Hi all I am installing CFDEM on a cluster, and I am having some issues. I followed the instructions on the documentation and I succeed installing OpenFOAM and LIGGGHTS. To install LIGGGHTS I had to to tweak the Makefile.auto to download the vtk lib ( USE_VTK ?= "OFF" and AUTOINSTALL_VTK ?= "ON").
Just in case I am using the step by step installation
cfdemCompLIG
cfdemCompCFDEMsrc
cfdemCompCFDEMsol
cfdemCompCFDEMuti
Apparently cannot open some heather files, I look for those files in the system (in $HOME e.i. find ./ -iname fvIOoptionList.H). I don't know how that can be possible.
I attached below the logs and the cfdemSysTest. Does anybody has an Idea of what could be the issue? Thanks in advance!
Regards,
Mauro
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cat log_compile_results_sol_fail
cfdemSolverPiso
cfdemSolverIB
cfdemSolverPisoScalar
cfdemSolverPisoSTM
cat log_compile_results_src_fail
cfdemParticle
cat log_compile_results_src_success
scalarTransportModelsCFDEM
fvOptionsCFDEM
cat log_compileCFDEMcoupling_cfdemSolverPiso
// log_compileCFDEMcoupling_cfdemSolverPiso_cfdemSolverPiso-2018-03-02-18:12 //
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/applications/solvers/cfdemSolverPiso
removing all .dep files ...
Making dependency list for source file cfdemSolverPiso.C
could not open file fvIOoptionList.H for source file cfdemSolverPiso.C due to No such file or directory
could not open file omp.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file openmpi/ompi/mpi/cxx/mpicxx.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file math.h for source file cfdemSolverPiso.C due to No such file or directory
could not open file cfdemCloudRotation.H for source file cfdemSolverPiso.C due to No such file or directory
could not open file cfdemCloudRotationSuperquadric.H for source file cfdemSolverPiso.C due to No such file or directory
could not open file readPISOControls.H for source file cfdemSolverPiso.C due to No such file or directory
g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -DSUPERQUADRIC_ACTIVE_FLAG -DNONSPHERICAL_ACTIVE_FLAG -DCFDEMWMPROJECTVERSION="50" -I/apps/OpenMPI/2.0.2-gcc/include -pthread -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/TurbulenceModels/turbulenceModels/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/TurbulenceModels/incompressible/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/fvOptions/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/transportModels -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/transportModels/incompressible/singlePhaseTransportModel -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/finiteVolume/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/meshTools/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/fvOptions/lnInclude -I/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/src/lagrangian/cfdemParticle/lnInclude -I/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/src/lagrangian/cfdemParticle/cfdTools -I/home/hpc/iwsp/iwsp009h/LIGGGHTS/LIGGGHTS-PUBLIC/src -IlnInclude -I. -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/OSspecific/POSIX/lnInclude -fPIC -c cfdemSolverPiso.C -o Make/linux64GccDPInt32Opt/cfdemSolverPiso.o
g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -DSUPERQUADRIC_ACTIVE_FLAG -DNONSPHERICAL_ACTIVE_FLAG -DCFDEMWMPROJECTVERSION="50" -I/apps/OpenMPI/2.0.2-gcc/include -pthread -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/TurbulenceModels/turbulenceModels/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/TurbulenceModels/incompressible/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/fvOptions/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/transportModels -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/transportModels/incompressible/singlePhaseTransportModel -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/finiteVolume/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/meshTools/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/fvOptions/lnInclude -I/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/src/lagrangian/cfdemParticle/lnInclude -I/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/src/lagrangian/cfdemParticle/cfdTools -I/home/hpc/iwsp/iwsp009h/LIGGGHTS/LIGGGHTS-PUBLIC/src -IlnInclude -I. -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude -I/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/src/OSspecific/POSIX/lnInclude -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPInt32Opt/cfdemSolverPiso.o -L/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/platforms/linux64GccDPInt32Opt/lib \
-L/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib -lturbulenceModels -lincompressibleTurbulenceModels -lfvOptions -lincompressibleTransportModels -lfiniteVolume -lmeshTools -lfvOptions -llagrangianCFDEM-PUBLIC-5.x -lOpenFOAM -ldl \
-lm -o /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/bin/cfdemSolverPiso
/usr/bin/ld: warning: libvtkCommonCore-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkIOCore-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkIOXML-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkIOLegacy-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkIOImage-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkCommonDataModel-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkIOParallelXML-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkParallelCore-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkParallelMPI-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkCommonExecutionModel-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkFiltersCore-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtksys-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkCommonMisc-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkCommonTransforms-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkCommonMath-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkIOXMLParser-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkCommonSystem-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkDICOMParser-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libvtkmetaio-8.0.so.1, needed by /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so, not found (try using -rpath or -rpath-link)
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkPolyData::SetVerts(vtkCellArray*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkOStreamWrapper::operator<<(int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLPPolyDataWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkObject::GetGlobalWarningDisplay()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkSmartPointerBase::vtkSmartPointerBase(vtkObjectBase*, vtkSmartPointerBase::NoReference const&)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkMultiBlockDataSet::GetBlock(unsigned int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkDebugLeaksManager::vtkDebugLeaksManager()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLUnstructuredGridWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkCommunicator::Receive(vtkDataObject*, int, int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkSmartPointerBase::vtkSmartPointerBase(vtkObjectBase*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkMultiProcessController::GetGlobalController()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkHexahedron::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkObjectFactoryRegistryCleanup::vtkObjectFactoryRegistryCleanup()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkPolyData::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkFieldData::GetAbstractArray(int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLPRectilinearGridWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLPolyDataWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkSmartPointerBase::operator=(vtkSmartPointerBase const&)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkPolyDataAlgorithm::GetOutput()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkOStrStreamWrapper::vtkOStrStreamWrapper()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkRectilinearGridWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkDataObjectTree::GetChildMetaData(unsigned int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkDataSetAlgorithm::SetInputData(vtkDataObject*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkCellDataToPointData::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLWriter::SetDataModeToBinary()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkWriter::SetInputData(vtkDataObject*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkOStreamWrapper::operator<<(void*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkDebugLeaksManager::~vtkDebugLeaksManager()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkFieldData::GetArray(int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkAppendPolyData::AddInputData(vtkPolyData*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkSmartPointerBase::operator=(vtkObjectBase*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkOStrStreamWrapper::freeze(int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkCommunicator::Send(vtkDataObject*, int, int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLWriter::Write()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkDataSetAlgorithm::GetOutput()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkPolyData::SetLines(vtkCellArray*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLPUnstructuredGridWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkPolyData::SetPolys(vtkCellArray*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkPointDataToCellData::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLWriter::SetDataModeToAscii()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkIdList::SetNumberOfIds(long long)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkUnstructuredGridWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLWriter::SetCompressorType(int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkMPIController::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkOStreamWrapper::operator<<(char const*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkStringArray::InsertNextValue(char const*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkUnstructuredGrid::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkOStrStreamWrapper::rdbuf()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkMultiBlockDataSet::GetNumberOfBlocks()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkRectilinearGrid::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkCompositeDataSet::NAME()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkMultiBlockDataSet::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkLine::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkRectilinearGrid::SetDimensions(int, int, int)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkSmartPointerBase::vtkSmartPointerBase()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkCellArray::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkObject::GetDebug()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkObjectBase::GetClassName() const'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkSmartPointerBase::vtkSmartPointerBase(vtkSmartPointerBase const&)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkDoubleArray::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkInformation::Set(vtkInformationStringKey*, char const*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLRectilinearGridWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkStringArray::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkMultiBlockDataSet::SetBlock(unsigned int, vtkDataObject*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkOStrStreamWrapper::str()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkObjectFactoryRegistryCleanup::~vtkObjectFactoryRegistryCleanup()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLMultiBlockDataWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkAOSDataArrayTemplate::WritePointer(long long, long long)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkOStrStreamWrapper::~vtkOStrStreamWrapper()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkAppendPolyData::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkSmartPointerBase::~vtkSmartPointerBase()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLPImageDataWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkTriangle::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkPolyDataWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkIntArray::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkMultiProcessController::SetGlobalController(vtkMultiProcessController*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkOutputWindowDisplayDebugText(char const*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLImageDataWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLWriter::SetInputData(vtkDataObject*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkPoints::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkFieldData::AddArray(vtkAbstractArray*)'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkXMLPMultiBlockDataWriter::New()'
/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so: undefined reference to `vtkUnstructuredGrid::SetCells(int, vtkCellArray*)'
collect2: error: ld returned 1 exit status
make: *** [/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/bin/cfdemSolverPiso] Error 1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
cfdemSysTest
*********************************************
* C F D E M (R) c o u p l i n g *
* *
* by DCS Computing GmbH *
* www.dcs-computing.com *
*********************************************
*********************************
CFDEM(R)coupling system settings:
*********************************
CFDEM_VERSION=PUBLIC
couple to OF_VERSION=5.x
compile option=Opt
check if paths are set correctly
valid:yes critical:yes - $CFDEM_PROJECT_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x
valid:yes critical:no - $CFDEM_PROJECT_USER_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/iwsp009h-PUBLIC-5.x
valid:yes critical:yes - $CFDEM_SRC_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/src
valid:yes critical:yes - $CFDEM_SOLVER_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/applications/solvers
valid:yes critical:yes - $CFDEM_TUT_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/tutorials
valid:yes critical:yes - $CFDEM_LIGGGHTS_SRC_DIR = /home/hpc/iwsp/iwsp009h/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:yes critical:yes - $CFDEM_LIGGGHTS_LIB_PATH = /home/hpc/iwsp/iwsp009h/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:yes critical:yes - $CFDEM_LPP_DIR = /home/hpc/iwsp/iwsp009h/LIGGGHTS/lpp/src
valid:yes critical:yes - $CFDEM_ADD_LIBS_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/src/lagrangian/cfdemParticle/etc/addLibs_universal
valid:yes critical:yes - $CFDEM_LIB_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib
valid:yes critical:yes - $CFDEM_APP_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/bin
valid:yes critical:no - $CFDEM_USER_LIB_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/iwsp009h-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib
valid:yes critical:no - $CFDEM_USER_APP_DIR = /home/hpc/iwsp/iwsp009h/CFDEM/iwsp009h-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/bin
valid:yes critical:no - $CFDEM_TEST_HARNESS_PATH = /home/hpc/iwsp/iwsp009h/CFDEM/iwsp009h-PUBLIC-5.x/log/logFilesCFDEM-PUBLIC-5.x
valid:NO critical:no - $C3PO_SRC_DIR = does not exist
library names
$CFDEM_LIGGGHTS_LIB_NAME = lmp_auto
$CFDEM_LIB_NAME = lagrangianCFDEM-PUBLIC-5.x
$LD_LIBRARY_PATH = /home/hpc/iwsp/iwsp009h/CFDEM/iwsp009h-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib:/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib:/home/hpc/iwsp/iwsp009h/OpenFOAM/ThirdParty-5.x/platforms/linux64Gcc/gperftools-svn/lib:/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/platforms/linux64GccDPInt32Opt/lib/openmpi-system:/home/hpc/iwsp/iwsp009h/OpenFOAM/ThirdParty-5.x/platforms/linux64GccDPInt32/lib/openmpi-system:/apps/OpenMPI/2.0.2-gcc/lib:/home/hpc/iwsp/iwsp009h/OpenFOAM/iwsp009h-5.x/platforms/linux64GccDPInt32Opt/lib:/home/hpc/iwsp/iwsp009h/OpenFOAM/site/5.x/platforms/linux64GccDPInt32Opt/lib:/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/platforms/linux64GccDPInt32Opt/lib:/home/hpc/iwsp/iwsp009h/OpenFOAM/ThirdParty-5.x/platforms/linux64GccDPInt32/lib:/home/hpc/iwsp/iwsp009h/OpenFOAM/OpenFOAM-5.x/platforms/linux64GccDPInt32Opt/lib/dummy:/home/hpc/iwsp/iwsp009h/CFDEM/iwsp009h-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib:/home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib:/apps/boost/1.61.0-sysgcc/lib:/apps/gcc/gcc-6.1.0-x86_64/lib64:/apps/gcc/gcc-6.1.0-x86_64/lib:/apps/git/2.2.1/lib
$WM_NCOMPPROCS = 24
$WM_LABEL_SIZE = 32
Additional lib settings
CFDEM_ADD_LIBS_DIR/CFDEM_ADD_LIBS_NAME = /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/src/lagrangian/cfdemParticle/etc/addLibs_universal/additionalLibs_5.x
CFDEM_ADD_LIB_PATHS =
CFDEM_ADD_LIBS =
LIGGGHTS library link (created during compilation of CFDEM)
lrwxrwxrwx 1 iwsp009h iwsp 67 Mar 2 18:09 /home/hpc/iwsp/iwsp009h/CFDEM/CFDEMcoupling-PUBLIC-5.x/platforms/linux64GccDPInt32Opt/lib/liblmp_auto.so -> /home/hpc/iwsp/iwsp009h/LIGGGHTS/LIGGGHTS-PUBLIC/src/liblmp_auto.so
*******************
g++:
/apps/gcc/gcc-6.1.0-x86_64/bin/g++
g++ (GCC) 6.1.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
gcc:
/apps/gcc/gcc-6.1.0-x86_64/bin/gcc
gcc (GCC) 6.1.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
mpic++:
/apps/OpenMPI/2.0.2-gcc/bin/mpic++
g++ (GCC) 6.1.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
mpirun:
/apps/OpenMPI/2.0.2-gcc/bin/mpirun
mpirun (Open MPI) 2.0.2
Report bugs to http://www.open-mpi.org/community/help/
**********************
additional packages...
mbaldini | Mon, 03/05/2018 - 18:16
Hi, I realized that the
Hi, I realized that the problem it's related with how I installed the vtk libraries. If I'm not wrong, I should tell the compiler to look into where I installed the vtk library (LIGGGHTS/LIGGGHTS-PUBLIC/lib/vtk). Should I do this by using the CFDEM_ADD_LIB_PATHS and CFDEM_ADD_LIBS? Or do I need to modify the existing make files?
Thanks
Mauro
mbaldini | Tue, 03/06/2018 - 18:16
Hi all, just wanted to give
Hi all, just wanted to give feedback just in case that somebody faces the same issue in the future. I finally managed to compile CFDEM by setting CFDEM_ADD_LIB_PATHS and CFDEM_ADD_LIBS in additionalLibs_5.x the following way:
CFDEM_ADD_LIB_PATHS = -Wl,-rpath,/home/usr/LIGGGHTS/LIGGGHTS-PUBLIC/lib/vtk/install/lib -L/home/usr/LIGGGHTS/LIGGGHTS-PUBLIC/lib/vtk/install/lib
CFDEM_ADD_LIBS = -lvtkCommonCore-8.0 -lvtkIOCore-8.0 -lvtkIOXML-8.0 -lvtkIOLegacy-8.0 -lvtkIOImage-8.0 -lvtkCommonDataModel-8.0 - lvtkIOParallelXML-8.0 -lvtkParallelCore-8.0 -lvtkParallelMPI-8.0 -lvtkCommonExecutionModel-8.0 -lvtkFiltersCore-8.0 -lvtksys-8.0 -lvtkCommonMisc-8.0 -lvtkCommonTransforms-8.0 -lvtkCommonMath-8.0 -lvtkIOXMLParser-8.0 -lvtkCommonSystem-8.0 -lvtkDICOMParser-8.0 -lvtkmetaio-8.0
Being /home/usr/LIGGGHTS/LIGGGHTS-PUBLIC/lib/vtk/install/lib the path where LIGGGHTS installed the vtk llibs.
Regards,
Mauro
AlexisEspinosa | Mon, 11/19/2018 - 01:33
How do you know the list for CFDEM_ADD_LIBS?
Dear Mauro,
Your trick worked perfectly for me, but I'm wondering how you figured out the list of libraries to set for CFDEM_ADD_LIBS?
Many thanks,
Alexis
Min Zhang | Tue, 07/31/2018 - 04:42
Hello Mauro,
Hello Mauro,
I am trying to install the latest CFDEM version on my university cluster. I am wondering whether you could be so kind to have a look at my post. Thanks in advance!
This is the post link:
https://www.cfdem.com/forums/install-latest-cfdem-versions#comment-19535
Thanks and best regards,
Min