Cardinal with DAGMC installation issues

[nancysemwal]

Hello

I am trying to again build Cardinal without MOOSE's conda environment but this time with ENABLE_DAGMC set to true. I have the 2 builds in 2 separate folders (/cardinal and /cardinal_dagmc) in my /home (just to keep things clean) and the one built without DAGMC works fine. However, the newer build is failing with the following error while linking the cardinal-opt executable:

Linking Executable /home/nancy/cardinal_dagmc/cardinal/cardinal-opt...
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateGradient(Moose::ElemSideQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/modules/stochastic_tools/lib/libstochastic_tools-opt.so: undefined reference to `FunctionInterface::hasFunctionByName(FunctionName const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluate(Moose::ElemSideQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `FunctionInterface::getFunction(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `FunctionInterface::validParams()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::residualSetup()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `typeinfo for Function'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::jacobianSetup()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateDot(Moose::ElemSideQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateDot(Moose::FaceArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateGradient(Moose::ElemQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluate(Moose::ElemArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/modules/thermal_hydraulics/lib/libthermal_hydraulics-opt.so: undefined reference to `MooseParsedFunctionBase::MooseParsedFunctionBase(InputParameters const&)'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateGradient(Moose::ElemQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateGradient(Moose::FaceArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::residualSetup()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluate(Moose::FaceArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::curl(double, libMesh::Point const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::timestepSetup()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::gradient(double, libMesh::Point const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateGradient(Moose::ElemPointArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/modules/thermal_hydraulics/lib/libthermal_hydraulics-opt.so: undefined reference to `MooseParsedFunctionBase::~MooseParsedFunctionBase()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::div(double, libMesh::Point const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluate(Moose::ElemQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateGradient(Moose::NodeArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::jacobianSetup()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::customSetup(MooseEnumItem const&)'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateDot(Moose::NodeArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::residualSetup()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluate(Moose::NodeArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `typeinfo for PiecewiseBase'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateGradient(Moose::FaceArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::timeIntegral(double, double, libMesh::Point const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::customSetup(MooseEnumItem const&)'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateDot(Moose::NodeArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::average() const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/modules/thermal_hydraulics/lib/libthermal_hydraulics-opt.so: undefined reference to `typeinfo for ConstantFunction'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/modules/thermal_hydraulics/lib/libthermal_hydraulics-opt.so: undefined reference to `Function::value(double, libMesh::Point const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateDot(Moose::ElemQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateDot(Moose::ElemQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/modules/thermal_hydraulics/lib/libthermal_hydraulics-opt.so: undefined reference to `MooseParsedFunctionBase::validParams()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateGradient(Moose::NodeArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::timestepSetup()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateDot(Moose::ElemPointArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::jacobianSetup()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `FunctionInterface::FunctionInterface(MooseObject const*)'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluate(Moose::ElemArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluate(Moose::ElemPointArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `typeinfo for PiecewiseLinear'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/modules/thermal_hydraulics/lib/libthermal_hydraulics-opt.so: undefined reference to `MooseParsedFunctionBase::verifyFunction(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateGradient(Moose::ElemArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateDot(Moose::ElemPointArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateGradient(Moose::ElemPointArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/modules/solid_mechanics/lib/libsolid_mechanics-opt.so: undefined reference to `Function::value(MetaPhysicL::DualNumber<double, double, false> const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateDot(Moose::FaceArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluate(Moose::ElemQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::~Function()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::timeDerivative(double, libMesh::Point const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::integral() const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluate(Moose::FaceArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateDot(Moose::ElemArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::value(MetaPhysicL::DualNumber<double, MetaPhysicL::SemiDynamicSparseNumberArray<double, unsigned long, MetaPhysicL::NWrapper<64ul> >, true> const&, libMesh::VectorValue<MetaPhysicL::DualNumber<double, MetaPhysicL::SemiDynamicSparseNumberArray<double, unsigned long, MetaPhysicL::NWrapper<64ul> >, true> > const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateGradient(Moose::ElemSideQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::Function(InputParameters const&)'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluate(Moose::NodeArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `FunctionInterface::getFunctionByName(FunctionName const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::validParams()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::evaluateDot(Moose::ElemSideQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateGradient(Moose::ElemArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/modules/thermal_hydraulics/lib/libthermal_hydraulics-opt.so: undefined reference to `typeinfo for MooseParsedFunctionBase'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluate(Moose::ElemPointArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::customSetup(MooseEnumItem const&)'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluate(Moose::ElemSideQpArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::evaluateDot(Moose::ElemArg const&, Moose::StateArg const&) const'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `non-virtual thunk to Function::timestepSetup()'
/usr/bin/ld: /home/nancy/cardinal_dagmc/cardinal/contrib/moose/framework/libmoose-opt.so: undefined reference to `Function::vectorValue(double, libMesh::Point const&) const'
collect2: error: ld returned 1 exit status

How do I proceed?

My /contrib/moose/scripts/diagnostics.sh gives me a PASSED message so I understand that there's nothing wrong with the Python/conda environment setup.

contrib/moose/scripts/diagnostics.sh 
####################################################################################################
Influential Environment Variables

CC=mpicc
CONDA_CHANNEL=https://conda.software.inl.gov/public
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/nancy/miniconda3/bin/conda
CONDA_PREFIX=/home/nancy/miniconda3
CONDA_PROMPT_MODIFIER=(base) 
CONDA_PYTHON_EXE=/home/nancy/miniconda3/bin/python
CONDA_SHLVL=1
CURL_CA_BUNDLE=
CXX=mpicxx
F77=mpif77
F90=mpif90
FC=mpif90
http_proxy=http://nancy:[email protected]:8080/
https_proxy=http://nancy:[email protected]:8080/
HTTPS_PROXY=http://proxy.barcv.gov.in:8080/
LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib64
LIBMESH_JOBS=8
MOOSE_JOBS=6
PATH=/home/nancy/miniconda3/bin:/home/nancy/miniconda3/bin/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:.
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
####################################################################################################
Compiler(s) (CC CXX FC F77 F90):

which $CC; /usr/bin/mpicc
$CC --version; gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
$CC -show; gcc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi

which $CXX; /usr/bin/mpicxx
$CXX --version; g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
$CXX -show; g++ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_cxx -lmpi

which $FC; /usr/bin/mpif90
$FC --version; GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
$FC -show; gfortran -I/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib/fortran/gfortran -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen-rte -lopen-pal -lhwloc -levent_core -levent_pthreads -lm -lz

which $F77; /usr/bin/mpif77
$F77 --version; GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
$F77 -show; gfortran -I/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib/fortran/gfortran -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen-rte -lopen-pal -lhwloc -levent_core -levent_pthreads -lm -lz

which $F90; /usr/bin/mpif90
$F90 --version; GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
$F90 -show; gfortran -I/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib/fortran/gfortran -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen-rte -lopen-pal -lhwloc -levent_core -levent_pthreads -lm -lz

OK
####################################################################################################
Python Sanity Checks

/usr/bin/env python3 --version; (reporting as: Python 3.12.7) matches
which python3 python;

/home/nancy/miniconda3/bin/python3 --version; == Python 3.12.7
/home/nancy/miniconda3/bin/python --version; == Python 3.12.7

OK
####################################################################################################
Python Modules (TestHarness, run-ability)

OK
####################################################################################################
MOOSE Repository/Conda Version Checks

WARNING: Not using Conda MOOSE packages, or conda activate moose not performed


checks PASSED

I am ignoring the conda activate moose not performed warning since I do not want to use the MOOSE's conda environment as I want to be able to use NekRS.

Are there any other diagnostics to perform that might point me in the right direction?

[aprilnovak]

I believe this question is a duplicate of #1004, so I will close this one. Please feel free to re-post if that is not the case!