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Segmentation Fault in fluent3DMeshToFoam

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Old   September 8, 2008, 09:56
Default Hi, I have received the follow
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John Wang
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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:stream&) 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?
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Old   September 8, 2008, 11:09
Default Can you post or send the case?
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Mattijs Janssens
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Can you post or send the case?

Mattijs
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Old   September 9, 2008, 04:48
Default Umm...how do I post the file?
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John Wang
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Umm...how do I post the file?
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Old   September 9, 2008, 05:25
Default Hello, I'm getting the same
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Etienne Lorriaux
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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.
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Old   September 9, 2008, 05:26
Default oh, checked the forum document
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John Wang
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oh, checked the forum documentation, here's the file.


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Old   September 9, 2008, 05:43
Default file's too big, can't upload i
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John Wang
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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
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Old   September 9, 2008, 09:27
Default says the file does not exist w
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Mattijs Janssens
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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)
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Old   September 10, 2008, 08:55
Default Pushed a changed fluent3DMeshT
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Pushed a changed fluent3DMeshToFoam.L to the 1.5.x git which reads your file. Let me know if it breaks anything else ;-)
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Old   September 11, 2008, 05:26
Default I couldn't seems to access the
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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
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Old   September 11, 2008, 06:10
Default I have just pulled and pushed
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I have just pulled and pushed and it was fine. It looks like you have an unreliable connection, could you try again later?

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Old   September 11, 2008, 06:52
Default humm...well, it never worked f
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John Wang
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humm...well, it never worked for me, I've tried updating it for a while, and was always stuck at the git clone step.
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Old   September 16, 2008, 08:50
Default Have you examined the mesh in
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Ameya Durve
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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
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Old   November 19, 2008, 05:27
Default Hi, I got the same sequence of
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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:stream&) 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
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Old   November 19, 2008, 05:36
Default We have pushed a new version t
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We have pushed a new version to the 1.5.x git repository, could you try that?

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Old   November 19, 2008, 06:08
Default Will do that, as soon as I hav
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Radu Mustata
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Will do that, as soon as I have some spare time.
Thanks anyway,
Radu
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Old   November 19, 2008, 12:01
Default Good morning, with the new
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Pierre-Olivier Dallaire
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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
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Old   November 19, 2008, 13:43
Default Which version of flex are you
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Which version of flex are you using?

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Old   November 19, 2008, 14:26
Default I have just pushed a small cha
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I have just pushed a small change which should keep old versions of flex happy.

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Old   November 19, 2008, 19:20
Default Thanks ! I will give it a t
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Pierre-Olivier Dallaire
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Thanks !

I will give it a try later tonight

-> flex 2.5.33

Regards,

PO
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Old   November 20, 2008, 04:28
Default We are now using flex 2.5.35 w
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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.

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