dolfin team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

This commit resulted in the following error when using PETSc 3.2:

[  0%] Building CXX object
dolfin/CMakeFiles/dolfin.dir/la/PETScPreconditioner.cpp.o
/home/johannr/dev/fenics/src/dolfin/trunk/dolfin/la/PETScPreconditioner.cpp:
In member function ‘virtual void
dolfin::PETScPreconditioner::set(dolfin::PETScKrylovSolver&)’:
/home/johannr/dev/fenics/src/dolfin/trunk/dolfin/la/PETScPreconditioner.cpp:573:71:
error: invalid conversion from ‘std::vector<double>::size_type {aka
long unsigned int}’ to ‘PetscReal* {aka double*}’ [-fpermissive]
/home/johannr/dev/fenics/src/dolfin/trunk/dolfin/la/PETScPreconditioner.cpp:573:71:
error: too many arguments to function ‘PetscErrorCode
PCSetCoordinates(PC, PetscInt, PetscReal*)’
In file included from /usr/lib/petscdir/3.2/include/petscksp.h:6:0,
                 from
/home/johannr/dev/fenics/src/dolfin/trunk/dolfin/la/PETScPreconditioner.cpp:27:
/usr/lib/petscdir/3.2/include/petscpc.h:398:23: note: declared here

The attached patch fixes the problem. Does it look like the correct fix?

Johannes

On Tue, Feb 19, 2013 at 11:18 PM,  <noreply@xxxxxxxxxxxxx> wrote:
> ------------------------------------------------------------
> revno: 7446
> committer: Garth N. Wells <gnw20@xxxxxxxxx>
> branch nick: petsc-dev
> timestamp: Tue 2013-02-19 20:46:47 +0000
> message:
>   Expose some more ML options.
> modified:
>   dolfin/fem/DofMap.cpp
>   dolfin/la/GenericPreconditioner.h
>   dolfin/la/PETScPreconditioner.cpp
>   dolfin/la/PETScPreconditioner.h
>
>
> --
> lp:dolfin
> https://code.launchpad.net/~dolfin-core/dolfin/trunk
>
> Your team DOLFIN Core Team is subscribed to branch lp:dolfin.
> To unsubscribe from this branch go to https://code.launchpad.net/~dolfin-core/dolfin/trunk/+edit-subscription
>
> === modified file 'dolfin/fem/DofMap.cpp'
> --- dolfin/fem/DofMap.cpp       2013-02-19 19:19:30 +0000
> +++ dolfin/fem/DofMap.cpp       2013-02-19 20:46:47 +0000
> @@ -311,11 +311,15 @@
>      // Copy dof coordinates into vector
>      for (std::size_t i = 0; i < dofs.size(); ++i)
>      {
> -      const std::size_t local_index = dofs[i] - offset;
> -      for (std::size_t j = 0; j < gdim; ++j)
> +      const std::size_t dof = dofs[i];
> +      if (dof >=  _ownership_range.first && dof < _ownership_range.second)
>        {
> -        dolfin_assert(gdim*local_index + j < x.size());
> -        x[gdim*local_index + j] = coordinates[i][j];
> +        const std::size_t local_index = dof - offset;
> +        for (std::size_t j = 0; j < gdim; ++j)
> +        {
> +          dolfin_assert(gdim*local_index + j < x.size());
> +          x[gdim*local_index + j] = coordinates[i][j];
> +        }
>        }
>      }
>    }
>
> === modified file 'dolfin/la/GenericPreconditioner.h'
> --- dolfin/la/GenericPreconditioner.h   2012-11-09 20:57:58 +0000
> +++ dolfin/la/GenericPreconditioner.h   2013-02-19 20:46:47 +0000
> @@ -42,7 +42,18 @@
>      virtual void set_nullspace(const std::vector<const GenericVector*> nullspace)
>      {
>        dolfin_error("GenericPreconditioner.h",
> -                   "set nullspace for precontioner operator",
> +                   "set nullspace for preconditioner operator",
> +                   "Not supported by current preconditioner type");
> +    }
> +
> +    /// Set the coordinates of the operator (matrix) rows. This is
> +    /// can be used by required for certain preconditioners, e.g. ML.
> +    /// The input for this function can be generated using
> +    /// GenericDofMap::tabulate_all_dofs.
> +    virtual void set_coordinates(const std::vector<double>& x)
> +    {
> +      dolfin_error("GenericPreconditioner.h",
> +                   "set coordinates for preconditioner operator",
>                     "Not supported by current preconditioner type");
>      }
>
>
> === modified file 'dolfin/la/PETScPreconditioner.cpp'
> --- dolfin/la/PETScPreconditioner.cpp   2013-02-19 12:58:48 +0000
> +++ dolfin/la/PETScPreconditioner.cpp   2013-02-19 20:46:47 +0000
> @@ -135,13 +135,10 @@
>    p_ml.add<int>("energy_minimization", -1, 4);
>    p_ml.add<double>("energy_minimization_threshold");
>    p_ml.add<double>("auxiliary_threshold");
> -
> -  std::set<std::string> aggregation_schemes;
> -  aggregation_schemes.insert("Uncoupled");
> -  aggregation_schemes.insert("Coupled");
> -  aggregation_schemes.insert("MIS");
> -  aggregation_schemes.insert("METIS");
> -  p_ml.add<std::string>("aggregation_scheme", aggregation_schemes);
> +  p_ml.add<bool>("repartition");
> +  p_ml.add<std::string>("repartition_type", boost::assign::list_of("Zoltan")("ParMETIS"));
> +  p_ml.add<std::string>("zoltan_repartition_scheme", boost::assign::list_of("RCB")("hypergraph")("fast_hypergraph"));
> +  p_ml.add<std::string>("aggregation_scheme", boost::assign::list_of("Uncoupled")("Coupled")("MIS")("METIS"));
>    p.add(p_ml);
>
>    // Hypre/ParaSails parameters
> @@ -185,7 +182,7 @@
>    // Do nothing
>  }
>  //-----------------------------------------------------------------------------
> -void PETScPreconditioner::set(PETScKrylovSolver& solver) const
> +void PETScPreconditioner::set(PETScKrylovSolver& solver)
>  {
>    dolfin_assert(solver.ksp());
>
> @@ -341,7 +338,6 @@
>      if (parameters("ml")["energy_minimization"].is_set())
>      {
>        const int method = parameters("ml")["energy_minimization"];
> -      cout << "Setting energy min" << endl;
>        PetscOptionsSetValue("-pc_ml_EnergyMinimization",
>                              boost::lexical_cast<std::string>(method).c_str());
>
> @@ -355,12 +351,31 @@
>      }
>
>      // Auxiliary threshold drop tolerance
> +    /*
> +    PetscOptionsSetValue("-pc_ml_Aux", "1");
>      if (parameters("ml")["auxiliary_threshold"].is_set())
>      {
>        const double threshold = parameters("ml")["auxiliary_threshold"];
>        PetscOptionsSetValue("-pc_ml_AuxThreshold",
>                              boost::lexical_cast<std::string>(threshold).c_str());
>      }
> +    */
> +
> +    // Allow ML to re-partition problem
> +    if (parameters("ml")["repartition"].is_set())
> +    {
> +      const bool repartition = parameters("ml")["repartition"];
> +      if (repartition)
> +      {
> +        PetscOptionsSetValue("-pc_ml_repartition", "1");
> +        if (parameters("ml")["repartition_type"].is_set())
> +          PetscOptionsSetValue("-pc_ml_repartitionType", parameters("ml")["repartition_type"].value_str().c_str());
> +        if (parameters("ml")["zoltan_repartition_scheme"].is_set())
> +          PetscOptionsSetValue("-pc_ml_repartitionZoltanScheme", parameters("ml")["zoltan_repartition_scheme"].value_str().c_str());
> +      }
> +      else
> +        PetscOptionsSetValue("-pc_ml_repartition", "0");
> +    }
>
>      // --- PETSc parameters
>
> @@ -553,6 +568,13 @@
>    // Make sure options are set
>    PCSetFromOptions(pc);
>
> +  // Set physical coordinates for row dofs
> +  if (!_coordinates.empty())
> +    PCSetCoordinates(pc, 3, _coordinates.size()/3, _coordinates.data());
> +
> +  // Clear memeory
> +  _coordinates.clear();
> +
>    // Print preconditioner information
>    const bool report = parameters["report"];
>    if (report)
> @@ -600,6 +622,11 @@
>    #endif
>  }
>  //-----------------------------------------------------------------------------
> +void PETScPreconditioner::set_coordinates(const std::vector<double>& x)
> +{
> +  _coordinates = x;
> +}
> +//-----------------------------------------------------------------------------
>  std::string PETScPreconditioner::str(bool verbose) const
>  {
>    std::stringstream s;
>
> === modified file 'dolfin/la/PETScPreconditioner.h'
> --- dolfin/la/PETScPreconditioner.h     2012-11-09 20:57:58 +0000
> +++ dolfin/la/PETScPreconditioner.h     2013-02-19 20:46:47 +0000
> @@ -58,7 +58,7 @@
>      virtual ~PETScPreconditioner();
>
>      /// Set the precondtioner type and parameters
> -    virtual void set(PETScKrylovSolver& solver) const;
> +    virtual void set(PETScKrylovSolver& solver);
>
>      /// Set the (approximate) null space of the preconditioner operator
>      /// (matrix). This is required for certain preconditioner types,
> @@ -69,6 +69,12 @@
>      boost::shared_ptr<const MatNullSpace> nullspace() const
>      { return petsc_nullspace; }
>
> +    /// Set the coordinates of the operator (matrix) rows. This is
> +    /// can be used by required for certain preconditioners, e.g. ML.
> +    /// The input for this function can be generated using
> +    /// GenericDofMap::tabulate_all_dofs.
> +    void set_coordinates(const std::vector<double>& x);
> +
>      /// Return informal string representation (pretty-print)
>      std::string str(bool verbose) const;
>
> @@ -99,6 +105,9 @@
>      // the future.
>      boost::shared_ptr<MatNullSpace> petsc_nullspace;
>
> +    // Operator row coordinates
> +    std::vector<double> _coordinates;
> +
>    };
>
>  }
>
>

Attachment: petsc3.2.patch
Description: Binary data