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-   -   Segmentation Fault in fluent3DMeshToFoam (https://www.cfd-online.com/Forums/openfoam-bugs/62366-segmentation-fault-fluent3dmeshtofoam.html)

cwang5 September 8, 2008 09:56

Hi, I have received the follow
 
Hi, I have received the following error message when converting fluent 3d mesh using fluent3DMeshToFoam:

Dimension of grid: 3
Number of points: 702
PointGroup: 1 start: 0 end: 701. Reading points...done.
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
Number of cells: 470
CellGroup: 2 start: 0 end: 469 type: 1
Zone: 2 name: fluid type: fluid. Reading zone data...done.
Zone: 3 name: inlet type: velocity-inlet. Reading zone data...done.
Zone: 4 name: outlet type: pressure-outlet. Reading zone data...done.
Zone: 5 name: floorceiling type: symmetry. Reading zone data...done.
Zone: 6 name: sidewall type: symmetry. Reading zone data...done.
Zone: 7 name: wall type: wall. Reading zone data...done.
Zone: 9 name: default-interior type: interior. Reading zone data...done.

FINISHED LEXING

--> FOAM Warning :
From function boundBox::boundBox(const pointField& points)
in file meshes/boundBox/boundBox.C at line 52
Cannot find bounding box for zero sized pointField, returning zero
Creating cellZone 0 name: fluid type: fluid
#0 Foam::error::printStack(Foam:http://www.cfd-online.com/OpenFOAM_D...part/proud.gifstream&) in "/home/john/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libOpenFOAM.so"
#1 Foam::sigSegv::sigSegvHandler(int) in "/home/john/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libOpenFOAM.so"
#2 Uninterpreted: [0xffffe420]
#3 Foam::polyTopoChange::getFaceOrder(int, Foam::List<int> const&, Foam::List<int> const&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const in "/home/john/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libdynamicMesh.so"
#4 Foam::polyTopoChange::compact(bool, bool, int&, Foam::List<int>&, Foam::List<int>&) in "/home/john/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libdynamicMesh.so"
#5 Foam::polyTopoChange::compactAndReorder(Foam::poly Mesh const&, bool, bool, bool, int&, Foam::Field<foam::vector<double> >&, Foam::List<int>&, Foam::List<int>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::map<int> >&, Foam::List<int>&, Foam::List<int>&, Foam::List<foam::map<int> >&) in "/home/john/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libdynamicMesh.so"
#6 Foam::polyTopoChange::changeMesh(Foam::polyMesh&, bool, bool, bool, bool) in "/home/john/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libdynamicMesh.so"
#7 main in "/home/john/OpenFOAM/OpenFOAM-1.5/applications/bin/linuxGccDPOpt/fluent3DMeshToF oam"
#8 __libc_start_main in "/lib/libc.so.6"
#9 __gxx_personality_v0 in "/home/john/OpenFOAM/OpenFOAM-1.5/applications/bin/linuxGccDPOpt/fluent3DMeshToF oam"
Segmentation fault



I tried converting the same .msh file using fluemtMeshToFoam and it worked fine. I'm wondering what might have caused it?

mattijs September 8, 2008 11:09

Can you post or send the case?
 
Can you post or send the case?

Mattijs

cwang5 September 9, 2008 04:48

Umm...how do I post the file?
 
Umm...how do I post the file?

elorriaux September 9, 2008 05:25

Hello, I'm getting the same
 
Hello,

I'm getting the same kind of error with fluent3DMeshToFoam and OF-1.5. I did not try the fluentMeshToFoam yet.

My mesh is generated with gambit-2.2.

Mattjis, i can send you an http link with my .msh, but it's quite big (more than one million cells).

Regards,

Etienne.

cwang5 September 9, 2008 05:26

oh, checked the forum document
 
oh, checked the forum documentation, here's the file.



cwang5 September 9, 2008 05:43

file's too big, can't upload i
 
file's too big, can't upload it, I'm uploading it to rapidshare, here's the link.

http://rapidshare.de/files/40430130/...id.msh.gz.html

let me know when you have received the file. Thanks

mattijs September 9, 2008 09:27

says the file does not exist w
 
says the file does not exist when I try to download it. Can you try again and send link to me? (m dot janssens at opencfd.co.uk)

mattijs September 10, 2008 08:55

Pushed a changed fluent3DMeshT
 
Pushed a changed fluent3DMeshToFoam.L to the 1.5.x git which reads your file. Let me know if it breaks anything else ;-)

cwang5 September 11, 2008 05:26

I couldn't seems to access the
 
I couldn't seems to access the git repository. The git update process is stuck at "Indexing 9605 objects... 0% (1/9605) done. Any idea how to fix that? Thanks

henry September 11, 2008 06:10

I have just pulled and pushed
 
I have just pulled and pushed and it was fine. It looks like you have an unreliable connection, could you try again later?

H

cwang5 September 11, 2008 06:52

humm...well, it never worked f
 
humm...well, it never worked for me, I've tried updating it for a while, and was always stuck at the git clone step.

ameya September 16, 2008 08:50

Have you examined the mesh in
 
Have you examined the mesh in gambit or fluent before exporing it to OpenFOAM? May be you hav some highly skewed elements.

I recoomend you not only peform grid check but also use hexahedral mesh as far as pssible

r2d2 November 19, 2008 04:27

Hi, I got the same sequence of
 
Hi, I got the same sequence of errors when using fluent3DMeshToFoam when using OF1.5 but it all went smooth with the OF1.4.1. Did anything change in-between, some lib somewhere?
Just for the record, if it helps:

In 1.5 it says:
Create time

Dimension of grid: 3
Number of points: 119966
PointGroup: 1 start: 0 end: 119965. Reading points...done.
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
--> FOAM Warning : Found unknown block of type: "13"
Number of cells: 93916
CellGroup: 2 start: 0 end: 54143 type: 1
CellGroup: 3 start: 54144 end: 93915 type: 1
Zone: 2 name: fluid type: fluid. Reading zone data...done.
Zone: 3 name: gdlH2 type: solid. Reading zone data...done.
Zone: 4 name: wall type: wall. Reading zone data...done.
Zone: 5 name: outletGDLH2 type: pressure-outlet. Reading zone data...done.
Zone: 6 name: outletH2 type: pressure-outlet. Reading zone data...done.
Zone: 7 name: inletH2 type: mass-flow-inlet. Reading zone data...done.
Zone: 9 name: default-interior type: interior. Reading zone data...done.

FINISHED LEXING

--> FOAM Warning :
From function boundBox::boundBox(const pointField& points)
in file meshes/boundBox/boundBox.C at line 52
Cannot find bounding box for zero sized pointField, returning zero
Creating cellZone 0 name: fluid type: fluid
Creating cellZone 1 name: gdlH2 type: solid
#0 Foam::error::printStack(Foam:http://www.cfd-online.com/OpenFOAM_D...part/proud.gifstream&) in "/home/radu/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#1 Foam::sigSegv::sigSegvHandler(int) in "/home/radu/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#2 ?? in "/lib/libc.so.6"
#3 Foam::polyTopoChange::getFaceOrder(int, Foam::List<int> const&, Foam::List<int> const&, Foam::List<int>&, Foam::List<int>&, Foam::List<int>&) const in "/home/radu/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#4 Foam::polyTopoChange::compact(bool, bool, int&, Foam::List<int>&, Foam::List<int>&) in "/home/radu/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#5 Foam::polyTopoChange::compactAndReorder(Foam::poly Mesh const&, bool, bool, bool, int&, Foam::Field<foam::vector<double> >&, Foam::List<int>&, Foam::List<int>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::map<int> >&, Foam::List<int>&, Foam::List<int>&, Foam::List<foam::map<int> >&) in "/home/radu/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#6 Foam::polyTopoChange::changeMesh(Foam::polyMesh&, bool, bool, bool, bool) in "/home/radu/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#7 main in "/home/radu/OpenFOAM/OpenFOAM-1.5/applications/bin/linux64GccDPOpt/fluent3DMeshT oFoam"
#8 __libc_start_main in "/lib/libc.so.6"
#9 __gxx_personality_v0 in "/home/radu/OpenFOAM/OpenFOAM-1.5/applications/bin/linux64GccDPOpt/fluent3DMeshT oFoam"
Segmentation fault



...and in 1.4.1

Dimension of grid: 3
Number of points: 119966
PointGroup: 1 start: 0 end: 119965. Reading points...done.
Number of faces: 309635
FaceGroup: 4 start: 0 end: 52438. Reading mixed faces...done.
FaceGroup: 5 start: 52439 end: 62381. Reading mixed faces...done.
FaceGroup: 6 start: 62382 end: 62413. Reading mixed faces...done.
FaceGroup: 7 start: 62414 end: 62445. Reading mixed faces...done.
FaceGroup: 9 start: 62446 end: 309634. Reading mixed faces...done.
Number of cells: 93916
CellGroup: 2 start: 0 end: 54143 type: 1
CellGroup: 3 start: 54144 end: 93915 type: 1
Zone: 2 name: fluid type: fluid. Reading zone data...done.
Zone: 3 name: gdlH2 type: solid. Reading zone data...done.
Zone: 4 name: wall type: wall. Reading zone data...done.
Zone: 5 name: outletGDLH2 type: pressure-outlet. Reading zone data...done.
Zone: 6 name: outletH2 type: pressure-outlet. Reading zone data...done.
Zone: 7 name: inletH2 type: mass-flow-inlet. Reading zone data...done.
Zone: 9 name: default-interior type: interior. Reading zone data...done.

FINISHED LEXING

--> FOAM Warning :
From function boundBox::boundBox(const pointField& points)
in file meshes/boundBox/boundBox.C at line 52
cannot find bounding box for zero sized pointFieldreturning zero
Creating patch 0 for zone: 4 name: wall type: wall
Creating patch 1 for zone: 5 name: outletGDLH2 type: pressure-outlet
Creating patch 2 for zone: 6 name: outletH2 type: pressure-outlet
Creating patch 3 for zone: 7 name: inletH2 type: mass-flow-inlet
Creating cellZone 0 name: fluid type: fluid
Creating cellZone 1 name: gdlH2 type: solid
patch 0 from Fluent indices: 0 to: 52438 type: wall
patch 1 from Fluent indices: 52439 to: 62381 type: pressure-outlet
patch 2 from Fluent indices: 62382 to: 62413 type: pressure-outlet
patch 3 from Fluent indices: 62414 to: 62445 type: mass-flow-inlet

Writing mesh to "/home/radu/OpenFOAM/radu-1.4.1/run/pila3D/pila10x10/cascada/simpleFoam/constant /region0"

End

henry November 19, 2008 04:36

We have pushed a new version t
 
We have pushed a new version to the 1.5.x git repository, could you try that?

H

r2d2 November 19, 2008 05:08

Will do that, as soon as I hav
 
Will do that, as soon as I have some spare time.
Thanks anyway,
Radu

podallaire November 19, 2008 11:01

Good morning, with the new
 
Good morning,

with the new changes, fluent3DMeshToFoam does not compile for me :

fluent3DMeshToFoam.L: In function 'int main(int, char**)':
fluent3DMeshToFoam.L:932: error: expected `]' before ')' token
fluent3DMeshToFoam.L:932: error: expected `]' before ')' token
fluent3DMeshToFoam.L:933: error: expected `)' before '{' token
fluent3DMeshToFoam.L:936: error: expected primary-expression before '}' token
fluent3DMeshToFoam.L:936: error: expected `;' before '}' token
fluent3DMeshToFoam.L: At global scope:
fluent3DMeshToFoam.L:1340: error: expected unqualified-id before ']' token


Regards,

PO

henry November 19, 2008 12:43

Which version of flex are you
 
Which version of flex are you using?

H

henry November 19, 2008 13:26

I have just pushed a small cha
 
I have just pushed a small change which should keep old versions of flex happy.

H

podallaire November 19, 2008 18:20

Thanks ! I will give it a t
 
Thanks !

I will give it a try later tonight

-> flex 2.5.33

Regards,

PO

henry November 20, 2008 03:28

We are now using flex 2.5.35 w
 
We are now using flex 2.5.35 which comes with SuSE 11 and other recent Linux releases or can be downloaded and compiled from sources. There is a bug in the .skel file in version 2.3.33 (fixed in 2.5.35) which means that "]]" in the "C" code throws and error but "] ]" is OK. The fix I uploaded should solve the problem for you.

H

wassja December 3, 2008 07:50

Hi, So this means I've got t
 
Hi,
So this means I've got to check out the files with git and compile them manually? This may be hard because my linux-system doesn't have a connection to the Internet.... I'd be glad if I could download a compiled 64bit version of this new fluent3DMeshToFoam so I can convert my porous zones from fluent to OF. Otherwise I could try to use the 1.4.1 version, but I'm quite happy with 1.5 and don't know if it's possible to use fluent3DMeshToFoam in version 1.4.1 and then run in 1.5.

Regards
Wassja

lakeat March 16, 2009 02:59

Quote:

Originally Posted by mattijs (Post 208138)
Pushed a changed fluent3DMeshToFoam.L to the 1.5.x git which reads your file. Let me know if it breaks anything else ;-)

I met the same problem, and using the new fluent3DMeshToFoam.L works, Thanks

ksr March 16, 2009 03:28

3D fluent mesh
 
Dear friend,

you can do the remeshing starting from lines, areasand then volume mesh. you will get the 3d mesh only after error free 2d mesh.Try again.

martals April 13, 2011 15:37

ERROR sigsegv
 
Hello,

I am new in OpenFOAM and I´m trying to convert a 2d mesh (.msh) from Fluent to OpenFOAM usinf FluentMeshToFoam. (OF 1.7.1.)

I got the same error "SigSev" and also "Printstack".

It appears this message in OF:

hemodynamics@marioc-PowerEdge-R300:~/OpenFOAM/hemodynamics-1.7.1/run/marta/poiseuille_mesh$ fluentMeshToFoam ascii.msh
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.7.x |
| \\ / A nd | Web: www.OpenFOAM.com |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 1.7.x-3776603e4c6c
Exec : fluentMeshToFoam ascii.msh
Date : Apr 11 2011
Time : 22:45:41
Host : marioc-PowerEdge-R300
PID : 13356
Case : /home/hemodynamics/OpenFOAM/hemodynamics-1.7.1/run/marta/poiseuille_mesh
nProcs : 1
SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

number of faces: 1643
Number of points: 203
Reading uniform faces
Reading points


FINISHED LEXING


#0 Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam171/lib/linux64GccDPOpt/libOpenFOAM.so"


#1 Foam::sigSegv::sigSegvHandler(int) in "/opt/openfoam171/lib/linux64GccDPOpt/libOpenFOAM.so"

#2 in "/lib/libc.so.6"
#3
in "/opt/openfoam171/applications/bin/linux64GccDPOpt/fluentMeshToFoam"
#4 __libc_start_main in "/lib/libc.so.6"
#5
in "/opt/openfoam171/applications/bin/linux64GccDPOpt/fluentMeshToFoam"
Violación de segmento
hemodynamics@marioc-PowerEdge-R300:~/OpenFOAM/hemodynamics-1.7.1/run/marta/poiseuille_mesh$


Does anybody now what this errors mean? I don´t know how to solve them! I would appreciate any help! Thanks in advance!!


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