checkMesh and decomposePar crashes with salome IDEAS mesh

pajofego · June 23, 2011, 09:43

Hello at all,

I'm trying to use salome as a meshing tool for my cases. Creating meshes works well in salome. The mesh were exported in *.unv file format. After converting the ideas mesh to openfoam format via ideasUnvToFoam and typing checkMesh it crashes after a few output lines:

Code:

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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-131caa989cd3
Exec   : checkMesh
Date   : Jun 23 2011
Time   : 14:35:58
Host   : pajofego-laptop
PID    : 19513
Case   : /home/pajofego/OpenFOAM/pajofego-1.7.1/run/heat/Kugelkammer
nProcs : 1
SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create polyMesh for time = 0

Time = 0

Mesh stats
    points:           114218
    faces:            1215560
    internal faces:   1162052
    cells:            594403
    boundary patches: 4
    point zones:      0
    face zones:       1
    cell zones:       1

Overall number of cells of each type:
    hexahedra:     0
    prisms:        0
    wedges:        0
    pyramids:      0
    tet wedges:    0
    tetrahedra:    594403
    polyhedra:     0

Checking topology...
    Boundary definition OK.
#0  Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam171/lib/linuxGccDPOpt/libOpenFOAM.so"
#1  Foam::sigSegv::sigSegvHandler(int) in "/opt/openfoam171/lib/linuxGccDPOpt/libOpenFOAM.so"
#2  Uninterpreted: 
#3  Foam::faceZone::checkParallelSync(bool) const in "/opt/openfoam171/lib/linuxGccDPOpt/libOpenFOAM.so"
#4  
 in "/opt/openfoam171/applications/bin/linuxGccDPOpt/checkMesh"
#5  
 in "/opt/openfoam171/applications/bin/linuxGccDPOpt/checkMesh"
#6  __libc_start_main in "/lib/tls/i686/cmov/libc.so.6"
#7  
 in "/opt/openfoam171/applications/bin/linuxGccDPOpt/checkMesh"
Speicherzugriffsfehler

But the case runs well with simpleFoam or with another solver...! The same problem occurs with the command decomposePar:

Code:

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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-131caa989cd3
Exec   : decomposePar
Date   : Jun 23 2011
Time   : 14:38:14
Host   : pajofego-laptop
PID    : 19535
Case   : /home/pajofego/OpenFOAM/pajofego-1.7.1/run/heat/Kugelkammer
nProcs : 1
SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Time = 0
Create mesh

Calculating distribution of cells
Selecting decompositionMethod scotch

Finished decomposition in 11.23 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Calculating processor boundary addressing

Distributing points to processors

Constructing processor meshes
*** glibc detected *** decomposePar: malloc(): memory corruption: 0x0c8d1f00 ***
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6(+0x6b591)[0x36f591]
/lib/tls/i686/cmov/libc.so.6(+0x6e395)[0x372395]
/lib/tls/i686/cmov/libc.so.6(__libc_malloc+0x5c)[0x373f9c]
/usr/lib/libstdc++.so.6(_Znwj+0x27)[0x866c07]
/usr/lib/libstdc++.so.6(_Znaj+0x1d)[0x866d3d]
/opt/openfoam171/lib/linuxGccDPOpt/libOpenFOAM.so(_ZN4Foam5error10printStackERNS_7OstreamE+0x81)[0x911ba21]
/opt/openfoam171/lib/linuxGccDPOpt/libOpenFOAM.so(_ZN4Foam7sigSegv14sigSegvHandlerEi+0x55)[0x9112495]
[0xa32400]
decomposePar[0x814ca71]
decomposePar[0x809389e]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6)[0x31abd6]
decomposePar[0x808e0b1]
======= Memory map: ========
00110000-00126000 r-xp 00000000 08:01 794780     /opt/openfoam171/lib/linuxGccDPOpt/liblagrangian.so
00126000-00127000 ---p 00016000 08:01 794780     /opt/openfoam171/lib/linuxGccDPOpt/liblagrangian.so
00127000-00128000 r--p 00016000 08:01 794780     /opt/openfoam171/lib/linuxGccDPOpt/liblagrangian.so
00128000-00129000 rw-p 00017000 08:01 794780     /opt/openfoam171/lib/linuxGccDPOpt/liblagrangian.so
00129000-001c4000 r-xp 00000000 08:01 794798     /opt/openfoam171/lib/linuxGccDPOpt/libgenericPatchFields.so
001c4000-001c5000 ---p 0009b000 08:01 794798     /opt/openfoam171/lib/linuxGccDPOpt/libgenericPatchFields.so
001c5000-001c7000 r--p 0009b000 08:01 794798     /opt/openfoam171/lib/linuxGccDPOpt/libgenericPatchFields.so
001c7000-001c8000 rw-p 0009d000 08:01 794798     /opt/openfoam171/lib/linuxGccDPOpt/libgenericPatchFields.so
001c8000-001ec000 r-xp 00000000 08:01 5898464    /lib/tls/i686/cmov/libm-2.11.1.so
001ec000-001ed000 r--p 00023000 08:01 5898464    /lib/tls/i686/cmov/libm-2.11.1.so
001ed000-001ee000 rw-p 00024000 08:01 5898464    /lib/tls/i686/cmov/libm-2.11.1.so
001ee000-0020b000 r-xp 00000000 08:01 5767251    /lib/libgcc_s.so.1
0020b000-0020c000 r--p 0001c000 08:01 5767251    /lib/libgcc_s.so.1
0020c000-0020d000 rw-p 0001d000 08:01 5767251    /lib/libgcc_s.so.1
0020d000-00215000 r-xp 00000000 08:01 794749     /opt/openfoam171/lib/linuxGccDPOpt/openmpi-system/libPstream.so
00215000-00216000 r--p 00007000 08:01 794749     /opt/openfoam171/lib/linuxGccDPOpt/openmpi-system/libPstream.so
00216000-00217000 rw-p 00008000 08:01 794749     /opt/openfoam171/lib/linuxGccDPOpt/openmpi-system/libPstream.so
00217000-00284000 r-xp 00000000 08:01 794788     /opt/openfoam171/lib/linuxGccDPOpt/libtriSurface.so
00284000-00285000 r--p 0006c000 08:01 794788     /opt/openfoam171/lib/linuxGccDPOpt/libtriSurface.so
00285000-00286000 rw-p 0006d000 08:01 794788     /opt/openfoam171/lib/linuxGccDPOpt/libtriSurface.so
00286000-00291000 r-xp 00000000 08:01 794769     /opt/openfoam171/lib/linuxGccDPOpt/libscotchDecomp.so
00291000-00292000 r--p 0000a000 08:01 794769     /opt/openfoam171/lib/linuxGccDPOpt/libscotchDecomp.so
00292000-00293000 rw-p 0000b000 08:01 794769     /opt/openfoam171/lib/linuxGccDPOpt/libscotchDecomp.so
00293000-00297000 r-xp 00000000 08:01 794776     /opt/openfoam171/lib/linuxGccDPOpt/dummy/libmetisDecomp.so
00297000-00298000 r--p 00003000 08:01 794776     /opt/openfoam171/lib/linuxGccDPOpt/dummy/libmetisDecomp.so
00298000-00299000 rw-p 00004000 08:01 794776     /opt/openfoam171/lib/linuxGccDPOpt/dummy/libmetisDecomp.so
00299000-0029d000 r-xp 00000000 08:01 794773     /opt/openfoam171/lib/linuxGccDPOpt/dummy/libparMetisDecomp.so
0029d000-0029e000 r--p 00003000 08:01 794773     /opt/openfoam171/lib/linuxGccDPOpt/dummy/libparMetisDecomp.so
0029e000-0029f000 rw-p 00004000 08:01 794773     /opt/openfoam171/lib/linuxGccDPOpt/dummy/libparMetisDecomp.so
0029f000-002b2000 r-xp 00000000 08:01 5767366    /lib/libz.so.1.2.3.3
002b2000-002b3000 r--p 00012000 08:01 5767366    /lib/libz.so.1.2.3.3
002b3000-002b4000 rw-p 00013000 08:01 5767366    /lib/libz.so.1.2.3.3
002b4000-002c7000 r-xp 00000000 08:01 5898466    /lib/tls/i686/cmov/libnsl-2.11.1.so
002c7000-002c8000 r--p 00012000 08:01 5898466    /lib/tls/i686/cmov/libnsl-2.11.1.so
002c8000-002c9000 rw-p 00013000 08:01 5898466    /lib/tls/i686/cmov/libnsl-2.11.1.so
002c9000-002cb000 rw-p 00000000 00:00 0 
002cb000-002cd000 r-xp 00000000 08:01 5898481    /lib/tls/i686/cmov/libutil-2.11.1.so
002cd000-002ce000 r--p 00001000 08:01 5898481    /lib/tls/i686/cmov/libutil-2.11.1.so
002ce000-002cf000 rw-p 00002000 08:01 5898481    /lib/tls/i686/cmov/libutil-2.11.1.so
002cf000-002d0000 r-xp 00000000 08:01 3541205    /usr/lib/libscotcherrexit-5.1.so
002d0000-002d1000 r--p 00000000 08:01 3541205    /usr/lib/libscotcherrexit-5.1.so
002d1000-002d2000 rw-p 00001000 08:01 3541205    /usr/lib/libscotcherrexit-5.1.so
002d2000-002d3000 r-xp 00000000 08:01 3541204    /usr/lib/libscotcherr-5.1.so
002d3000-002d4000 r--p 00000000 08:01 3541204    /usr/lib/libscotcherr-5.1.so
002d4000-002d5000 rw-p 00001000 08:01 3541204    /usr/lib/libscotcherr-5.1.so
002d5000-002dc000 r-xp 00000000 08:01 5898478    /lib/tls/i686/cmov/librt-2.11.1.so
002dc000-002dd000 r--p 00006000 08:01 5898478    /lib/tls/i686/cmov/librt-2.11.1.so
002dd000-002de000 rw-p 00007000 08:01 5898478    /lib/tls/i686/cmov/librt-2.11.1.so
002de000-002e4000 r-xp 00000000 08:01 5898467    /lib/tls/i686/cmov/libnss_compat-2.11.1.so
002e4000-002e5000 r--p 00006000 08:01 5898467    /lib/tls/i686/cmov/libnss_compat-2.11.1.so
002e5000-002e6000 rw-p 00007000 08:01 5898467    /lib/tls/i686/cmov/libnss_compat-2.11.1.so
002e6000-00302000 r-xp 00000000 08:01 794757     /opt/openfoam171/lib/linuxGccDPOpt/libdecompositionMethods.so
00302000-00303000 r--p 0001b000 08:01 794757     /opt/openfoam171/lib/linuxGccDPOpt/libdecompositionMethods.so
00303000-00304000 rw-p 0001c000 08:01 794757     /opt/openfoam171/lib/linuxGccDPOpt/libdecompositionMethods.so
00304000-00457000 r-xp 00000000 08:01 5898460    /lib/tls/i686/cmov/libc-2.11.1.so
00457000-00458000 ---p 00153000 08:01 5898460    /lib/tls/i686/cmov/libc-2.11.1.so
00458000-0045a000 r--p 00153000 08:01 5898460    /lib/tls/i686/cmov/libc-2.11.1.so
0045a000-0045b000 rw-p 00155000 08:01 5898460    /lib/tls/i686/cmov/libc-2.11.1.so
0045b000-0045e000 rw-p 00000000 00:00 0 
0045e000-004a0000 r-xp 00000000 08:01 6167050    /usr/lib/openmpi/lib/libopen-rte.so.0.0.0
004a0000-004a1000 r--p 00041000 08:01 6167050    /usr/lib/openmpi/lib/libopen-rte.so.0.0.0
004a1000-004a3000 rw-p 00042000 08:01 6167050    /usr/lib/openmpi/lib/libopen-rte.so.0.0.0
004a3000-004a4000 rw-p 00000000 00:00 0 
004a5000-006e1000 r-xp 00000000 08:01 794783     /opt/openfoam171/lib/linuxGccDPOpt/libmeshTools.so
006e1000-006e2000 ---p 0023c000 08:01 794783     /opt/openfoam171/lib/linuxGccDPOpt/libmeshTools.so
006e2000-006e5000 r--p 0023c000 08:01 794783     /opt/openfoam171/lib/linuxGccDPOpt/libmeshTools.so
006e5000-006e7000 rw-p 0023f000 08:01 794783     /opt/openfoam171/lib/linuxGccDPOpt/libmeshTools.soAbgebrochen

Maybe this is a bug?!?

In salome I used the netgen 1-2-3 D with other algorithms including a boundary prism layer the conversion to openfoam as also starting a simulation with e.x. simpleFoam crashes.

My question is, did anyone know if there are some limitations with the conversion capability of the ideasUnvToFoam tool with the actual salome version 6.3.0?

Thanks in advance.
pajofego