View Issue Details
| ID | Project | Category | View Status | Date Submitted | Last Update |
|---|---|---|---|---|---|
| 0003587 | OpenFOAM | Bug | public | 2020-11-03 09:48 | 2020-11-06 11:21 |
| Reporter | maxdre91 | Assigned To | henry | ||
| Priority | high | Severity | crash | Reproducibility | always |
| Status | resolved | Resolution | no change required | ||
| Platform | Linux | OS | Ubuntu | OS Version | 18.04 |
| Summary | 0003587: fluent3DMeshToFoam and mergeMeshes crash with large (around 170 mio cells) meshes | ||||
| Description | During Mesh conversion from ICEM-generated .msh files (written in ASCII) i come across errors when i try to convert large meshes (around 170 mio. cells) via fluent3DMeshToFoam. As a workaround i tried to split my mesh into 3 smaller parts in order to merge them after the conversion with fluent3DMeshToFoam. For all of these 3 parts of the mesh, the conversion via fluent3DMeshToFoam is successfull and checkMeshes also provide good results. Now when i try to merge them in any possibility (1&2; 1&3; 2&3) mergeMesh crashes witht he same error output as in the fluent3DMeshToFoam of the large mesh. I attached the log-file from mergeMeshes. As you can see it was performed under OF7. As these issues only occur with large mesh sizes, i am not sure how to provide a minimum working example. Any help would be very appreciated, thanks. M. Drexelius | ||||
| Additional Information | Further info on the meshes: Total cells: 172,114,578 hexahedral cells Part 1: 8.6 GB data; 44,166,906 hexa cells; 24 boundary patches Part 2: 11.2 GB data; 57,232,114 hexa cells; 27 boundary patches Part 3: 14.0 GB data; 70,715,558 hexa cells; 27 boundary patches | ||||
| Tags | No tags attached. | ||||
|
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log_mergeMesh (8,173 bytes)
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Version: 6
\\/ M anipulation |
\*---------------------------------------------------------------------------*/
Build : 6
Exec : mergeMeshes /hpcwork/********/TestMesh_fluid1 /hpcwork/********/TestMesh_fluid2
Date : Oct 31 2020
Time : 09:44:13
Host : "****.hpc.itc.rwth-aachen.de"
PID : 238804
I/O : uncollated
Case : /rwthfs/rz/cluster/hpcwork/********/********
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Master: "/hpcwork/********/TestMesh_fluid1" region region0
mesh to add: "/hpcwork/********/TestMesh_fluid2" region region0
Create Times
Reading master mesh for time = 0
Create mesh
Reading mesh to add for time = 0
Create mesh
Writing combined mesh to 0.000100000000000000005
patch names:
42
(
ABSORBER_SUED
DACH_SUED
STRAHLUNGSSCHUTZ_SUED
DACH
STRAHLUNGSSCHUTZ_AUSSEN
BODEN
TURM
AMBIENT_BOTTOM
AMBIENT_TOP
ELR_SUED
AMBIENT_RIGHT
AMBIENT_INLET
TRICHTER_TEMP
TEMP_WUERFEL
MESHINTERFACE1
MESHINTERFACE2
MESHINTERFACE3
MESHINTERFACE4
MESHINTERFACE5
MESHINTERFACE6
MESHINTERFACE7
MESHINTERFACE8
MESHINTERFACE5A
MESHINTERFACE1A
ABSORBER_NO
ELR_NO
STRAHLUNGSSCHUTZ_NO
DACH_NO
AMBIENT_OUTLET
MESHINTERFACE1_2
MESHINTERFACE2_2
MESHINTERFACE3_2
MESHINTERFACE4_2
MESHINTERFACE9_2
MESHINTERFACE11_2
MESHINTERFACE12_2
MESHINTERFACE13_2
MESHINTERFACE14_2
MESHINTERFACE1A_2
MESHINTERFACE10_2
MESHINTERFACE15_2
MESHINTERFACE16_2
)
patch dicts:
42
(
{
type wall;
inGroups 1 ( wall );
nFaces 16020;
startFace 132077097;
}
{
type wall;
inGroups 1 ( wall );
nFaces 12504;
startFace 132093117;
}
{
type wall;
inGroups 1 ( wall );
nFaces 48276;
startFace 132105621;
}
{
type wall;
inGroups 1 ( wall );
nFaces 18492;
startFace 132153897;
}
{
type wall;
inGroups 1 ( wall );
nFaces 50612;
startFace 132172389;
}
{
type wall;
inGroups 1 ( wall );
nFaces 18492;
startFace 132223001;
}
{
type wall;
inGroups 1 ( wall );
nFaces 37252;
startFace 132241493;
}
{
type wall;
inGroups 1 ( wall );
nFaces 92670;
startFace 132278745;
}
{
type wall;
inGroups 1 ( wall );
nFaces 31030;
startFace 132371415;
}
{
type wall;
inGroups 1 ( wall );
nFaces 3240;
startFace 132402445;
}
{
type wall;
inGroups 1 ( wall );
nFaces 71258;
startFace 132405685;
}
{
type wall;
inGroups 1 ( wall );
nFaces 87043;
startFace 132476943;
}
{
type wall;
inGroups 1 ( wall );
nFaces 5628;
startFace 132563986;
}
{
type wall;
inGroups 1 ( wall );
nFaces 56012;
startFace 132569614;
}
{
type wall;
inGroups 1 ( wall );
nFaces 19062;
startFace 132625626;
}
{
type wall;
inGroups 1 ( wall );
nFaces 108680;
startFace 132644688;
}
{
type wall;
inGroups 1 ( wall );
nFaces 26609;
startFace 132753368;
}
{
type wall;
inGroups 1 ( wall );
nFaces 1449;
startFace 132779977;
}
{
type wall;
inGroups 1 ( wall );
nFaces 19062;
startFace 132781426;
}
{
type wall;
inGroups 1 ( wall );
nFaces 1449;
startFace 132800488;
}
{
type wall;
inGroups 1 ( wall );
nFaces 108680;
startFace 132801937;
}
{
type wall;
inGroups 1 ( wall );
nFaces 10824;
startFace 132910617;
}
{
type wall;
inGroups 1 ( wall );
nFaces 1449;
startFace 132921441;
}
{
type wall;
inGroups 1 ( wall );
nFaces 1449;
startFace 132922890;
}
{
type wall;
inGroups 1 ( wall );
nFaces 13083;
startFace 171184653;
}
{
type wall;
inGroups 1 ( wall );
nFaces 2499;
startFace 171197736;
}
{
type wall;
inGroups 1 ( wall );
nFaces 38867;
startFace 171200235;
}
{
type wall;
inGroups 1 ( wall );
nFaces 8428;
startFace 171239102;
}
{
type wall;
inGroups 1 ( wall );
nFaces 105534;
startFace 171569817;
}
{
type wall;
inGroups 1 ( wall );
nFaces 19062;
startFace 171852943;
}
{
type wall;
inGroups 1 ( wall );
nFaces 108680;
startFace 171872005;
}
{
type wall;
inGroups 1 ( wall );
nFaces 26609;
startFace 171980685;
}
{
type wall;
inGroups 1 ( wall );
nFaces 1449;
startFace 172007294;
}
{
type wall;
inGroups 1 ( wall );
nFaces 67199;
startFace 172008743;
}
{
type wall;
inGroups 1 ( wall );
nFaces 1449;
startFace 172075942;
}
{
type wall;
inGroups 1 ( wall );
nFaces 6552;
startFace 172077391;
}
{
type wall;
inGroups 1 ( wall );
nFaces 1449;
startFace 172083943;
}
{
type wall;
inGroups 1 ( wall );
nFaces 12510;
startFace 172085392;
}
{
type wall;
inGroups 1 ( wall );
nFaces 1449;
startFace 172097902;
}
{
type wall;
inGroups 1 ( wall );
nFaces 14421;
startFace 172099351;
}
{
type wall;
inGroups 1 ( wall );
nFaces 14421;
startFace 172113772;
}
{
type wall;
inGroups 1 ( wall );
nFaces 79838;
startFace 172128193;
}
)
point zone names: 0()
face zone names: 1(int_FLUID)
cell zone names: 1(FLUID)
Copying old patches
Adding new patches.
#0 Foam::error::printStack(Foam::Ostream&) at ??:?
#1 Foam::sigSegv::sigHandler(int) at ??:?
#2 ? in "/lib64/libc.so.6"
#3 Foam::polyTopoChange::makeCells(int, Foam::List<int>&, Foam::List<int>&) const at ??:?
#4 Foam::polyTopoChange::compact(bool, bool, int&, Foam::List<int>&, Foam::List<int>&) at ??:?
#5 Foam::polyTopoChange::compactAndReorder(Foam::polyMesh 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> >&) at ??:?
#6 Foam::polyTopoChange::changeMesh(Foam::polyMesh&, bool, bool, bool, bool) at ??:?
#7 ? at ??:?
#8 ? at ??:?
#9 __libc_start_main in "/lib64/libc.so.6"
#10 ? at ??:?
|
|
|
log_mergeMeshes_v7 (9,123 bytes)
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Version: 7
\\/ M anipulation |
\*---------------------------------------------------------------------------*/
Build : 7
Exec : mergeMeshes /hpcwork/********/TestMesh_fluid2 /hpcwork/********/TestMesh_fluid3
Date : Nov 02 2020
Time : 19:03:06
Host : "ncm0535.hpc.itc.rwth-aachen.de"
PID : 126513
I/O : uncollated
Case : /rwthfs/rz/cluster/hpcwork/********/TestMesh_fluid2u3
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Master: "/hpcwork/********/TestMesh_fluid2" region region0
mesh to add: "/hpcwork/********/TestMesh_fluid3" region region0
Create Times
Reading master mesh for time = 0
Create mesh
Reading mesh to add for time = 0
Create mesh
Writing combined mesh to 0.000100000000000000005
patch names:
46
(
ABSORBER_NO
ELR_NO
STRAHLUNGSSCHUTZ_NO
DACH_NO
DACH
STRAHLUNGSSCHUTZ_AUSSEN
BODEN
TURM
AMBIENT_BOTTOM
AMBIENT_TOP
AMBIENT_OUTLET
AMBIENT_RIGHT
TRICHTER_TEMP
TEMP_WUERFEL
MESHINTERFACE1_2
MESHINTERFACE2_2
MESHINTERFACE3_2
MESHINTERFACE4_2
MESHINTERFACE9_2
MESHINTERFACE11_2
MESHINTERFACE12_2
MESHINTERFACE13_2
MESHINTERFACE14_2
MESHINTERFACE1A_2
MESHINTERFACE10_2
MESHINTERFACE15_2
MESHINTERFACE16_2
ELR_NW
ABSORBER_NW
STRAHLUNGSSCHUTZ_NW
DACH_NW
AMBIENT_LEFT
AMBIENT_INLET
MESHINTERFACE5_3
MESHINTERFACE6_3
MESHINTERFACE7_3
MESHINTERFACE8_3
MESHINTERFACE9_3
MESHINTERFACE15_3
MESHINTERFACE11_3
MESHINTERFACE12_3
MESHINTERFACE13_3
MESHINTERFACE14_3
MESHINTERFACE5A_3
MESHINTERFACE10_3
MESHINTERFACE16_3
)
patch dicts:
46
(
{
type wall;
inGroups List<word> 1(wall);
nFaces 13083;
startFace 171184653;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 2499;
startFace 171197736;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 38867;
startFace 171200235;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 8428;
startFace 171239102;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 19182;
startFace 171247530;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 61091;
startFace 171266712;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 19182;
startFace 171327803;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 38642;
startFace 171346985;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 124065;
startFace 171385627;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 60125;
startFace 171509692;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 105534;
startFace 171569817;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 113652;
startFace 171675351;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 5838;
startFace 171789003;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 58102;
startFace 171794841;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 19062;
startFace 171852943;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 108680;
startFace 171872005;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 26609;
startFace 171980685;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 1449;
startFace 172007294;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 67199;
startFace 172008743;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 1449;
startFace 172075942;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 6552;
startFace 172077391;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 1449;
startFace 172083943;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 12510;
startFace 172085392;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 1449;
startFace 172097902;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 14421;
startFace 172099351;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 14421;
startFace 172113772;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 79838;
startFace 172128193;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 2737;
startFace 211528736;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 14329;
startFace 211531473;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 41786;
startFace 211545802;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 9233;
startFace 211587588;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 184008;
startFace 212076699;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 73062;
startFace 212260707;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 19062;
startFace 212425309;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 1449;
startFace 212444371;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 108680;
startFace 212445820;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 10824;
startFace 212554500;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 67199;
startFace 212565324;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 14421;
startFace 212632523;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 1449;
startFace 212646944;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 6552;
startFace 212648393;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 1449;
startFace 212654945;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 12510;
startFace 212656394;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 1449;
startFace 212668904;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 14421;
startFace 212670353;
}
{
type wall;
inGroups List<word> 1(wall);
nFaces 79838;
startFace 212684774;
}
)
point zone names: 0()
face zone names: 1(int_FLUID)
cell zone names: 1(FLUID)
Copying old patches
Adding new patches.
#0 Foam::error::printStack(Foam::Ostream&) at ??:?
#1 Foam::sigSegv::sigHandler(int) at ??:?
#2 ? in "/lib64/libc.so.6"
#3 Foam::polyTopoChange::makeCells(int, Foam::List<int>&, Foam::List<int>&) const at ??:?
#4 Foam::polyTopoChange::compact(bool, bool, int&, Foam::List<int>&, Foam::List<int>&) at ??:?
#5 Foam::polyTopoChange::compactAndReorder(Foam::polyMesh 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> >&) at ??:?
#6 Foam::polyTopoChange::changeMesh(Foam::polyMesh&, bool, bool, bool, bool) at ??:?
#7 ? at ??:?
#8 ? at ??:?
#9 __libc_start_main in "/lib64/libc.so.6"
#10 ? at ??:?
|
|
|
Try compiling with 64bit labels. |
|
|
Thanks alot for your reply. Could you elaborate on how to do that? |
|
|
I guesss you are refering to: /etc/bashrc changing WM_LABEL_SIZE=32 to 64. I will try that and give feedback on the results when its done |
|
|
I managed to compile it with WM_LABEL_SIZE=64 which seems to do the trick! fluent3DMeshToFoam ran successfully this time. Thanks a lot. |
| Date Modified | Username | Field | Change |
|---|---|---|---|
| 2020-11-03 09:48 | maxdre91 | New Issue | |
| 2020-11-03 09:48 | maxdre91 | File Added: log_mergeMesh | |
| 2020-11-03 09:56 | maxdre91 | File Added: log_mergeMeshes_v7 | |
| 2020-11-03 10:15 | henry | Note Added: 0011655 | |
| 2020-11-03 11:07 | maxdre91 | Note Added: 0011656 | |
| 2020-11-03 11:17 | maxdre91 | Note Added: 0011657 | |
| 2020-11-06 08:16 | maxdre91 | Note Added: 0011662 | |
| 2020-11-06 11:21 | wyldckat | Assigned To | => henry |
| 2020-11-06 11:21 | wyldckat | Status | new => resolved |
| 2020-11-06 11:21 | wyldckat | Resolution | open => no change required |
