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Commit edb2158b authored by Praetorius, Simon's avatar Praetorius, Simon
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solvers are reworked and a lot of thingt corrected in the parallel petsc backend

parent d93ad598
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AMDiS/src/AMDiS.cc
View file @ edb2158b
......@@ -29,6 +29,10 @@
#endif
#include "boost/program_options.hpp"
#if defined HAVE_PETSC || defined HAVE_SEQ_PETSC || defined HAVE_PARALLEL_PETSC
#include <petsc.h>
#endif
namespace AMDiS {
using namespace std;
......
AMDiS/src/AMDiS.h
View file @ edb2158b
......@@ -154,9 +154,7 @@
#include "parallel/StdMpi.h"
#include "parallel/ParallelProblemStat.h"
#if HAVE_PARALLEL_MTL4
// #include "parallel/PMTL4Solver.h"
#else
#if !HAVE_PARALLEL_MTL4
#include "parallel/PetscSolver.h"
#include "parallel/PetscSolverNavierStokes.h"
#endif
......
AMDiS/src/AMDiS_fwd.h
View file @ edb2158b
......@@ -35,6 +35,7 @@ namespace AMDiS {
class AdaptStationary;
class Assembler;
class BasisFunction;
struct BlockMTLMatrix;
class BoundaryManager;
// class CGSolver;
class CoarseningManager;
......
AMDiS/src/CreatorMap.cc
View file @ edb2158b
......@@ -25,6 +25,7 @@
#include "MTL4Types.h"
#include "solver/LinearSolver.h"
#include "solver/ITL_Solver.h"
#include "solver/BITL_Solver.h"
#include "solver/ITL_Preconditioner.h"
#include "solver/UmfPackSolver.h"
#include "solver/KrylovPreconditioner.h"
......@@ -61,6 +62,9 @@ namespace AMDiS {
{
LinearSolverCreator *creator;
// creators for MTL4 krylov solvers
// _________________________________________________________________________
creator = new CGSolver::Creator;
addCreator("mtl_cg", creator);
......@@ -115,11 +119,64 @@ namespace AMDiS {
addCreator("mtl_hypre", creator);
#endif
// creators for block krylov solvers
// _________________________________________________________________________
creator = new B_CGSolver::Creator;
addCreator("bmtl_cg", creator);
creator = new B_CGSSolver::Creator;
addCreator("bmtl_cgs", creator);
// creator = new B_BiCGSolver::Creator;
// addCreator("mtl_bicg", creator);
creator = new B_BiCGStabSolver::Creator;
addCreator("bmtl_bicgstab", creator);
// creator = new B_BiCGStab2Solver::Creator;
// addCreator("bmtl_bicgstab2", creator); // MTL Error
// creator = new B_BiCGStabEllSolver::Creator;
// addCreator("bmtl_bicgstab_ell", creator); // MTL Error
// creator = new QMRSolver::Creator;
// addCreator("mtl_qmr", creator);
creator = new B_TFQMRSolver::Creator;
addCreator("bmtl_tfqmr", creator);
creator = new B_GMResSolver::Creator;
addCreator("bmtl_gmres", creator);
creator = new B_GcrSolver::Creator;
addCreator("bmtl_gcr", creator);
creator = new B_FGMResSolver::Creator;
addCreator("bmtl_fgmres", creator);
// creator = new B_IDRsSolver::Creator;
// addCreator("bmtl_idr_s", creator); // MTL Error
creator = new B_MinResSolver::Creator;
addCreator("bmtl_minres", creator);
creator = new B_PreOnly::Creator;
addCreator("bmtl_preonly", creator);
addCreator("bmtl_richardson", creator);
// creators for PETSc solvers
// _________________________________________________________________________
#if defined HAVE_SEQ_PETSC
// sequential PETSc-Solver
creator = new PetscSolver<>::Creator;
creator = new PetscSolver::Creator;
addCreator("petsc_petsc", creator); // standard creator for petsc solver
addCreator("petsc", creator);
LinearSolverCreator* creator2 = new PetscSolverNested::Creator;
addCreator("bpetsc_petsc", creator2); // standard creator for petsc solver
addCreator("bpetsc", creator2);
std::map<std::string,std::string>::iterator it;
PetscParameters params;
......@@ -127,7 +184,8 @@ namespace AMDiS {
it!= params.solverMap.end();
it++) {
CreatorMap< LinearSolver >::addCreator("petsc_" + it->first, creator);
}
CreatorMap< LinearSolver >::addCreator("bpetsc_" + it->first, creator2);
}
#endif
}
......@@ -159,6 +217,22 @@ namespace AMDiS {
}
template<>
void CreatorMap<ITL_BasePreconditioner<BlockMTLMatrix, MTLTypes::MTLVector> >::addDefaultCreators()
{
addCreator("no", new BlockIdentityPreconditioner::Creator);
addCreator("diag", new BlockDiagonalPreconditioner::Creator);
}
#if defined HAVE_SEQ_PETSC
template<>
void CreatorMap<PetscPreconditioner>::addDefaultCreators() { }
template<>
void CreatorMap<PetscPreconditionerNested>::addDefaultCreators() { }
#endif
template<>
void CreatorMap<Estimator>::addDefaultCreators()
{
......
AMDiS/src/CreatorMap.h
View file @ edb2158b
......@@ -43,13 +43,16 @@ namespace AMDiS {
template<typename BaseClass>
class CreatorMap
{
public:
typedef std::map< std::string, CreatorInterface<BaseClass>* > CreatorMapType;
public:
/// Adds a new creator together with the given key to the map.
static void addCreator(std::string key, CreatorInterface<BaseClass>* creator)
{
FUNCNAME("CreatorMap::addCreator()");
init();
TEST_EXIT(creatorMap[key] == nullptr)
TEST_EXIT(creatorMap[key] == NULL)
("there is already a creator for key %s\n",key.c_str());
creatorMap[key] = creator;
}
......@@ -66,8 +69,10 @@ namespace AMDiS {
FUNCNAME("CreatorMap::getCreator()");
init();
CreatorInterface<BaseClass> *creator = creatorMap[key];
TEST_EXIT(creator)("No creator for key \"%s\" defined in init file for parameter \"%s\"\n",
key.c_str(), initFileStr.c_str());
TEST_EXIT(creator)
("No creator for key \"%s\" defined in init file for parameter \"%s\"\n",
key.c_str(), initFileStr.c_str());
return creator;
}
......@@ -89,13 +94,13 @@ namespace AMDiS {
protected:
/// STL map containing the pairs of keys and creators.
static std::map< std::string, CreatorInterface<BaseClass>* > creatorMap;
static CreatorMapType creatorMap;
static bool initialized;
};
template<typename BaseClass>
std::map< std::string, CreatorInterface<BaseClass>* > CreatorMap<BaseClass>::creatorMap;
typename CreatorMap<BaseClass>::CreatorMapType CreatorMap<BaseClass>::creatorMap;
template<typename BaseClass>
bool CreatorMap<BaseClass>::initialized = false;
......
AMDiS/src/DOFMatrix.cc
View file @ edb2158b
......@@ -67,10 +67,6 @@ namespace AMDiS {
if (!colFeSpace)
colFeSpace = rowFeSpace;
#if 0
if (rowFeSpace && rowFeSpace->getAdmin())
(const_cast<DOFAdmin*>(rowFeSpace->getAdmin()))->addDOFIndexed(this);
#endif
boundaryManager = new BoundaryManager(rowFeSpace);
nRow = rowFeSpace->getBasisFcts()->getNumber();
......@@ -87,10 +83,6 @@ namespace AMDiS {
FUNCNAME("DOFMatrix::DOFMatrix()");
*this = rhs;
#if 0
if (rowFeSpace && rowFeSpace->getAdmin())
(const_cast<DOFAdmin*>( rowFeSpace->getAdmin()))->addDOFIndexed(this);
#endif
TEST_EXIT(rhs.inserter == 0)("Cannot copy during insertion!\n");
inserter = 0;
}
......@@ -98,10 +90,6 @@ namespace AMDiS {
DOFMatrix::~DOFMatrix()
{
#if 0
if (rowFeSpace && rowFeSpace->getAdmin())
(const_cast<DOFAdmin*>(rowFeSpace->getAdmin()))->removeDOFIndexed(this);
#endif
if (boundaryManager)
delete boundaryManager;
if (inserter)
......@@ -116,43 +104,6 @@ namespace AMDiS {
}
bool DOFMatrix::symmetric()
{
double tol = 1e-5;
using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
namespace traits= mtl::traits;
typedef base_matrix_type Matrix;
traits::row<Matrix>::type row(matrix);
traits::col<Matrix>::type col(matrix);
traits::const_value<Matrix>::type value(matrix);
typedef traits::range_generator<major, Matrix>::type cursor_type;
typedef traits::range_generator<nz, cursor_type>::type icursor_type;
for (cursor_type cursor = begin<major>(matrix), cend = end<major>(matrix); cursor != cend; ++cursor)
for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); icursor != icend; ++icursor)
// Compare each non-zero entry with its transposed
if (abs(value(*icursor) - matrix[col(*icursor)][row(*icursor)]) > tol)
return false;
return true;
}
void DOFMatrix::test()
{
FUNCNAME("DOFMatrix::test()");
int non_symmetric = !symmetric();
if (non_symmetric)
MSG("Matrix `%s' not symmetric.\n", name.data());
else
MSG("Matrix `%s' is symmetric.\n", name.data());
}
DOFMatrix& DOFMatrix::operator=(const DOFMatrix& rhs)
{
rowFeSpace = rhs.rowFeSpace;
......@@ -290,14 +241,11 @@ namespace AMDiS {
}
#if 0
double DOFMatrix::logAcc(DegreeOfFreedom a, DegreeOfFreedom b) const
{
return matrix[a][b];
}
#if 0
void DOFMatrix::freeDOFContent(int index)
{}
#endif
void DOFMatrix::assemble(double factor,
......@@ -418,7 +366,7 @@ namespace AMDiS {
void DOFMatrix::finishAssembling()
{
// call the operatos cleanup procedures
// call the operators cleanup procedures
for (std::vector<Operator*>::iterator it = operators.begin();
it != operators.end(); ++it)
(*it)->finishAssembling();
......@@ -436,7 +384,7 @@ namespace AMDiS {
return fillFlag;
}
#if 0
void DOFMatrix::axpy(double a, const DOFMatrix& x, const DOFMatrix& y)
{
matrix += a * x.matrix + y.matrix;
......@@ -447,7 +395,7 @@ namespace AMDiS {
{
matrix *= b;
}
#endif
void DOFMatrix::addOperator(Operator *op, double* factor, double* estFactor)
{
......
AMDiS/src/DOFMatrix.h
View file @ edb2158b
......@@ -69,6 +69,9 @@ namespace AMDiS {
/// Symbolic constant for an unused entry which is not followed by any
/// used entry in this row
static const int NO_MORE_ENTRIES = -2;
/// Minimal slot-size used for the inserter. See \ref startInsertion for details.
static const int MIN_NNZ_PER_ROW = 20;
public:
DOFMatrix();
......@@ -100,56 +103,7 @@ namespace AMDiS {
{
return matrix;
}
#if 0
// Only to get rid of the abstract functions, I hope they are not used
std::vector<bool>::iterator begin()
{
ERROR_EXIT("Shouldn't be used, only fake."); std::vector<bool> v;
return v.begin();
}
std::vector<bool>::iterator end()
{
ERROR_EXIT("Shouldn't be used, only fake."); std::vector<bool> v;
return v.end();
}
// Only to get rid of the abstract functions, I hope they are not used
std::vector<bool>::const_iterator begin() const
{
ERROR_EXIT("Shouldn't be used, only fake."); std::vector<bool> v;
return v.begin();
}
std::vector<bool>::const_iterator end() const
{
ERROR_EXIT("Shouldn't be used, only fake."); std::vector<bool> v;
return v.end();
}
bool dummy; // Must be deleted later
reference operator[](DegreeOfFreedom i)
{
ERROR_EXIT("Shouldn't be used, only fake.");
std::vector<bool> d; d.push_back(dummy);
return d[0];
}
const_reference operator[](DegreeOfFreedom i) const
{
ERROR_EXIT("Shouldn't be used, only fake.");
std::vector<bool> d; d.push_back(dummy);
return d[0];
}
/// DOFMatrix does not need to be compressed before assembling, when using MTL4.
void compressDOFIndexed(int first, int last, std::vector<DegreeOfFreedom> &newDOF)
{}
/// Implements DOFIndexedBase::freeDOFContent()
virtual void freeDOFContent(int index);
#endif
/// Returns \ref coupleMatrix.
inline bool isCoupleMatrix()
{
......@@ -162,11 +116,13 @@ namespace AMDiS {
coupleMatrix = c;
}
#if 0
/// a * x + y
void axpy(double a, const DOFMatrix& x, const DOFMatrix& y);
/// Multiplication with a scalar.
void scal(double s);
#endif
/// Adds an operator to the DOFMatrix. A factor, that is multipled to the
/// operator, and a multilier factor for the estimator may be also given.
......@@ -267,7 +223,7 @@ namespace AMDiS {
/// entries per row (per column for CCS matrices). Choosing this parameter
/// too small can induce perceivable overhead for compressed matrices. Thus,
/// it's better to choose a bit too large than too small.
void startInsertion(int nnz_per_row = 10);
void startInsertion(int nnz_per_row = MIN_NNZ_PER_ROW);
/// Finishes insertion. For compressed matrix types, this is where the
/// compression happens.
......@@ -281,15 +237,6 @@ namespace AMDiS {
inserter= 0;
}
#if 0
/// Returns whether restriction should be performed after coarsening
/// (false by default)
virtual bool coarseRestrict()
{
return false;
}
#endif
/// Returns const \ref rowFeSpace
const FiniteElemSpace* getRowFeSpace() const
{
......@@ -332,12 +279,6 @@ namespace AMDiS {
return name;
}
#if 0
/// Resizes \ref matrix to n rows
inline void resize(int n)
{
TEST_EXIT_DBG(n >= 0)("Can't resize DOFMatrix to negative size\n");
}
#endif
/// Returns value at logical indices a,b
double logAcc(DegreeOfFreedom a, DegreeOfFreedom b) const;
......@@ -349,6 +290,7 @@ namespace AMDiS {
void addSparseDOFEntry(double sign,
int irow, int jcol, double entry,
bool add = true);
#endif
void clearDirichletRows();
......@@ -361,11 +303,6 @@ namespace AMDiS {
set_to_zero(matrix);
}
/// Test whether \ref matrix is symmetric. Exits if not.
void test();
bool symmetric();
inline std::vector<Operator*>& getOperators()
{
return operators;
......@@ -398,8 +335,8 @@ namespace AMDiS {
if (num_rows(matrix) != 0)
nnzPerRow = int(double(matrix.nnz()) / num_rows(matrix) * 1.2);
if (nnzPerRow < 20)
nnzPerRow = 20;
if (nnzPerRow < MIN_NNZ_PER_ROW)
nnzPerRow = MIN_NNZ_PER_ROW;
}
/// Returns \ref nnzPerRow.
......
AMDiS/src/DOFVector.cc
View file @ edb2158b
......@@ -110,7 +110,7 @@ namespace AMDiS {
delete oldElInfo;
} else
inside = mesh->findElInfoAtPoint(p, elInfo, lambda, nullptr, nullptr, nullptr);
if (oldElInfo)
oldElInfo = elInfo;
......@@ -122,7 +122,7 @@ namespace AMDiS {
value = basFcts->evalUh(lambda, uh);
} else {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
return 0.0;
value = 0.0;
#else
ERROR_EXIT("Can not eval DOFVector at point p, because point is outside geometry.");
#endif
......@@ -132,6 +132,9 @@ namespace AMDiS {
if (oldElInfo == nullptr)
delete elInfo;
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
Parallel::mpi::globalAdd(value);
#endif
return value;
}
......
AMDiS/src/GenericOperatorTerm.h
View file @ edb2158b
......@@ -315,7 +315,7 @@ struct GenericSecondOrderTerm_1 : public SecondOrderTerm
l1lt(grdLambda, LALt[iq], term(iq));
}
/// Implenetation of SecondOrderTerm::eval().
/// Implemetation of SecondOrderTerm::eval().
void eval(int nPoints,
const mtl::dense_vector<double>& uhAtQP,
const mtl::dense_vector<WorldVector<double> >& grdUhAtQP,
......@@ -336,7 +336,7 @@ struct GenericSecondOrderTerm_1 : public SecondOrderTerm
}
}
/// Implenetation of SecondOrderTerm::weakEval().
/// Implemetation of SecondOrderTerm::weakEval().
void weakEval(const std::vector<WorldVector<double> > &grdUhAtQP,
std::vector<WorldVector<double> > &result)
{
......@@ -521,25 +521,6 @@ inline void addZOT(Operator& op, double term)
addZOT(op, constant(term));
}
// .............................................................................
// Rosenbrock method
// template <typename Term>
// void addZOT_(Operator* op, const Term& term)
// {
// if (op->getUhOld()) {
// addZOT(op, jacobian(term,0) * ...
//
// }
// template <typename Term>
// void addZOT(Operator& op, const Term& term)
// {
// op.addZeroOrderTerm(new GenericZeroOrderTerm<Term>(term));
// }
// _____________________________________________________________________________
// first order term using FirstOrderTerm::l1
......@@ -775,7 +756,7 @@ inline expressions::Function1<expressions::Wrapper<TOut,WorldVector<double> >, e
eval(AbstractFunction<TOut, WorldVector<double> >* fct) { return function_(wrap(fct), X()); }
/// Integrate an expression over a domain.
/** IF the expression does not contain any DOFVector, a mesh must be given as second argument */
/** If the expression does not contain any DOFVector, a mesh must be given as second argument */
template<typename Term>
inline typename boost::enable_if<typename traits::is_expr<Term>::type, typename Term::value_type>::type
integrate(Term term, Mesh* mesh_ = NULL);
......
AMDiS/src/Global.cc
View file @ edb2158b
......@@ -188,7 +188,11 @@ namespace AMDiS {
PRINT_LINE((*error), buff);
va_end(arg);
#if defined HAVE_PARALLEL_DOMAIN_AMDIS && !defined HAVE_PARALLEL_MTL4 && (DEBUG == 0 || defined NDEBUG)
#if (PETSC_VERSION_MINOR >= 5)
PetscError(MPI_COMM_WORLD, __LINE__, "Msg::print_error_exit", "Global.cc", 1, PETSC_ERROR_INITIAL, buff);
#else
PetscError(MPI_COMM_WORLD, __LINE__, "Msg::print_error_exit", "Global.cc", "src/", 1, PETSC_ERROR_INITIAL, buff);
#endif
#else
throw std::runtime_error(buff);
#endif
......
AMDiS/src/LinearAlgebra.h 0 → 100644
View file @ edb2158b
/******************************************************************************
*
* AMDiS - Adaptive multidimensional simulations
*
* Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
* Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
*
* Authors:
* Simon Vey, Thomas Witkowski, Andreas Naumann, Simon Praetorius, et al.
*
* This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
* WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
*
*
* This file is part of AMDiS
*
* See also license.opensource.txt in the distribution.
*
******************************************************************************/
/// This file is work in progress and may replace the assembling now part of
/// DOFMatrix directly. The idea is to assemble matrices to a data-structure
/// provided by a linear algebra backend. You have to specify how an element-
/// matrix can be added to the global matrix, how a Dirichlet-row is inserted
/// and how the matrix is initialized/finalized.
/** \file LinearAlgebra.h */
#ifndef AMDIS_LINEAR_ALGEBRA_H
#define AMDIS_LINEAR_ALGEBRA_H
#include "utility/calculate_nnz.hpp"
namespace AMDiS {
namespace tag
{
struct distributed {};
struct non_distributed {};
// backends
struct mtl {};
struct pmtl {};
struct petsc {};
struct p_petsc {};
}
namespace traits
{
template< class T >
struct distributed_tag : boost::mpl::if_<
mtl::traits::is_distributed< T >,
tag::distributed,
tag::non_distributed
> {};
}
namespace detail
{
template< class Dummy = void >
struct DefaultParameters {};
}
/** fill for each backend a linear algebra class that
* contains the following typedefs and functions
**/
template< class Backend = tag::mtl, class Value = double, class Parameters = detail::DefaultParameters<> >
struct LinearAlgebra
{
public: // typedefs
typedef Value ValueType;
typedef unsigned int SizeType;
typedef mtl::matrix::parameters<mtl::row_major, mtl::index::c_index, mtl::non_fixed::dimensions, false, SizeType> MatrixPara;
typedef mtl::matrix::compressed2D<ValueType, MatrixPara> MatrixBase;