[petsc-users] How to use petsc in a dynamically loaded shared library?

[Florian]

Am Mittwoch, den 18.07.2012, 09:15 -0500 schrieb Jed Brown:
> On Wed, Jul 18, 2012 at 8:52 AM, Florian Beck <Flo.44 at gmx.de> wrote:
>         [0]PETSC ERROR:
>         ------------------------------------------------------------------------
>         [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>         Violation, probably memory access out of range
>         [0]PETSC ERROR: Try option -start_in_debugger or
>         -on_error_attach_debugger
>         [0]PETSC ERROR: or see
>         http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>         [0]PETSC ERROR: configure using --with-debugging=yes,
>         recompile, link, and run
>         [0]PETSC ERROR: to get more information on the crash.
>         [0]PETSC ERROR: --------------------- Error Message
>         ------------------------------------
>         [0]PETSC ERROR: Signal received!
>         [0]PETSC ERROR:
>         ------------------------------------------------------------------------
>         [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 3, Fri Jun
>          4 15:34:52 CDT 2010
>         [0]PETSC ERROR: See docs/changes/index.html for recent
>         updates.
>         [0]PETSC ERROR: See docs/faq.html for hints about trouble
>         shooting.
>         [0]PETSC ERROR: See docs/index.html for manual pages.
>         [0]PETSC ERROR:
>         ------------------------------------------------------------------------
>         [0]PETSC ERROR: -no_signal_handler,--with-dynamic-loading on a
>         linux-gnu named riemann by beck Wed Jul 18 15:41:20 2012
>         [0]PETSC ERROR: Libraries linked
>         from /home/hazelsct/repositories/petsc/linux-gnu-c-opt/lib
>         [0]PETSC ERROR: Configure run at Wed Aug  4 15:00:14 2010
>         [0]PETSC ERROR: Configure options --with-shared
>         --with-debugging=0 --useThreads 0 --with-clanguage=C++
>         --with-c-support --with-fortran-interfaces=1
>         --with-mpi-dir=/usr/lib/openmpi --with-mpi-shared=1
>         --with-blas-lib=-lblas --with-lapack-lib=-llapack
>         --with-umfpack=1
>         --with-umfpack-include=/usr/include/suitesparse
>         --with-umfpack-lib="[/usr/lib/libumfpack.so,/usr/lib/libamd.so]" --with-spooles=1 --with-spooles-include=/usr/include/spooles --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1 --with-hypre-dir=/usr --with-scotch=1 --with-scotch-include=/usr/include/scotch --with-scotch-lib=/usr/lib/libscotch.so --with-hdf5=1 --with-hdf5-dir=/usr
>         [0]PETSC ERROR:
>         ------------------------------------------------------------------------
>         [0]PETSC ERROR: User provided function() line 0 in unknown
>         directory unknown file
>         --------------------------------------------------------------------------
>         MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>         with errorcode 59.
>         
> 
> This is in your code. Run in a debugger to find out what's wrong.
>  
>         

I have used ddd and when I step into the VecDestroy function I get the
signal 11. I have three Vectors and it's only possible to destroy one of
them. Do I have consider something special before I destroy them? I read
values from the Vector which I'm able to destroy. 


>         NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
>         processes.
>         You may or may not see output from other processes, depending
>         on
>         exactly when Open MPI kills them.
>         --------------------------------------------------------------------------
>         
>         
>         > > Of course I have a memory leak, because I'm not using the
>         functions to
>         > > destroy my vectors. Is there a simple example how to use
>         the
>         > petsc-library
>         > > in a program like the following pseudo-code:
>         > >
>         >
>         > Is MPI initialized before this is called? Did you plan to do
>         this in
>         > parallel? Are you linking PETSc dynamically (as in, you
>         dlopen and dlsym
>         > PETSc functions to call them, or perhaps you declare weak
>         symbols in your
>         > code), linking your app-specific solver module (you call
>         PETSc normally
>         > and
>         > use dlsym at a higher level), or something else? Remember to
>         configure
>         > PETSc --with-dynamic-loading if necessary.
>         
>         
>         I plan to use it parallel, but first I want to calculate
>         serial. I'm using dlopen to link my library.
>         
>         What happens if I call the PetsInitalize function several
>         times? I call it in every function call.
> 
> You can call it multiple times, but MPI_Init() can only be called
> once. We usually recommend that people only call PetscInitialize once
> (the logging/profiling/debugging infrastructure is more useful that
> way).