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

Wed Oct 4 18:08:18 CDT 2017

On Wed, Oct 4, 2017 at 6:52 PM, Klaus Burkart <k_burkart at yahoo.com> wrote:

> Thank you for the hint, the problem becomes clearer, it's looking for
> libpetsc.so.3.7   which is not found  but is located in the same directory
> as libpetsc.so  but doesn't come with the .so ending
>
> ldd
>
>     libpetsc.so.3.7 => not found
>

The build system you have is adding a spurious suffix to the library. You
can either fix it, or make a link
to that name in the lib directory.

   Matt

> Jed Brown <jed at jedbrown.org> schrieb am 22:51 Mittwoch, 4.Oktober 2017:
>
>
> Klaus Burkart <k_burkart at yahoo.com> writes:
>
> > Adding the path to LD_LIBRARY_PATH doesn't help, the problems remain the
> same, it has no effect
>
> You're having a problem linking correctly from the plugin, and maybe
> some error messages are being swallowed, but this is not a PETSc issue.
> You can use ldd to check whether the plugin was linked correctly (it
> should find libpetsc.so).
>
>
> >
> >    Jed Brown <jed at jedbrown.org> schrieb am 21:39 Mittwoch, 4.Oktober
> 2017:
> >
> >
> >  Klaus Burkart <k_burkart at yahoo.com> writes:
> >
> >> When I link the petsc library, the application side code is not
> properly compiled and the solver is not available for selection
> >>
> >> --> FOAM FATAL IO ERROR:
> >> Unknown asymmetric matrix solver petGMRES
> >
> > There must be some earlier error message.
> >
> >> Valid asymmetric matrix solvers are :
> >>
> >> 4
> >> (
> >> GAMG
> >> PBiCG
> >> PBiCGStab
> >> smoothSolver
> >> )
> >> I added the following to my makefile to link the petsc library
> >>
> >>     -L$(PETSC_DIR)/arch-linux2-c-debug/lib    -lpetsc
> >
> > In this case, you'd need to add that path to LD_LIBRARY_PATH so the
> > loader can find it.  None of these are PETSc issues, just linking
> > dynamic libraries.
> >
> >>    Jed Brown <jed at jedbrown.org> schrieb am 18:45 Mittwoch, 4.Oktober
> 2017:
> >>
> >>
> >>  Klaus Burkart <k_burkart at yahoo.com> writes:
> >>
> >>> My setup:
> >>>
> >>> .bashrc
> >>> export PETSC_DIR=/home/klaus/OpenFOAM/klaus-5.0/petsc-3.7.6
> >>> export PETSC_ARCH=arch-linux2-c-debug
> >>> export PETSC_CONFIGDIR=${PETSC_DIR}/lib/petsc
> >>>
> >>>
> >>> make options
> >>>     -I$(PETSC_CONFIGDIR)/conf \
> >>
> >> The above should not be needed.
> >>
> >>>     -I$(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
> >>
> >> How have you linked libpetFoam.so to libpetsc.so and did you use RPATH?
> >> That seems to be the problem.
> >>
> >>> 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.
> >>
> >> That's fine.  You can use the PETSC_OPTIONS environment variable or a
> >> configuration file to get run-time options to PETSc.
> >>
> >>> 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
> >>>
> >>>
> >>
> >>
> >
> >
>
>
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
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