
Default Parallel snappyHexMesh
  #1
Member
 
Muhammad Waqas
Join Date: Jul 2014
Posts: 53
Rep Power: 2
mwaqas is on a distinguished road
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
mwaqas is offline   Reply With Quote

Old   July 17, 2014, 03:30
Default
  #2
Member
 
matej forman
Join Date: Mar 2009
Location: Brno, Czech Republic
Posts: 91
Rep Power: 8
matejfor is on a distinguished road
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
matejfor is offline   Reply With Quote

Old   July 17, 2014, 08:23
Default
  #3
Member
 
Muhammad Waqas
Join Date: Jul 2014
Posts: 53
Rep Power: 2
mwaqas is on a distinguished road
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)
mwaqas is offline   Reply With Quote

Old   July 17, 2014, 10:54
Default
  #4
Member
 
matej forman
Join Date: Mar 2009
Location: Brno, Czech Republic
Posts: 91
Rep Power: 8
matejfor is on a distinguished road
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
matejfor is offline   Reply With Quote

Old   July 17, 2014, 14:01
Default
  #5
Member
 
Muhammad Waqas
Join Date: Jul 2014
Posts: 53
Rep Power: 2
mwaqas is on a distinguished road
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.
mwaqas is offline   Reply With Quote

Old   July 23, 2014, 08:04
Default
  #6
Member
 
matej forman
Join Date: Mar 2009
Location: Brno, Czech Republic
Posts: 91
Rep Power: 8
matejfor is on a distinguished road
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.
matejfor is offline   Reply With Quote

Old   July 23, 2014, 08:55
Default
  #7
Senior Member
 
chegdan's Avatar
 
Daniel P. Combest
Join Date: Mar 2009
Location: St. Louis, USA
Posts: 530
Rep Power: 18
chegdan will become famous soon enough
@Mwaqas

Post your case somewhere and let some people debug the setup. This will be the quickest way possible.
mwaqas likes this.
__________________
Dan

Developer, Trainer, and Support Engineer at www.engys.com
Find me on twitter @dancombest and LinkedIn
chegdan is offline   Reply With Quote

Old   August 19, 2014, 18:05
Default
  #8
Member
 
Pete Bachant
Join Date: Jun 2012
Location: NH, USA
Posts: 87
Rep Power: 4
pbachant is on a distinguished road
Sounds like you want to run

Code:
snappyHexMesh -overwrite
mwaqas likes this.
__________________
Home | Twitter | GitHub
pbachant is offline   Reply With Quote

Old   September 4, 2014, 14:39
Default
  #9
New Member
 
Khiem Pham
Join Date: Nov 2013
Posts: 23
Rep Power: 3
Bachduong is on a distinguished road
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",
Quote:
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!
Bachduong is offline   Reply With Quote

Old   September 5, 2014, 03:41
Default
  #10
Member
 
matej forman
Join Date: Mar 2009
Location: Brno, Czech Republic
Posts: 91
Rep Power: 8
matejfor is on a distinguished road
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
matejfor is offline   Reply With Quote

Old   September 5, 2014, 06:37
Default
  #11
New Member
 
Khiem Pham
Join Date: Nov 2013
Posts: 23
Rep Power: 3
Bachduong is on a distinguished road
Quote:
Originally Posted by matejfor View Post
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
Quote:
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / 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).
Bachduong is offline   Reply With Quote

Reply

Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
SnappyHexMesh in Parallel problem swifty OpenFOAM Meshing & Mesh Conversion 5 February 24, 2015 09:31
snappyHexMesh in parallel shailesh.nitk OpenFOAM Native Meshers: snappyHexMesh and Others 18 January 6, 2014 07:13
simpleFoam parallel AndrewMortimer OpenFOAM Running, Solving & CFD 10 November 12, 2013 18:03
SnappyHexMesh OF-1.6-ext crashes on a parallel run norman1981 OpenFOAM Bugs 5 December 7, 2011 13:48
Parallel mesh generation using snappyHexMesh aki_yafuji OpenFOAM Mesh Utilities 0 December 25, 2010 04:49


All times are GMT -4. The time now is 07:54.