dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

On 20 February 2013 09:23, Johannes Ring <johannr@xxxxxxxxx> wrote:
> 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?
>

Looks good.

Garth

> 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;
>> +
>>    };
>>
>>  }
>>
>>
>
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