Memory corruption error in SNESSolve

Tue Jan 22 19:39:15 CST 2008

Dave is correct. Also I would point out that based upon your example code,
you probably want to use FormFunctionLocal() instead. For this, please
refer to SNES ex5.

  Thanks,

     Matt

On Jan 22, 2008 6:55 PM, Dave May <dave.mayhem23 at gmail.com> wrote:
> Hey Vijay,
>     I can spot something wrong. VecGetSize gives you the global length of
> the vector. However VecGetArray only gives you access to the LOCAL portion
> of the vector data for that processor. Thus you need to use a local index if
> you are going to set the values directly into the array.
>
> In parallel, xx[n-1] will always be outside the bounds of the processors
> local portion of the vector if n is the global vector length.
>
> Cheers,
>     Dave.
>
>
>
>
>
> > Here's the function.
> >
> > PetscErrorCode FormFunction(SNES snes,Vec x,Vec f,void *ctx)
> > {
> >  PetscScalar    *xx,*ff,d;
> >  PetscErrorCode ierr;
> >  PetscInt       i,n;
> >
> >  PetscFunctionBegin;
> >  ierr = VecGetArray(x,&xx);CHKERRQ(ierr);
> >  ierr = VecGetArray(f,&ff);CHKERRQ(ierr);
> >  ierr = VecGetSize(x,&n);CHKERRQ(ierr);
> >
> >  double h = 1.0/(n-1) ;
> >  d = (PetscReal)(n - 1); d = d*d;
> >  double pos ;
> >
> >  ff[0]   = xx[0];      // left boundary with Dirichlet = 0
> >  // residual : (un-1 -2*un + un+1)/h^2 + Reaction*u - f
> >  for (i=1; i<n-1; i++) {
> >    pos = i*h ;
> >    ff[i] = -Diffusion(pos, 0, 0, 0, xx[i])*d*(xx[i-1] - 2.0*xx[i] +
> > xx[i+1]) + Reaction(pos, 0, 0, 0, xx[i])*xx[i] - RHS(pos, 0, 0, 0,
> > xx[i]) ;
> >  }
> >  ff[n-1] = xx[n-1] - 1.0;            // right boundary with Dirichlet = 1
> >
> >  ierr = VecRestoreArray(x,&xx);CHKERRQ(ierr);
> >  ierr = VecRestoreArray(f,&ff);CHKERRQ(ierr);
> >  PetscFunctionReturn(0);
> > }
> >
> > One question though. If i use GetArray and RestoreArray to change the
> > values directly in memory, do i still have to make the
> > VecAssemblyBegin-End calls ?
> >
> > Thanks again for the help Matt.
> >
> > Vijay
> >
> >
> >
> >
> > On Jan 22, 2008 5:02 PM, Matthew Knepley <knepley at gmail.com> wrote:
> > > On Jan 22, 2008 3:54 PM, Vijay M < vijay.m at gmail.com> wrote:
> > > > Hi all,
> > > >
> > > > I am currently trying to use LibMesh with PETSc SNES solver to solve a
> > > > nonlinear Diffusion-reaction problem. The code works fine with 1
> > > > processor but when i use 2 processors for the exact same problem, it
> > > > throws me this error regarding memory corruption. I am not sure what
> > > > this error is about and was wondering if someone can help me out on
> > > > this. Note: My residual function is being called successfully and
> > > > returns the residual back without any problem since i can see some
> > > > print message at the end of the call ! Hence, this problem is not in
> > > > my custom FormFunction.
> > >
> > > Actually, it is very likely that the problem is in your FormFunction.
> The
> > > error is being reported because after every call to FormFunction, we
> > > walk the PETSc heap and validate all the pieces of memory we allocated.
> > > Something wrote over a piece of memory we already own, so the OS
> > > did not complain and you saw your printout, however there is still
> corruption.
> > > I would advise you to run 'valgrind' on the code. It is the best tool I
> have
> > > used for finding these kind of errors.
> > >
> > >   Matt
> > >
> > >
> > > > [1]PETSC ERROR: PetscMallocValidate: error detected at
> > > > SNESComputeFunction() line 950 in src/snes/interface/snes.c
> > > > [1]PETSC ERROR: Memory at address 0xa5cf40 is corrupted
> > > > [1]PETSC ERROR: Probably write past beginning or end of array
> > > > [1]PETSC ERROR: Last intact block allocated in PetscStrallocpy() line
> > > > 82 in src/sys/utils/str.c
> > > > [0]PETSC ERROR: PetscMallocValidate: error detected at
> > > > SNESComputeFunction() line 950 in src/snes/interface/snes.c
> > > > [0]PETSC ERROR: Memory at address 0xa5cf30 is corrupted
> > > > [0]PETSC ERROR: Probably write past beginning or end of array
> > > > [0]PETSC ERROR: Last intact block allocated in PetscStrallocpy() line
> > > > 82 in src/sys/utils/str.c
> > > > [0]PETSC ERROR: --------------------- Error Message
> > > > ------------------------------------
> > > > [0]PETSC ERROR: Memory corruption!
> > > > [0]PETSC ERROR:  !
> > > > [0]PETSC ERROR:
> > > >
> ------------------------------------------------------------------------
> > > > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 7, Fri Oct 26
> > > > 14:21:35 CDT 2007 HG revision:
> > > > 2e223033ba960114833e1f9713ab393ec78c056f
> > > > [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: ./myProg-opt on a linux-gnu named [1]PETSC ERROR:
> > > > --------------------- Error Message
> > > > ------------------------------------
> > > > [1]PETSC ERROR: Memory corruption!
> > > > [1]PETSC ERROR:  !
> > > > [1]PETSC ERROR:
> > > >
> ------------------------------------------------------------------------
> > > > [1]PETSC ERROR: Petsc Release Version 2.3.3, Patch 7, Fri Oct 26
> > > > 14:21:35 CDT 2007 HG revision:
> > > > 2e223033ba960114833e1f9713ab393ec78c056f
> > > > [1]PETSC ERROR: See docs/changes/index.html for recent updates.
> > > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > > > [1]PETSC ERROR: See docs/index.html for manual pages.
> > > > [1]PETSC ERROR: ----------------------------[cli_0]: aborting job:
> > > > application called MPI_Abort(comm=0x84000000, 78) - process 0
> > > > [cli_1]: aborting job:
> > > > application called MPI_Abort(comm=0x84000000, 78) - process 1
> > > > grove.ne.tamu.edu by vijaysm Tue Jan 22 15:47:58 2008
> > > > [0]PETSC ERROR: Libraries linked from
> > > > /state/partition1/local/petsc-2.3.3-p7/lib/linux-gnu-c-debug
> > > > [0]PETSC ERROR: Configure run at Fri Nov  9 15:02:46 2007
> > > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=ifort
> > > > --with-cxx=g++ --download-f-blas-lapack=1 --download-mpich=1
> > > > --with-shared=1
> > > > [0]PETSC ERROR:
> > > >
> ------------------------------------------------------------------------
> > > > [0]PETSC ERROR: PetscMallocValidate() line 139 in src/sys/memory/mtr.c
> > > > [0]PETSC ERROR: SNESComputeFunction() line 950 in
> src/snes/interface/snes.c
> > > > [0]PETSC ERROR: SNESSolve_LS() line 158 in src/snes/impls/ls/ls.c
> > > > [0]PETSC ERROR: SNESSolve() line 1871 in src/snes/interface/snes.c
> > > > [0]PETSC ERROR: main() line 395 in unknowndirectory/myProg.C
> > > >
> > > > If you need some more information, feel free to let me know. Thanks in
> advance !
> > > >
> > > > Vijay
> > > >
> > > >
> > >
> > >
> > >
> > > --
> > > 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
> > >
> > >
> >
> >
>
>

-- 
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