[pct]

Good morning everybody,

i'm not sure if this is actually a bug or just an unfortunate effect of different wrong settings or a bad mesh, but since it's not a regular OF-error but a memory-corruption i'll post it here.

i'm currently doing my diploma-thesis at university, which includes working with OpenFoam. (v. 2.2.x)
From one of my predecessors working on the project i have a basic case for mesh generation, including several *.stl-files for the geometry, which resembles a turbine-cascade. The problem occurs while processing the outlet.stl and looks like this:

*** glibc detected *** snappyHexMesh: malloc(): memory corruption: 0x0000000006051b50 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x76518)[0x7f6bf117e518]
/lib64/libc.so.6(+0x794cf)[0x7f6bf11814cf]
/lib64/libc.so.6(__libc_malloc+0x77)[0x7f6bf11835a7]
/usr/lib64/libstdc++.so.6(_Znwm+0x1d)[0x7f6bf175259d]
/usr/lib64/libstdc++.so.6(_Znam+0x9)[0x7f6bf17526b9]
/usr/local/share/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64IccDPOpt/lib/libautoMesh.so(_ZN4Foam9syncTools13syncPointListINS_6VectorIdEENS_13minMagSqrEqOpIS3_EENS_13mapDistribute9transformEEEvRKNS_8polyMeshERKNS_4ListIiEERNSB_IT_EERKT0_RKSF_RKT1_+0x154)[0x7f6bf29f06b4]
/usr/local/share/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64IccDPOpt/lib/libautoMesh.so(_ZNK4Foam14autoSnapDriver25calcNearestSurfaceFeatureERKNS_14snapParametersEiddRKNS_5FieldIdEERKNS4_INS_6VectorIdEEEERNS_14motionSmootherE+0xc47)[0x7f6bf2a0afb7]
/usr/local/share/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64IccDPOpt/lib/libautoMesh.so(_ZN4Foam14autoSnapDriver6doSnapERKNS_10dictionaryES3_dRKNS_14snapParametersE+0xcba)[0x7f6bf29e2bca]
snappyHexMesh[0x40d237]
/lib64/libc.so.6(__libc_start_main+0xe6)[0x7f6bf1126c16]
snappyHexMesh[0x40b459]

The following memory-map is about 2 pages but i can post it, if anyone actually wants to see it.
Since i have no access to valgrind and next to zero experience with gdb i simply started digging, by searching for the provided info-strings to see where the error actually occured an traced it to:

/src/mesh/autoMesh/autoHexMesh/autoHexMeshDriver/autoSnapDriverFeature.C

the last output given was from line 2853 to 2888 (codeblock commented with "//Count")

By inserting my own Info-outputs i reached syncTools::syncPointList ( ...)

Of course by inserting said info-outputs i changed the memorymap and from a certain length of output-string onwards the whole error collapsed to:

snappyHexMesh: malloc.c:4625: _int_malloc: Assertion `(unsigned long)(size) >= (unsigned long)(nb)' failed.
Abbruch
Exitcode 134

I'm running just snappyHexMesh, no multicore/parallel-run for a decomposed-case of something like that.

Since something like that can always be the consequence of corrupted base-data:

surfaceCheck for said *.stl looks like this.

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Reading surface from "constant/triSurface/outlet.stl" ...

Statistics:
Triangles    : 18
Vertices     : 16
Bounding Box : (328.133 -10 561.695) (328.133 60 961.695)

Region  Size
------  ----
GEOM    18


Surface has no illegal triangles.

Triangle quality (equilateral=1, collapsed=0):
    0 .. 0.05  : 0
    0.05 .. 0.1  : 0
    0.1 .. 0.15  : 0
    0.15 .. 0.2  : 0.222222
    0.2 .. 0.25  : 0
    0.25 .. 0.3  : 0.555556
    0.3 .. 0.35  : 0.222222
    0.35 .. 0.4  : 0
    0.4 .. 0.45  : 0
    0.45 .. 0.5  : 0
    0.5 .. 0.55  : 0
    0.55 .. 0.6  : 0
    0.6 .. 0.65  : 0
    0.65 .. 0.7  : 0
    0.7 .. 0.75  : 0
    0.75 .. 0.8  : 0
    0.8 .. 0.85  : 0
    0.85 .. 0.9  : 0
    0.9 .. 0.95  : 0
    0.95 .. 1  : 0

    min 0.198651 for triangle 2
    max 0.340691 for triangle 4

Edges:
    min 21 for edge 1 points (328.133 39 841.695)(328.133 60 841.695)
    max 162.432 for edge 9 points (328.133 11 681.695)(328.133 39 841.695)

Checking for points less than 1e-6 of bounding box ((0 70 400) meter) apart.
Found 0 nearby points.

Surface is not closed since not all edges connected to two faces:
    connected to one face : 12
    connected to >2 faces : 0
Conflicting face labels:12
Dumping conflicting face labels to "problemFaces"
Paste this into the input for surfaceSubset

Number of unconnected parts : 1

Number of zones (connected area with consistent normal) : 1


End

and checkMesh gives:

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

Create polyMesh for time = 0

Time = 0

Mesh stats
    points:           828072
    faces:            2384496
    internal faces:   2286781
    cells:            778550
    faces per cell:   5.99997
    boundary patches: 11
    point zones:      0
    face zones:       0
    cell zones:       0

Overall number of cells of each type:
    hexahedra:     778527
    prisms:        23
    wedges:        0
    pyramids:      0
    tet wedges:    0
    tetrahedra:    0
    polyhedra:     0

Checking topology...
    Boundary definition OK.
    Cell to face addressing OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces...
    Patch               Faces    Points   Surface topology                  
    top                 33850    34503    ok (non-closed singly connected)  
    endwall             33850    34503    ok (non-closed singly connected)  
    inlet               2162     2280     ok (non-closed singly connected)  
    defaultFaces        9315     9792     ok (non-closed singly connected)  
    cut.stl_GEOM        92       120      ok (non-closed singly connected)  
    cyclic1             6486     6792     ok (non-closed singly connected)  
    cyclic2             6486     6792     ok (non-closed singly connected)  
    cyclic0             2599     2736     ok (non-closed singly connected)  
    cyclic3             2599     2736     ok (non-closed singly connected)  
    cyclic4             138      168      ok (non-closed singly connected)  
    cyclic5             138      168      ok (non-closed singly connected)  

Checking geometry...
    Overall domain bounding box (-225 0 -1.421085e-14) (390.985 50 906.612)
    Mesh (non-empty, non-wedge) directions (1 1 1)
    Mesh (non-empty) directions (1 1 1)
    Boundary openness (-1.250668e-15 -8.838649e-14 8.18473e-17) OK.
    Max cell openness = 3.526904e-16 OK.
    Max aspect ratio = 7.587198 OK.
    Minimum face area = 0.3513021. Maximum face area = 38.50867.  Face area magnitudes OK.
    Min volume = 0.7637002. Max volume = 35.89391.  Total volume = 5739637.  Cell volumes OK.
    Mesh non-orthogonality Max: 43.7972 average: 7.422812
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 0.8312743 OK.
    Coupled point location match (average 1.031287e-13) OK.

Mesh OK.

End

So, can anyone help me, or give me a tip where to look next? Is this actually a bug, or should i try messing around with different refinement/precision-parameters in the snappyHexMeshDict, or is this something different alltogehter?

If more data on the used geometry or one of the Dict-files is needed, just say so, i'll post it.

Any input is appreciated... thanks in advance..

Alex