Cardinal with DAGMC build 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?

[nuclearkevin]

Hi Nancy,

From what I can see, it looks like the linker errors you're encountering are caused by MOOSE and the MOOSE modules (which are independent of DAGMC). These are normally caused by mismatched header/source files (where a function definition in a C++ header doesn't match / is missing the corresponding function declaration in the source file); in your case I believe one of the following might be to blame:

1. An incomplete submodule init resulting in missing/mismatched source files (unlikely).
2. The MOOSE submodule may have been built previously, then Cardinal was rebuilt after pulling changes which include a submodule update (the most likely cause).
3. The MOOSE buildsystem is detecting the MOOSE headers in /home/nancy/cardinal/cardinal/contrib/moose/* (possibly through an include directory environment variable), which causes a mismatch iff the cloned versions of Cardinal are different (very unlikely).

My recommendation (given that you want to keep your working version of Cardinal) would be to delete the contents of /home/nancy/cardinal_dagmc/ and clone / rebuild Cardinal from scratch in that directory (following the tutorial). This should rule out 1. & 2.

If that doesn't end up working you can rebuild your working Cardinal installation with DAGMC. This can be done by running make clobberall in /home/nancy/cardinal_dagmc/cardinal/, then set

export ENABLE_DAGMC=yes
export ENABLE_OPENMC=yes
export ENABLE_NEK=yes

finally running scripts/get-dependencies.sh to fetch the newly declared DAGMC dependency and make -j NUM_PROC to rebuild Cardinal.

Hope this helps,
Kevin

[nancysemwal]

I ended up using an older commit of the devel branch (the same one using which I was able to build successfully last time ), instead of the newest one which was getting cloned by default. That solved my problem. Thank you @nuclearkevin for your pointers.