MATLAB bindings: error while compiling

Using preCICE
1

Hello,

I want to couple Matlab and Openfoam. Openfoam adapter is OK for me. But Matlab bindings is not OK for me. I am using Matlab 2020b now. I ran compile_matlab_bindings_for_precice.m, which I downloaded from Github. But it comes errors as follwing:

/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp: In member function
‘virtual void MexFunction::operator()(matlab::mex::ArgumentList, matlab::mex::ArgumentList)’:
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:176:70: warning: ‘bool
precice::SolverInterface::hasToEvaluateSurrogateModel() const’ is deprecated: The manifold mapping feature is no longer
supported. [-Wdeprecated-declarations]
                 bool result = interface->hasToEvaluateSurrogateModel();
                                                                      ^
In file included from
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:6:0:
/usr/include/precice/SolverInterface.hpp:260:79: note: declared here
   [[deprecated("The manifold mapping feature is no longer supported.")]] bool hasToEvaluateSurrogateModel() const;
                                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:182:65: warning: ‘bool
precice::SolverInterface::hasToEvaluateFineModel() const’ is deprecated: The manifold mapping feature is no longer
supported. [-Wdeprecated-declarations]
                 bool result = interface->hasToEvaluateFineModel();
                                                                 ^
In file included from
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:6:0:
/usr/include/precice/SolverInterface.hpp:275:79: note: declared here
   [[deprecated("The manifold mapping feature is no longer supported.")]] bool hasToEvaluateFineModel() const;
                                                                               ^~~~~~~~~~~~~~~~~~~~~~
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:217:65: warning:
‘std::set<int> precice::SolverInterface::getMeshIDs() const’ is deprecated: Use getMeshID() for specific mesh names instead.
[-Wdeprecated-declarations]
                 const std::set<int> ids = interface->getMeshIDs();
                                                                 ^
In file included from
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:6:0:
/usr/include/precice/SolverInterface.hpp:350:84: note: declared here
   [[deprecated("Use getMeshID() for specific mesh names instead.")]] std::set<int> getMeshIDs() const;
                                                                                    ^~~~~~~~~~
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:247:100: warning:
narrowing conversion of ‘matlab::data::TypedArray<T>::operator[](size_t) const [with T = int; size_t = long unsigned
int](0).matlab::data::ArrayElementTypedRef<int, true>::operator matlab::data::ArrayElementTypedRef<int, true>::reference()’
from ‘matlab::data::ArrayElementTypedRef<int, true>::reference {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
                 outputs[0] = factory.createArrayFromBuffer<int32_t>({1,size[0]}, std::move(ids_ptr));
                                                                                                    ^
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:258:105: warning:
narrowing conversion of ‘matlab::data::TypedArray<T>::operator[](size_t) const [with T = int; size_t = long unsigned
int](0).matlab::data::ArrayElementTypedRef<int, true>::operator matlab::data::ArrayElementTypedRef<int, true>::reference()’
from ‘matlab::data::ArrayElementTypedRef<int, true>::reference {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
                 outputs[0] = factory.createArrayFromBuffer<double>({1,size[0]}, std::move(positions_ptr));
                                                                                                         ^
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:269:100: warning:
narrowing conversion of ‘matlab::data::TypedArray<T>::operator[](size_t) const [with T = int; size_t = long unsigned
int](0).matlab::data::ArrayElementTypedRef<int, true>::operator matlab::data::ArrayElementTypedRef<int, true>::reference()’
from ‘matlab::data::ArrayElementTypedRef<int, true>::reference {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
                 outputs[0] = factory.createArrayFromBuffer<int32_t>({1,size[0]}, std::move(ids_ptr));
                                                                                                    ^
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:335:105: warning:
narrowing conversion of ‘matlab::data::TypedArray<T>::operator[](size_t) const [with T = int; size_t = long unsigned
int](0).matlab::data::ArrayElementTypedRef<int, true>::operator matlab::data::ArrayElementTypedRef<int, true>::reference()’
from ‘matlab::data::ArrayElementTypedRef<int, true>::reference {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
                 outputs[0] = factory.createArrayFromBuffer<double>({1,size[0]}, std::move(positions_ptr));
                                                                                                         ^
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:336:96: error: no
matching function for call to ‘matlab::data::ArrayFactory::createArrayFromBuffer<int32_t>(<brace-enclosed initializer list>,
std::remove_reference<int*&>::type)’
                 outputs[1] = factory.createArrayFromBuffer<int32_t>({1,size[0]}, std::move(ids));
                                                                                                ^
In file included from /home/u0148289/software/matlab/R2020b/extern/include/MatlabDataArray.hpp:22:0,
                 from /home/u0148289/software/matlab/R2020b/extern/include/mexAdapter.hpp:10,
                 from
                 /home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:3:
/home/u0148289/software/matlab/R2020b/extern/include/MatlabDataArray/ArrayFactory.hpp:556:19: note: candidate:
template<class T> matlab::data::TypedArray<T>
matlab::data::ArrayFactory::createArrayFromBuffer(matlab::data::ArrayDimensions, matlab::data::buffer_ptr_t<T>,
matlab::data::MemoryLayout)
     TypedArray<T> createArrayFromBuffer(ArrayDimensions dims,
                   ^~~~~~~~~~~~~~~~~~~~~
/home/u0148289/software/matlab/R2020b/extern/include/MatlabDataArray/ArrayFactory.hpp:556:19: note:   template argument
deduction/substitution failed:
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:336:91: note:   cannot
convert ‘std::move<int*&>(ids)’ (type ‘std::remove_reference<int*&>::type {aka int*}’) to type
‘matlab::data::buffer_ptr_t<int> {aka std::unique_ptr<int [], void (*)(void*)>}’
                 outputs[1] = factory.createArrayFromBuffer<int32_t>({1,size[0]}, std::move(ids));
                                                                                  ~~~~~~~~~^~~~~
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:417:104: warning:
narrowing conversion of ‘dim’ from ‘int32_t {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
                 outputs[0] = factory.createArrayFromBuffer<double>({dim,size[0]}, std::move(values_ptr));
                                                                                                        ^
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:417:104: warning:
narrowing conversion of ‘dim’ from ‘int32_t {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:417:104: warning:
narrowing conversion of ‘matlab::data::TypedArray<T>::operator[](size_t) const [with T = int; size_t = long unsigned
int](0).matlab::data::ArrayElementTypedRef<int, true>::operator matlab::data::ArrayElementTypedRef<int, true>::reference()’
from ‘matlab::data::ArrayElementTypedRef<int, true>::reference {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:428:97: warning:
narrowing conversion of ‘dim’ from ‘int32_t {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
                 outputs[0] = factory.createArrayFromBuffer<double>({dim,1}, std::move(value_ptr));
                                                                                                 ^
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:428:97: warning:
narrowing conversion of ‘dim’ from ‘int32_t {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:449:104: warning:
narrowing conversion of ‘sizeA’ from ‘int32_t {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
                 outputs[0] = factory.createArrayFromBuffer<double>({sizeA,sizeB}, std::move(values_ptr));
                                                                                                        ^
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:449:104: warning:
narrowing conversion of ‘sizeA’ from ‘int32_t {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:449:104: warning:
narrowing conversion of ‘sizeB’ from ‘int32_t {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]
/home/u0148289/openfoam-adapter/matlab-bindings/+precice/@SolverInterface/private/preciceGateway.cpp:449:104: warning:
narrowing conversion of ‘sizeB’ from ‘int32_t {aka int}’ to ‘long unsigned int’ inside { } [-Wnarrowing]


Error in compile_matlab_bindings_for_precice (line 19)
mex(strcat(path_Interface,".cpp"),"-output",path_Interface,flags{:});

Any suggestions to solve this problem?

Best regards,
Jun

2

Hi @Yin_Jun,

the deprecation messages are not errors and this does not seem to be the reason this fails.

The main error is:

Error in compile_matlab_bindings_for_precice (line 19)
mex(strcat(path_Interface,".cpp"),"-output",path_Interface,flags{:});

Maybe @BenjaminRodenberg or @IshaanDesai have some clue of what could be going wrong here.

By the way, I see you opened a related issue: Error using mex · Issue #35 · precice/matlab-bindings · GitHub

3

Dear Makis,
Thank you for your kind reply. I remove the interface command " mex(strcat(path_Interface,".cpp"),"-output",path_Interface,flags{:});" Then the bindings works fine. I think the interface command caused this issue. Do you have some suggestions to solve this ?

image
image921×454 138 KB

4

Hi @Yin_Jun,

We found the problem which was leading to these errors and it was been fixed through Insert missing `_ptr` in `getMeshVerticesAndIDs` by erikscheurer · Pull Request #36 · precice/matlab-bindings · GitHub. Can you please try to use the latest develop branch of the MATLAB-bindings and see if you still get the compilation errors?

5

This topic was automatically closed 3 days after the last reply. New replies are no longer allowed.