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linhanGE / CFDEMcoupling-LG

CFDEM with modified multiscale CFD/VOF-DEM solvers developed by Linhan Ge
GNU General Public License v3.0
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Segmentation fault erro #5

Open sihaeri opened 1 year ago

sihaeri commented 1 year ago

Hi I am trying to run bubbleRisingAgainstParticles. I managed to build the code successfully but when running the case I get a segmentation fault error:

[0] #0  [1] #0  [2] #0  [3] #0  Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)--------------------------------------------------------------------------
A process has executed an operation involving a call to the
"fork()" system call to create a child process.  Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your job may hang, crash, or produce silent
data corruption.  The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.

The process that invoked fork was:

  Local host:          [[2591,1],0] (PID 19168)

If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
 at ??:?
[1] #1  Foam::sigSegv::sigHandler(int) at ??:?
 at ??:?
[2] #1  Foam::sigSegv::sigHandler(int)[3] #1  Foam::sigSegv::sigHandler(int) at ??:?
[0] #1  Foam::sigSegv::sigHandler(int) at ??:?
[1] #2  ? at ??:?
[2]  at ??:?
#2  ?[3] #2  ? at ??:?
[0] #2  ? in "/lib64/libpthread.so.0"
[1] #3  Foam::curvatureModels::vofsmooth::smoothen(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>&) const in "/lib64/libpthread.so.0"
[2] #3  Foam::curvatureModels::vofsmooth::smoothen(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>&) const in "/lib64/libpthread.so.0"
[3] #3  Foam::curvatureModels::vofsmooth::smoothen(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>&) const in "/lib64/libpthread.so.0"
[0] #3  Foam::curvatureModels::vofsmooth::smoothen(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>&) const at ??:?
[3] #4  Foam::curvatureModels::vofsmooth::calculateK(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh>&) const at ??:?
[1] #4  Foam::curvatureModels::vofsmooth::calculateK(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh>&) const at ??:?
[2] #4   at ??:?
[0] #4  Foam::curvatureModels::vofsmooth::calculateK(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh>&) constFoam::curvatureModels::vofsmooth::calculateK(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh>&) const at ??:?
[1] #5  Foam::interfaceProperties::interfaceProperties(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::IOdictionary const&) at ??:?
[0] #5  Foam::interfaceProperties::interfaceProperties(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::IOdictionary const&) at ??:?
[2] #5  Foam::interfaceProperties::interfaceProperties(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::IOdictionary const&) at ??:?
[3] #5  Foam::interfaceProperties::interfaceProperties(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::IOdictionary const&) at ??:?
[0] #6  Foam::immiscibleIncompressibleTwoPhaseMixture::immiscibleIncompressibleTwoPhaseMixture(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&) at ??:?
[1] #6  Foam::immiscibleIncompressibleTwoPhaseMixture::immiscibleIncompressibleTwoPhaseMixture(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&) at ??:?
[2] #6  Foam::immiscibleIncompressibleTwoPhaseMixture::immiscibleIncompressibleTwoPhaseMixture(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&) at ??:?
[3] #6  Foam::immiscibleIncompressibleTwoPhaseMixture::immiscibleIncompressibleTwoPhaseMixture(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&) at ??:?
[1] #7   at ??:?
[0] #7   at ??:?
[2] #7   at ??:?
[3] #7  ???? at ??:?
[2] #8  __libc_start_main at ??:?
[1] #8  __libc_start_main at ??:?
[0] #8  __libc_start_main at ??:?
[3] #8  __libc_start_main in "/lib64/libc.so.6"
[2] #9   in "/lib64/libc.so.6"
[1] #9   in "/lib64/libc.so.6"
[0] #9   in "/lib64/libc.so.6"
[3] #9  ???? at ??:?
[workstation01:19168] *** Process received signal ***
[workstation01:19168] Signal: Segmentation fault (11)
[workstation01:19168] Signal code:  (-6)
[workstation01:19168] Failing at address: 0x100042c00004ae0
[workstation01:19168] [ 0]  at ??:?
 at ??:?
/lib64/libpthread.so.0(+0xf370)[0x7fd583e49370]
[workstation01:19168] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x7fd583e4923b]
[workstation01:19168] [ 2] /lib64/libpthread.so.0(+0xf370)[0x7fd583e49370]
[workstation01:19168] [ 3] [workstation01:19169] *** Process received signal ***
[workstation01:19170] *** Process received signal ***
/home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZNK4Foam15curvatureModels9vofsmooth8smoothenERNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x37)[0x7fd58add5ad7]
[workstation01:19168] [ 4] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZNK4Foam15curvatureModels9vofsmooth10calculateKERNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEERNS2_IdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x6c)[0x7fd58add658c]
[workstation01:19168] [ 5] [workstation01:19170] Signal: Segmentation fault (11)
[workstation01:19170] Signal code:  (-6)
[workstation01:19170] Failing at address: 0x100042c00004ae2
[workstation01:19169] Signal: Segmentation fault (11)
[workstation01:19169] Signal code:  (-6)
[workstation01:19169] Failing at address: 0x100042c00004ae1
/home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZN4Foam19interfacePropertiesC2ERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEERKNS1_INS_6VectorIdEES2_S3_EERKNS_12IOdictionaryE+0x7f6)[0x7fd58ad9be96]
[workstation01:19168] [ 6] /data/home/bb/aaa/OpenFOAM/OpenFOAM-5.x/platforms/linux64GccDPInt32Opt/lib/libimmiscibleIncompressibleTwoPhaseMixture.so(_ZN4Foam39immiscibleIncompressibleTwoPhaseMixtureC2ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEERKNS1_IdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x2a)[0x7fd5863d9d5a]
[workstation01:19168] [ 7] cfdemSolverVoF[0x44c92d]
[workstation01:19168] [ 8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7fd583a9ab35]
[workstation01:19168] [ 9] [workstation01:19169] [ 0] [workstation01:19170] [ 0] cfdemSolverVoF[0x456039]
[workstation01:19168] *** End of error message ***
/lib64/libpthread.so.0(+0xf370)[0x7febc943d370]
[workstation01:19169] [ 1] /lib64/libpthread.so.0(+0xf370)[0x7fc059e08370]
[workstation01:19170] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x7febc943d23b]
[workstation01:19169] [ 2] /lib64/libpthread.so.0(raise+0x2b)[0x7fc059e0823b]
[workstation01:19170] [ 2] /lib64/libpthread.so.0(+0xf370)[0x7fc059e08370]
/lib64/libpthread.so.0(+0xf370)[0x7febc943d370]
[workstation01:19169] [ 3] [workstation01:19170] [ 3] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZNK4Foam15curvatureModels9vofsmooth8smoothenERNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x37)[0x7fc060d94ad7]
[workstation01:19170] [ 4] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZNK4Foam15curvatureModels9vofsmooth8smoothenERNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x37)[0x7febd03c9ad7]
[workstation01:19169] [ 4] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZNK4Foam15curvatureModels9vofsmooth10calculateKERNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEERNS2_IdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x6c)[0x7fc060d9558c]
[workstation01:19170] [ 5] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZNK4Foam15curvatureModels9vofsmooth10calculateKERNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEERNS2_IdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x6c)[0x7febd03ca58c]
[workstation01:19169] [ 5] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZN4Foam19interfacePropertiesC2ERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEERKNS1_INS_6VectorIdEES2_S3_EERKNS_12IOdictionaryE+0x7f6)[0x7fc060d5ae96]
[workstation01:19170] [ 6] /data/home/bb/aaa/OpenFOAM/OpenFOAM-5.x/platforms/linux64GccDPInt32Opt/lib/libimmiscibleIncompressibleTwoPhaseMixture.so(_ZN4Foam39immiscibleIncompressibleTwoPhaseMixtureC2ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEERKNS1_IdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x2a)[0x7fc05c398d5a]
[workstation01:19170] [ 7] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZN4Foam19interfacePropertiesC2ERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEERKNS1_INS_6VectorIdEES2_S3_EERKNS_12IOdictionaryE+0x7f6)[0x7febd038fe96]
[workstation01:19169] [ 6] /data/home/bb/aaa/OpenFOAM/OpenFOAM-5.x/platforms/linux64GccDPInt32Opt/lib/libimmiscibleIncompressibleTwoPhaseMixture.so(_ZN4Foam39immiscibleIncompressibleTwoPhaseMixtureC2ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEERKNS1_IdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x2a)[0x7febcb9cdd5a]
[workstation01:19169] [ 7] cfdemSolverVoF[0x44c92d]
[workstation01:19170] [ 8] cfdemSolverVoF[0x44c92d]
[workstation01:19169] [ 8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7fc059a59b35]
[workstation01:19170] [ 9] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7febc908eb35]
[workstation01:19169] [ 9] cfdemSolverVoF[0x456039]
[workstation01:19169] *** End of error message ***
cfdemSolverVoF[0x456039]
[workstation01:19170] *** End of error message ***
 at ??:?
[workstation01:19171] *** Process received signal ***
[workstation01:19171] Signal: Segmentation fault (11)
[workstation01:19171] Signal code:  (-6)
[workstation01:19171] Failing at address: 0x100042c00004ae3
[workstation01:19171] [ 0] /lib64/libpthread.so.0(+0xf370)[0x7f11fe3ec370]
[workstation01:19171] [ 1] /lib64/libpthread.so.0(raise+0x2b)[0x7f11fe3ec23b]
[workstation01:19171] [ 2] /lib64/libpthread.so.0(+0xf370)[0x7f11fe3ec370]
[workstation01:19171] [ 3] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZNK4Foam15curvatureModels9vofsmooth8smoothenERNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x37)[0x7f1205378ad7]
[workstation01:19171] [ 4] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZNK4Foam15curvatureModels9vofsmooth10calculateKERNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEERNS2_IdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x6c)[0x7f120537958c]
[workstation01:19171] [ 5] /home/bb/aaa/OpenFOAM/aaa-5.x/platforms/linux64GccDPInt32Opt/lib/libkva_interfaceProperties.so(_ZN4Foam19interfacePropertiesC2ERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEERKNS1_INS_6VectorIdEES2_S3_EERKNS_12IOdictionaryE+0x7f6)[0x7f120533ee96]
[workstation01:19171] [ 6] /data/home/bb/aaa/OpenFOAM/OpenFOAM-5.x/platforms/linux64GccDPInt32Opt/lib/libimmiscibleIncompressibleTwoPhaseMixture.so(_ZN4Foam39immiscibleIncompressibleTwoPhaseMixtureC2ERKNS_14GeometricFieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshEEERKNS1_IdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x2a)[0x7f120097cd5a]
[workstation01:19171] [ 7] cfdemSolverVoF[0x44c92d]
[workstation01:19171] [ 8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f11fe03db35]
[workstation01:19171] [ 9] cfdemSolverVoF[0x456039]
[workstation01:19171] *** End of error message ***

Using OpenMPI 3 with GCC 8.2.0. All the components work independently, I can run the interFoam with vofsmooth and we can independently run CFDEM cases built independently.

Just wondering if you have had such errors before?

Thanks

LiChenyuRuber commented 2 weeks ago

Hi, I also have the same situation. I wanna know do you address it? I don't know if it is a case problem or if I wrongly installed it.