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Seg faults using scotch decomposition

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Old   August 14, 2013, 09:16
Default Seg faults using scotch decomposition
  #1
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Hi all,

I wonder if anyone has encountered the following:

If i decompose my mesh using scotch, often i get my solver throwing a seg fault fatal error at me. Occaisionally, though, the solver will run.

At the moment, i have to use simple type decomposition using a combination of zones which i have found works for the mesh.

I was wondering why scotch fails? surely the method can't "do anything funny!" such that the connectivity of the mesh gets messed up or similar problems?!

Has anyone else seen such a problem at all?

PS I want to use scotch rather than simple as it gives better balanced CPU loads etc.

many thanks for any ideas / comments in advance,
best regards
jonathan

Log
Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.1.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.1.1-221db2718bbb
Exec   : SRFSimpleFoam -parallel
Date   : Aug 14 2013
Time   : 15:07:31
Host   : "bergh01"
PID    : 23201
Case   : /media/data/temp1-meshing/ICEM/mesh_4/openFoam/3005144_mapFields_test2
nProcs : 8
Slaves : 
7
(
"bergh01.23202"
"bergh01.23203"
"bergh01.23204"
"bergh01.23205"
"bergh01.23206"
"bergh01.23207"
"bergh01.23208"
)

Pstream initialized with:
    floatTransfer     : 0
    nProcsSimpleSum   : 0
    commsType         : nonBlocking
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

[6] #0  Foam::error::printStack(Foam::Ostream&)[7] #0  Foam::error::printStack(Foam::Ostream&) in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[6] #1  Foam::sigFpe::sigHandler(int) in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[7] #1  Foam::sigSegv::sigHandler(int) in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[6] #2   in "/lib/x86_64-linux-gnu/libc.so.6"
[6] #3   in Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&)"/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[7] #2   in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[6] #4  Foam::polyBoundaryMesh::updateMesh() in "/lib/x86_64-linux-gnu/libc.so.6"
[7] #3  Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&) in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[6] #5  Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[6] #6  Foam::fvMesh::fvMesh(Foam::IOobject const&) in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[7] #4  Foam::polyBoundaryMesh::updateMesh() in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[7] #5  Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[7] #6  Foam::fvMesh::fvMesh(Foam::IOobject const&) in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
[7] #7   in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
[6] #7  

[7]  in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/bin/SRFSimpleFoam"
[7] #8  __libc_start_main[6]  in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/bin/SRFSimpleFoam"
[6] #8  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
[7] #9   in "/lib/x86_64-linux-gnu/libc.so.6"
[6] #9  

[7]  in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/bin/SRFSimpleFoam"
[bergh01:23208] *** Process received signal ***
[bergh01:23208] Signal: Segmentation fault (11)
[bergh01:23208] Signal code:  (-6)
[bergh01:23208] Failing at address: 0x3e800005aa8
[bergh01:23208] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f403b0bc4a0]
[bergh01:23208] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f403b0bc425]
[bergh01:23208] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f403b0bc4a0]
[bergh01:23208] [ 3] /home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam18processorPolyPatch10updateMeshERNS_14PstreamBuffersE+0x251) [0x7f403c1514d1]
[bergh01:23208] [ 4] /home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x1a9) [0x7f403c155449]
[bergh01:23208] [ 5] /home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam8polyMeshC2ERKNS_8IOobjectE+0xd61) [0x7f403c1a19b1]
[bergh01:23208] [ 6] /home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam6fvMeshC1ERKNS_8IOobjectE+0x19) [0x7f403cea09a9]
[bergh01:23208] [ 7] SRFSimpleFoam() [0x416623]
[bergh01:23208] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f403b0a776d]
[bergh01:23208] [ 9] SRFSimpleFoam() [0x41951d]
[bergh01:23208] *** End of error message ***
[6]  in "/home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/bin/SRFSimpleFoam"
[bergh01:23207] *** Process received signal ***
[bergh01:23207] Signal: Floating point exception (8)
[bergh01:23207] Signal code:  (-6)
[bergh01:23207] Failing at address: 0x3e800005aa7
[bergh01:23207] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7fc1ec9b44a0]
[bergh01:23207] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7fc1ec9b4425]
[bergh01:23207] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7fc1ec9b44a0]
[bergh01:23207] [ 3] /home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam18processorPolyPatch10updateMeshERNS_14PstreamBuffersE+0x243) [0x7fc1eda494c3]
[bergh01:23207] [ 4] /home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x1a9) [0x7fc1eda4d449]
[bergh01:23207] [ 5] /home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam8polyMeshC2ERKNS_8IOobjectE+0xd61) [0x7fc1eda999b1]
[bergh01:23207] [ 6] /home/jonathan/OpenFOAM/OpenFOAM-2.1.1/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam6fvMeshC1ERKNS_8IOobjectE+0x19) [0x7fc1ee7989a9]
[bergh01:23207] [ 7] SRFSimpleFoam() [0x416623]
[bergh01:23207] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fc1ec99f76d]
[bergh01:23207] [ 9] SRFSimpleFoam() [0x41951d]
[bergh01:23207] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 7 with PID 23208 on node bergh01 exited on signal 11 (Segmentation fault).
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Old   August 14, 2013, 13:16
Default fixed
  #2
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ok, for any interested others ...

seem to have fixed it - if you use the preservePatches keyword in your decomposeParDict and list your cyclic patches, you seem to not get this problem ...
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