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Adding Libraries to OpenFOAM

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Old   October 20, 2020, 06:07
Default Adding Libraries to OpenFOAM
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Mohammad Khojastehmehr
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Hi everybody, hope you are doing fine!

There is a library that I wanted to add to OpenFOAM called "Reaktoro". Here is a link to the source:
https://github.com/reaktoro/reaktoro

Unfortunately, I don't know much about C++ so I would be very appreciative if someone can help me with this in detail. I know it has something to do with options in the make folder but I don't know exactly how I can add this library in this case; since there are a bunch of folders in the source file.

I've read somethings about libraries in OpenFOAM but I'm a little bit confused; perhaps because I don't know the basics.
https://cfd.direct/openfoam/user-gui...-applications/

Thank you so much.
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Old   October 20, 2020, 11:45
Default Put the source in the make folder
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I realized all you have to do is to create a folder named lnInclude in your solver folder. Then put the whole source into this lnInclude.

Last edited by MCrossover97; October 21, 2020 at 08:42.
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Old   October 21, 2020, 08:49
Default undefined reference to ...
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Mohammad Khojastehmehr
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Now I'm getting some errors making the solver:
Code:
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 -Wno-attributes -O3  -DNoRepository -ftemplate-depth-100 -I/opt/openfoam8/src/finiteVolume/lnInclude -I/opt/openfoam8/src/meshTools/lnInclude -IlnInclude -I. -I/opt/openfoam8/src/OpenFOAM/lnInclude -I/opt/openfoam8/src/OSspecific/POSIX/lnInclude   -fPIC -fuse-ld=bfd -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPInt32Opt/reaktoroFOAM.o -L/opt/openfoam8/platforms/linux64GccDPInt32Opt/lib \
    -lfiniteVolume -lmeshTools -lOpenFOAM -ldl  \
     -lm -o /home/mcrossover97/OpenFOAM/mcrossover97-8/platforms/linux64GccDPInt32Opt/bin/reaktoroFOAM.C
Make/linux64GccDPInt32Opt/reaktoroFOAM.o: In function `main':
reaktoroFOAM.C:(.text.startup+0x60): undefined reference to `Reaktoro::ChemicalEditor::ChemicalEditor()'
reaktoroFOAM.C:(.text.startup+0x6f): undefined reference to `Reaktoro::StringList::StringList(char const*)'
reaktoroFOAM.C:(.text.startup+0x7a): undefined reference to `Reaktoro::ChemicalEditor::addAqueousPhaseWithElementsOf(Reaktoro::StringList const&)'
reaktoroFOAM.C:(.text.startup+0x82): undefined reference to `Reaktoro::StringList::~StringList()'
reaktoroFOAM.C:(.text.startup+0x91): undefined reference to `Reaktoro::StringList::StringList(char const*)'
reaktoroFOAM.C:(.text.startup+0x9c): undefined reference to `Reaktoro::ChemicalEditor::addGaseousPhase(Reaktoro::StringList const&)'
reaktoroFOAM.C:(.text.startup+0xa4): undefined reference to `Reaktoro::StringList::~StringList()'
reaktoroFOAM.C:(.text.startup+0xb3): undefined reference to `Reaktoro::StringList::StringList(char const*)'
reaktoroFOAM.C:(.text.startup+0xbe): undefined reference to `Reaktoro::ChemicalEditor::addMineralPhase(Reaktoro::StringList const&)'
reaktoroFOAM.C:(.text.startup+0xc6): undefined reference to `Reaktoro::StringList::~StringList()'
reaktoroFOAM.C:(.text.startup+0xd1): undefined reference to `Reaktoro::ChemicalEditor::operator Reaktoro::ChemicalSystem() const'
reaktoroFOAM.C:(.text.startup+0xe1): undefined reference to `Reaktoro::EquilibriumProblem::EquilibriumProblem(Reaktoro::ChemicalSystem const&)'
reaktoroFOAM.C:(.text.startup+0x11f): undefined reference to `Reaktoro::EquilibriumProblem::add(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
reaktoroFOAM.C:(.text.startup+0x179): undefined reference to `Reaktoro::EquilibriumProblem::add(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
reaktoroFOAM.C:(.text.startup+0x1d3): undefined reference to `Reaktoro::EquilibriumProblem::add(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
reaktoroFOAM.C:(.text.startup+0x22d): undefined reference to `Reaktoro::EquilibriumProblem::add(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
reaktoroFOAM.C:(.text.startup+0x263): undefined reference to `Reaktoro::equilibrate(Reaktoro::EquilibriumProblem const&)'
reaktoroFOAM.C:(.text.startup+0x282): undefined reference to `Reaktoro::ChemicalState::output(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int) const'
reaktoroFOAM.C:(.text.startup+0x29d): undefined reference to `Reaktoro::ChemicalState::~ChemicalState()'
reaktoroFOAM.C:(.text.startup+0x2a5): undefined reference to `Reaktoro::EquilibriumProblem::~EquilibriumProblem()'
reaktoroFOAM.C:(.text.startup+0x2ad): undefined reference to `Reaktoro::ChemicalSystem::~ChemicalSystem()'
reaktoroFOAM.C:(.text.startup+0x2b5): undefined reference to `Reaktoro::ChemicalEditor::~ChemicalEditor()'
reaktoroFOAM.C:(.text.startup+0x305): undefined reference to `Reaktoro::ChemicalState::~ChemicalState()'
reaktoroFOAM.C:(.text.startup+0x310): undefined reference to `Reaktoro::EquilibriumProblem::~EquilibriumProblem()'
reaktoroFOAM.C:(.text.startup+0x318): undefined reference to `Reaktoro::ChemicalSystem::~ChemicalSystem()'
reaktoroFOAM.C:(.text.startup+0x320): undefined reference to `Reaktoro::ChemicalEditor::~ChemicalEditor()'
reaktoroFOAM.C:(.text.startup+0x381): undefined reference to `Reaktoro::StringList::~StringList()'
collect2: error: ld returned 1 exit status
/opt/openfoam8/wmake/makefiles/general:140: recipe for target '/home/mcrossover97/OpenFOAM/mcrossover97-8/platforms/linux64GccDPInt32Opt/bin/reaktoroFOAM.C' failed
make: *** [/home/mcrossover97/OpenFOAM/mcrossover97-8/platforms/linux64GccDPInt32Opt/bin/reaktoroFOAM.C] Error 1
I can't understand what I'm missing. I'm still wondering is there anything I should have done more? Does it have anything to do with .so files? I can't see any .so file in the source folder so that I can put them in the option under EXE_LIBS. Should I somehow create these .so files? I'm confused. any help would be greatly appreciated.
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Old   October 21, 2020, 17:46
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Did you build the Reaktoro library? Following the guide for building Reaktoro you should end up with a directory called "build" that probably contains a folder with the .so files and another one with the headers (.H files).

Once you built Reaktoro you can use it in OpenFOAM by adding to the Make/options:
- The positions of the headers in EXE_INC
- The positions of the .so files and the name of the built libraries that you are using in EXE_LIBS. For example, if you build the boost libraries you end up with a folder containing two other folders: include and lib. "include" contains the headers, while "lib" contains the compiled libraries in .so files. One of these files is libboost_system.so. To add this file to the Make/options file you should write something like:

EXE_INC = \
...
-I<path/to/include> \
...

EXE_LIBS = \
...
-L<path/to/lib> \
-lboost_system \
...

The folder lnInclude is automatically generated when you use wmake to compile, you sould not create it
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Old   October 21, 2020, 19:17
Default error while loading shared libraries
  #5
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Mohammad Khojastehmehr
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Quote:
Originally Posted by EdoardoCip View Post
Did you build the Reaktoro library? Following the guide for building Reaktoro you should end up with a directory called "build" that probably contains a folder with the .so files and another one with the headers (.H files).

Once you built Reaktoro you can use it in OpenFOAM by adding to the Make/options:
- The positions of the headers in EXE_INC
- The positions of the .so files and the name of the built libraries that you are using in EXE_LIBS. For example, if you build the boost libraries you end up with a folder containing two other folders: include and lib. "include" contains the headers, while "lib" contains the compiled libraries in .so files. One of these files is libboost_system.so. To add this file to the Make/options file you should write something like:

EXE_INC = \
...
-I<path/to/include> \
...

EXE_LIBS = \
...
-L<path/to/lib> \
-lboost_system \
...

The folder lnInclude is automatically generated when you use wmake to compile, you sould not create it
Dear EdoardoCip,

Thank you so much for your answer. I build the library using miniconda with this command:
Code:
conda install reaktoro
I followed your instructions and now I am able to make the solver without any error; but now when I want to call my solver (reaktoroFOAM), it gives me this error:
Code:
reaktoroFOAM.C: error while loading shared libraries: libReaktoro.so: cannot open shared object file: No such file or directory
Did I miss something?

This is the body of the solver:
Code:
#include <Reaktoro/Reaktoro.hpp>
using namespace Reaktoro;

int main()
{
    ChemicalEditor editor;
    editor.addAqueousPhaseWithElementsOf("H2O NaCl CaCO3 CO2");
    editor.addGaseousPhase("CO2(g)");
    editor.addMineralPhase("Calcite");

    ChemicalSystem system(editor);

    EquilibriumProblem problem(system);
    problem.add("H2O", 1, "kg");
    problem.add("CO2", 1, "mol");
    problem.add("NaCl", 0.7, "mol");
    problem.add("CaCO3", 1, "g");

    ChemicalState state = equilibrate(problem);

    state.output("result.txt");
}
And this is what is in the option file:
Code:
EXE_INC = \
	-I/home/mcrossover97/miniconda3/include
	
	

EXE_LIBS = \
	-L/home/mcrossover97/miniconda3/lib \
	-lReaktoro
and make file:
Code:
reaktoroFOAM.C

EXE = $(FOAM_USER_APPBIN)/reaktoroFOAM.C
I appreciate your help so much,
Mohammad
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Old   October 22, 2020, 01:22
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Hi,

You might also have to location of the folder containing libReaktoro.so to the environment variable LD_LIBRARY_PATH

Hope this helps.

Cheers,
Antimony
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Old   October 22, 2020, 01:54
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You can update LD_LIBRARY_PATH with the position of libReaktoro.so. with the following command:
LD_LIBRARY_PATH=‘$LD_LIBRARY_PATH:<path/to/folder-with-libReaktoro.so>’

Also, you are missing return 0; at the end of the main.
int main()
{
...
state.output("result.txt");
return 0;
}

While the Make/file shuld be like this:

reaktoroFOAM.C

EXE = $(FOAM_USER_APPBIN)/reaktoroFOAM

Otherwise your exe would be called reaktoroFOAM.C
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Old   October 22, 2020, 06:33
Default Done!
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Mohammad Khojastehmehr
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Quote:
Originally Posted by Antimony View Post
You might also have to location of the folder containing libReaktoro.so to the environment variable LD_LIBRARY_PATH
Quote:
Originally Posted by EdoardoCip View Post
You can update LD_LIBRARY_PATH with the position of libReaktoro.so. with the following command:
LD_LIBRARY_PATH=‘$LD_LIBRARY_PATH:<path/to/folder-with-libReaktoro.so>’
I tried to update LD_LIBRARY_PATH with the following command:
Code:
LD_LIBRARY_PATH=‘$LD_LIBRARY_PATH:</home/mcrossover97/miniconda3/lib>’
It didn't give me any error but apparently, nothing had happened as I checked it to make sure it is updated:
Code:
echo $LD_LIBRARY_PATH
but it wasn't.

Then I tried to update the LD_LIBRARY_PATH with the following command:
Code:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/mcrossover97/miniconda3/lib
Now it works! Thank you so much for your help and time!
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Old   November 6, 2020, 02:42
Default Problem adding in Ubuntu
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Mohammad Khojastehmehr
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Hey Sorry to bother you guys again.


Now I want to do all the procedure in Ubuntu 18.04 (not WSL). I have done exactly the same things; but I cannot even make the solver, because it gives me this error:
Code:
(base) mohammad@mohammad-VirtualBox:~/OpenFOAM/mohammad-8/applications/solvers/reaktoroFoam$ wmake
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 -Wno-attributes -O3  -DNoRepository -ftemplate-depth-100 -I/opt/openfoam8/src/finiteVolume/lnInclude -I/opt/openfoam8/src/meshTools/lnInclude -I/home/mohammad/miniconda3/include -IlnInclude -I. -I/opt/openfoam8/src/OpenFOAM/lnInclude -I/opt/openfoam8/src/OSspecific/POSIX/lnInclude   -fPIC -fuse-ld=bfd -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPInt32Opt/reaktoroFoam.o -L/opt/openfoam8/platforms/linux64GccDPInt32Opt/lib \
    -L/home/mohammad/miniconda3/lib -lfiniteVolume -lmeshTools -lreaktoro -lOpenFOAM -ldl  \
     -lm -o /home/mohammad/OpenFOAM/mohammad-8/platforms/linux64GccDPInt32Opt/bin/reaktoroFoam
/usr/bin/ld.bfd: cannot find -lreaktoro
collect2: error: ld returned 1 exit status
/opt/openfoam8/wmake/makefiles/general:140: recipe for target '/home/mohammad/OpenFOAM/mohammad-8/platforms/linux64GccDPInt32Opt/bin/reaktoroFoam' failed
make: *** [/home/mohammad/OpenFOAM/mohammad-8/platforms/linux64GccDPInt32Opt/bin/reaktoroFoam] Error 1
The contents of the files are same as before:
Code:
EXE_INC = \
    -I$(LIB_SRC)/finiteVolume/lnInclude \
    -I$(LIB_SRC)/meshTools/lnInclude \
    -I/home/mohammad/miniconda3/include

EXE_LIBS = \
    -L/home/mohammad/miniconda3/lib \
    -lfiniteVolume \
    -lmeshTools \
    -lreaktoro
And the LD_LIBRARY_PATH is updated:
Code:
(base) mohammad@mohammad-VirtualBox:~/OpenFOAM/mohammad-8/applications/solvers/reaktoroFoam$ echo $LD_LIBRARY_PATH
 ‘/opt/ThirdParty-8/platforms/linux64Gcc/gperftools-svn/lib:/opt/paraviewopenfoam56/lib:/opt/openfoam8/platforms/linux64GccDPInt32Opt/lib/openmpi-system:/opt/ThirdParty-8/platforms/linux64GccDPInt32/lib/openmpi-system:/usr/lib/x86_64-linux-gnu/openmpi/lib:/home/mohammad/OpenFOAM/mohammad-8/platforms/linux64GccDPInt32Opt/lib:/opt/site/8/platforms/linux64GccDPInt32Opt/lib:/opt/openfoam8/platforms/linux64GccDPInt32Opt/lib:/opt/ThirdParty-8/platforms/linux64GccDPInt32/lib:/opt/openfoam8/platforms/linux64GccDPInt32Opt/lib/dummy::/home/mohammad/miniconda3/lib
What would possibly be different between WSL and Ubuntu on VirtualBox?
Thank you so much for your help again!
Mohammad
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Old   October 26, 2021, 06:37
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Im very late, but maybe it is because you seem to have double : before path to reaktoro library in your LD_LIBRARY_PATH
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Old   February 23, 2024, 02:34
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hi try changing your options as shown below

Quote:
EXE_INC = \
-I/home/mcrossover97/miniconda3/include



EXE_LIBS = \
-Wl,-rpath=/home/mcrossover97/miniconda3/lib \
-L/home/mcrossover97/miniconda3/lib \
-lReaktoro
it should work i think after this change
libReaktoro.so is a dynamically link so OS need to know its location at runtime an this can be done using -Wl,-rpath=<location of your library>
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