[petsc-users] Memory corruption with two-dimensional array and PetscMemzero

[Christophe Ortiz]

I found another problem when using two-dimensional arrays defined using
pointers of pointers.

When I use a "classical" two-dimensional array defined by

PetscScalar  array[dof][dof];

and then build the Jacobian using

ierr = MatSetValuesBlocked(*Jpre,1,&row,1,&col,&array[0][0],INSERT_VALUES);

It works fine.

The problem comes when I define the two-dimensional array as follows:

PetscScalar  **array;

 array = (PetscScalar**)malloc(sizeof(PetscScalar*) * dof);
 for (k = 0; k < dof; k++){
   array[k] = (PetscScalar*)malloc(sizeof(PetscScalar) * dof);
  }

When I pass it to MatSetValuesBlocked() there is a problem. Either Petsc
complains because I am not passing it the right way or when it accepts it,
wrong data is passed because the solution is not correct. Maybe Petsc
expect dof*dof values and only dof are passed ?

How a two-dimensional array declared with pointers of pointers should be
passed to MatSetValuesBlocked() ?

Many thanks in advance.
Christophe




On Thu, May 15, 2014 at 2:08 AM, Jed Brown <jed at jedbrown.org> wrote:

> Christophe Ortiz <christophe.ortiz at ciemat.es> writes:
>
> > Hi all,
> >
> > I am experiencing some problems of memory corruption with PetscMemzero().
> >
> > I set the values of the Jacobian by blocks using MatSetValuesBlocked().
> To
> > do so, I use some temporary two-dimensional arrays[dof][dof] that I must
> > reset at each loop.
> >
> > Inside FormIJacobian, for instance, I declare the following
> two-dimensional
> > array:
> >
> >    PetscScalar  diag[dof][dof];
> >
> > and then, to zero the array diag[][] I do
> >
> >    ierr = PetscMemzero(diag,dof*dof*sizeof(PetscScalar));
>
> Note that this can also be spelled
>
>   PetscMemzero(diag,sizeof diag);
>
> > Then, inside main(), once dof is determined, I allocate memory for diag
> as
> > follows:
> >
> >  diag = (PetscScalar**)malloc(sizeof(PetscScalar*) * dof);
> >
> >  for (k = 0; k < dof; k++){
> >   diag[k] = (PetscScalar*)malloc(sizeof(PetscScalar) * dof);
> >  }
> > That is, the classical way to allocate memory using the pointer notation.
>
> Note that you can do a contiguous allocation by creating a Vec, then use
> VecGetArray2D to get 2D indexing of it.
>
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