[petsc-users] How to interface with PETSc from another application?

[Klaus Burkart]

My setup:

.bashrc
export PETSC_DIR=/home/klaus/OpenFOAM/klaus-5.0/petsc-3.7.6
export PETSC_ARCH=arch-linux2-c-debug
export PETSC_CONFIGDIR=${PETSC_DIR}/lib/petsc


make options
    -I$(PETSC_CONFIGDIR)/conf \
    -I$(PETSC_DIR)/include \
    -I$(PETSC_DIR)/arch-linux2-c-debug/include

Installation and tests worked fine.

The output using:     PetscInitialize(0,0,NULL,NULL); at the beginning and PetscFinalize(); at the end of the code section including PETSc (solver section) is:

simpleFoam: symbol lookup error: /home/klaus/OpenFOAM/klaus-5.0/platforms/linux64GccDPInt32Opt/lib/libpetFoam.so: undefined symbol: PetscInitialize

No simulation is triggered


When I just declare Mat M; and call a function with M as a parameter which outputs "Petsc - Hello" and sets the matrix M to symmetric (using: MatSetOption(A, MAT_SYMMETRIC, PETSC_TRUE);), the execution of a simulation is triggered but MatSetOption is causing a problem, I assume because PetscInitialize is missing

Petsc - Hello nonepetGMRES:  Solving for Ux, Initial residual = 1, Final residual = 1, No Iterations 0
Petsc - Hello nonepetGMRES:  Solving for Uz, Initial residual = 1, Final residual = 1, No Iterations 0
simpleFoam: symbol lookup error: /home/klaus/OpenFOAM/klaus-5.0/platforms/linux64GccDPInt32Opt/lib/libpetFoam.so: undefined symbol: MatSetOption

Maybe important to know, there's no way to enter commmand line input in the terminal while a simulation is running because the application displays continuously the intermediate simulation results. That's why I use PetscInitialize(0,0,NULL,NULL); There's now way to provide command line input.

I came back to this simple test after writing "the complete code" which showed these problems and stripped it down, step-by-step, to figure out what causes the problem i.e. everything but a declaration. 

 

    Jed Brown <jed at jedbrown.org> schrieb am 17:17 Mittwoch, 4.Oktober 2017:
 

 Klaus Burkart <k_burkart at yahoo.com> writes:

> What's the concept to interface with PETSc from another application to solve a linear system with PETSc?
>
> The standard procedure of the job:
>
> 1: The application provides a matrix which needs to be converted and be loaded into PETSc
>
> 2: The application provides the rhs vector (containing pointers!) which needs to be loaded into PETSc 
>
> 3: The linear system is to be solved using PETSc
>
> 4: The application provides the result vector x, the PETSc result needs to be copied back to the application into vector x (also expecting pointers)
>
>
> The problem - maybe a completely wrong approach when it comes to using PETSc: 
>
> With other linear algebra libraries, I included the library functionality in the code of a new solver accessing the functionality usually via header files and created a plugin which can be called from the application when running a simulation. 
>
> Even so the mixed code including PETSc code can be compiled, the bit of the plugin, interfacing with the application is broken as soon as I include more than a PETSc declaration in the mixed code.

Sounds like maybe you haven't correctly linked to the PETSc library.
Sending us the commands run and output/errors would be helpful to debug.

> How to interface with PETSc from a software application?  (I am using c++ and Ubuntu)
>
> Klaus

   
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