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Commit 2aff8c3b authored by Praetorius, Simon's avatar Praetorius, Simon
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some corrections in the solvers

parent 0b5440f3
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AMDiS/AMDISConfig.cmake.in
View file @ 2aff8c3b
......@@ -255,6 +255,9 @@ int i ;
void *Symbolic, *Numeric ;
double stats [2];
umfpack_tic (stats);
(void) umfpack_di_symbolic (n, n, Ap, Ai, Ax, &Symbolic, null, null) ;
(void) umfpack_di_numeric (Ap, Ai, Ax, Symbolic, &Numeric, null, null) ;
......@@ -265,6 +268,7 @@ umfpack_di_free_symbolic (&Symbolic) ;
umfpack_di_free_numeric (&Numeric) ;
umfpack_toc (stats);
return (0) ;
......@@ -276,18 +280,30 @@ return (0) ;
OUTPUT_VARIABLE CHOLMOD_OUT)
if(NOT CHOLMOD_TEST)
find_library(CHOLMOD_LIB cholmod)
find_library(COLAMD_LIB colamd)
if(CHOLMOD_LIB)
list(APPEND AMDIS_LIBRARIES ${CHOLMOD_LIB})
else()
message(FATAL_ERROR "your umfpack seems to need cholmod, but cmake could not find it")
endif()
find_library(COLAMD_LIB colamd)
if(COLAMD_LIB)
list(APPEND AMDIS_LIBRARIES ${COLAMD_LIB})
else()
message(FATAL_ERROR "your umfpack seems to need colamd, but cmake could not find it")
endif()
try_compile(CHOLMOD_TEST2 ${_CHOLMOD_TEST_DIR}/build ${_CHOLMOD_TEST_DIR} cholmodTest
OUTPUT_VARIABLE CHOLMOD_OUT)
if(NOT CHOLMOD_TEST2)
find_library(SUITESPARSECONFIG_LIB libsuitesparseconfig)
if(SUITESPARSECONFIG_LIB)
list(APPEND AMDIS_LIBRARIES ${SUITESPARSECONFIG_LIB})
else()
message(FATAL_ERROR "your umfpack seems to need suitesparseconfig, but cmake could not find it")
endif()
endif()
endif()
endif(AMDIS_NEED_UMFPACK)
......
AMDiS/AMDISUse.cmake
View file @ 2aff8c3b
......@@ -53,8 +53,11 @@ elseif(AMDIS_NEED_SEQ_PETSC)
endif()
if(AMDIS_NEED_HYPRE)
find_package(HYPRE REQUIRED)
find_package(HYPRE REQUIRED HINTS ${AMDIS_DIR})
if(HAVE_HYPRE)
list(APPEND AMDIS_INCLUDE_DIRS ${HYPRE_INCLUDE_DIRECTORIES})
list(APPEND AMDIS_COMPILEFLAGS "-DMTL_HAS_HYPRE")
list(APPEND AMDIS_LIBRARIES ${HYPRE_LIBRARIES} )
if(NOT MPI_FOUND)
find_package(MPI REQUIRED)
if(MPI_FOUND)
......@@ -63,9 +66,6 @@ if(AMDIS_NEED_HYPRE)
list(APPEND AMDIS_INCLUDE_DIRS ${MPI_INCLUDE_PATH})
endif()
endif()
list(APPEND AMDIS_INCLUDE_DIRS ${HYPRE_INCLUDE_DIRECTORIES})
list(APPEND AMDIS_COMPILEFLAGS "-DMTL_HAS_HYPRE")
list(APPEND AMDIS_LIBRARIES ${HYPRE_LIBRARIES} )
endif()
endif(AMDIS_NEED_HYPRE)
......
AMDiS/CMakeLists.txt
View file @ 2aff8c3b
......@@ -340,10 +340,10 @@ endif(ENABLE_UMFPACK)
if(ENABLE_HYPRE)
include(FindHYPRE.cmake)
message("have hypre: ${HAVE_HYPRE}")
if(HAVE_HYPRE)
if(NOT MPI_FOUND)
if (HAVE_HYPRE)
if (NOT MPI_FOUND)
find_package(MPI REQUIRED)
if(MPI_FOUND)
if (MPI_FOUND)
list(APPEND COMPILEFLAGS "${MPI_COMPILE_FLAGS}")
include_directories(${MPI_INCLUDE_PATH})
endif()
......
AMDiS/src/Timer.cc
View file @ 2aff8c3b
......@@ -48,7 +48,7 @@ namespace AMDiS {
return MPI::Wtime() - first_mpi;
#else
time_duration td = microsec_clock::local_time()-first_seq;
return static_cast<double>(td.total_milliseconds())*1.e-3;
return static_cast<double>(td.total_microseconds())*1.e-6;
#endif
}
......
AMDiS/src/parallel/PetscSolver.cc
View file @ 2aff8c3b
......@@ -29,6 +29,8 @@
#include "parallel/PetscSolver.h"
#include "parallel/StdMpi.h"
#include "tools.h"
namespace AMDiS { namespace Parallel {
PetscSolver::PetscSolver(std::string name)
......@@ -86,10 +88,10 @@ namespace AMDiS { namespace Parallel {
MPI::COMM_WORLD.Barrier();
Timer t;
if (createMatrixData)
fillPetscMatrix(const_cast< Matrix< DOFMatrix* >* >(A.getOriginalMat()));
fillPetscMatrix(const_cast< Matrix< DOFMatrix* >* >(A.getOriginalMat()));
fillPetscRhs(&b);
INFO(info, 8)("creation of parallel data structures needed %.5f seconds\n",
......
AMDiS/src/parallel/PetscSolverGlobalMatrix.cc
View file @ 2aff8c3b
......@@ -66,6 +66,8 @@ namespace AMDiS { namespace Parallel {
Parameters::get(name + "->pc_type", precon);
if (!precon.size())
Parameters::get(name + "->left precon", precon);
if (!precon.size())
Parameters::get(name + "->right precon", precon);
if (!matSolverPackage && params.emptyParam.find(precon) == params.emptyParam.end()) {
precon = (params.preconMap.find(precon) != params.preconMap.end() ? params.preconMap[precon] : precon);
PetscOptionsInsertString(("-" + kspPrefix + "pc_type " + precon).c_str());
......
AMDiS/src/parallel/PetscSolverNavierStokes.cc
View file @ 2aff8c3b
......@@ -24,6 +24,8 @@
#include "parallel/PetscHelper.h"
#include "TransformDOF.h"
#include "tools.h"
namespace AMDiS { namespace Parallel {
using namespace std;
......@@ -114,6 +116,7 @@ namespace AMDiS { namespace Parallel {
{
FUNCNAME("PetscSolverNavierStokes::initSolver()");
printMem("begin(initSolver)");
// Create FGMRES based outer solver
MSG("CREATE POS 1: %p\n", &ksp);
......@@ -128,6 +131,8 @@ namespace AMDiS { namespace Parallel {
// Create null space information.
if (pressureNullSpace)
setConstantNullSpace(ksp, pressureComponent, true);
printMem("end(initSolver)");
}
......@@ -140,6 +145,9 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT(nu)("nu pointer not set!\n");
TEST_EXIT(invTau)("invtau pointer not set!\n");
TEST_EXIT(solution)("solution pointer not set!\n");
printMem("begin(initPreconditioner)");
int dim = componentSpaces[pressureComponent]->getMesh()->getDim();
......@@ -356,6 +364,9 @@ namespace AMDiS { namespace Parallel {
}
setConstantNullSpace(matShellContext.kspLaplace);
printMem("end(initPreconditioner)");
MSG("Setup of Navier-Stokes preconditioner needed %.5f seconds\n",
t.elapsed());
......
AMDiS/src/solver/ITL_Runner.h
View file @ 2aff8c3b
......@@ -89,11 +89,17 @@ namespace AMDiS {
TEST_EXIT(preconPair.l != nullptr)("there is no left preconditioner\n");
TEST_EXIT(preconPair.r != nullptr)("there is no right preconditioner\n");
typedef typename mtl::Collection<MatrixType>::value_type value_type;
VectorType r(A * x - b);
VectorType r(num_rows(b)); r = b;
if (two_norm(x) != 0) {
r = A * x ;
r -= b;
}
int error = 0;
if (oem.getInfo() == 0) {
itl::basic_iteration<typename MatrixType::value_type>
itl::basic_iteration<value_type>
iter(r, oem.getMaxIterations(), oem.getRelative(), oem.getTolerance());
error = solver(A, x, b, *(preconPair.l), *(preconPair.r), iter);
......@@ -101,7 +107,7 @@ namespace AMDiS {
oem.setIterations(iter.iterations());
oem.setResidual(iter.resid());
} else {
itl::cyclic_iteration<typename MatrixType::value_type>
itl::cyclic_iteration<value_type>
iter(r, oem.getMaxIterations(), oem.getRelative(), oem.getTolerance(),
oem.getPrint_cycle());
......@@ -122,29 +128,31 @@ namespace AMDiS {
TEST_EXIT(preconPair.l != nullptr)("there is no left preconditioner\n");
TEST_EXIT(preconPair.r != nullptr)("there is no right preconditioner\n");
mtl::matrix::transposed_view<const MatrixType> B(A);
VectorType r(B * x - b);
int error = 0;
if (oem.getInfo() == 0) {
itl::basic_iteration<typename MatrixType::value_type>
iter(r, oem.getMaxIterations(), oem.getRelative(), oem.getTolerance());
error = solver(B, x, b, *(preconPair.l), *(preconPair.r), iter);
oem.setErrorCode(error);
oem.setIterations(iter.iterations());
oem.setResidual(iter.resid());
} else {
itl::cyclic_iteration<typename MatrixType::value_type>
iter(r, oem.getMaxIterations(), oem.getRelative(), oem.getTolerance(),
oem.getPrint_cycle());
error = solver(B, x, b, *(preconPair.l), *(preconPair.r), iter);
oem.setErrorCode(error);
oem.setIterations(iter.iterations());
oem.setResidual(iter.resid());
}
return error;
// typedef typename mtl::Collection<MatrixType>::value_type value_type;
// mtl::matrix::transposed_view<const MatrixType> B(A);
// VectorType r(B * x - b);
// int error = 0;
// if (oem.getInfo() == 0) {
// itl::basic_iteration<value_type>
// iter(r, oem.getMaxIterations(), oem.getRelative(), oem.getTolerance());
//
// error = solver(B, x, b, *(preconPair.l), *(preconPair.r), iter);
// oem.setErrorCode(error);
// oem.setIterations(iter.iterations());
// oem.setResidual(iter.resid());
// } else {
// itl::cyclic_iteration<value_type>
// iter(r, oem.getMaxIterations(), oem.getRelative(), oem.getTolerance(),
// oem.getPrint_cycle());
//
// error = solver(B, x, b, *(preconPair.l), *(preconPair.r), iter);
// oem.setErrorCode(error);
// oem.setIterations(iter.iterations());
// oem.setResidual(iter.resid());
// }
//
// return error;
return 1;
}
......
AMDiS/src/solver/MTL4SolverBase.h
View file @ 2aff8c3b
......@@ -43,8 +43,8 @@ namespace AMDiS {
/// Constructor
MTL4SolverBase(LinearSolver* oem_)
: runner(oem_),
oem(*oem_),
matrix(0,0)
oem(*oem_)/*,
matrix(0,0)*/
{}
protected:
......
AMDiS/src/solver/MatrixStreams.h
View file @ 2aff8c3b
......@@ -56,8 +56,9 @@ namespace AMDiS {
mat(mat), mapper(m) {}
};
template< typename MTLMatrix, typename Mapper >
void operator<<(MTLMatrix& matrix, MatMap<const SolverMatrix<Matrix<DOFMatrix* > >, Mapper >& Asolver)
// requires MatrixType to have an inserter
template< typename MatrixType, typename Mapper >
void operator<<(MatrixType& matrix, MatMap<const SolverMatrix<Matrix<DOFMatrix* > >, Mapper >& Asolver)
{
const Matrix< DOFMatrix* >& A = *(Asolver.mat.getOriginalMat());
int ns = A.getSize();
......@@ -72,7 +73,7 @@ namespace AMDiS {
nnz += A[rb][cb]->getBaseMatrix().nnz();
{
typedef mtl::matrix::mapped_inserter< typename Collection< MTLMatrix >::Inserter, Mapper > Inserter;
typedef mtl::matrix::mapped_inserter< typename Collection< MatrixType >::Inserter, Mapper > Inserter;
Inserter ins(matrix, mapper, int(1.2 * nnz / matrix.dim1()));
for (int rb = 0; rb < ns; ++rb) {
mapper.setRow(rb);
......@@ -84,6 +85,37 @@ namespace AMDiS {
}
}
}
// requires MatrixType to have an inserter
template< typename MatrixType, typename Mapper >
void operator<<(MatrixType& matrix, MatMap<Matrix<MatrixType* >, Mapper >& Asolver)
{
Matrix< MatrixType* >& A = *(Asolver.mat);
int ns = A.getSize();
Mapper& mapper(Asolver.mapper);
set_to_zero(matrix);
int nnz = 0;
for (int rb = 0; rb < ns; ++rb)
for (int cb = 0; cb < ns; ++cb)
if (A[rb][cb])
nnz += A[rb][cb]->nnz();
{
typedef mtl::matrix::mapped_inserter< typename Collection< MatrixType >::Inserter, Mapper > Inserter;
Inserter ins(matrix, mapper, int(1.2 * nnz / matrix.dim1()));
for (int rb = 0; rb < ns; ++rb) {
mapper.setRow(rb);
for (int cb = 0; cb < ns; ++cb) {
mapper.setCol(cb);
if (A[rb][cb])
ins << (*A[rb][cb]);
}
}
}
}
template< typename Vector, typename CurMap >
void operator<<(Vector& dest, VecMap<DOFVector<double >, CurMap >& rhs)
......@@ -185,31 +217,31 @@ namespace AMDiS {
/// create and fill \ref PetscMatrix
inline void operator<<(PetscMatrix& mat, const SolverMatrix<Matrix<DOFMatrix*> >& Asolver)
{
const Matrix< DOFMatrix* >& A = *(Asolver.getOriginalMat());
if(mat.isNested) {
std::vector<PetscInt> nnz;
mat.nestMat.resize(A.getNumRows() * A.getNumCols());
for (size_t i = 0; i < static_cast<size_t>(A.getNumRows()); i++) {
for (size_t j = 0; j < static_cast<size_t>(A.getNumCols()); j++) {
size_t idx = i * A.getNumCols() + j;
if (A[i][j] == nullptr
|| num_rows(A[i][j]->getBaseMatrix()) == 0
|| num_cols(A[i][j]->getBaseMatrix()) == 0
|| A[i][j]->getBaseMatrix().nnz() == 0) {
mat.nestMat[idx] = PETSC_NULL;
continue;
}
const Matrix< DOFMatrix* >& A = *(Asolver.getOriginalMat());
if (mat.isNested) {
mat.nestMat[idx] << *(A[i][j]);
}
}
std::vector<PetscInt> nnz;
mat.nestMat.resize(A.getNumRows() * A.getNumCols());
for (size_t i = 0; i < static_cast<size_t>(A.getNumRows()); i++) {
for (size_t j = 0; j < static_cast<size_t>(A.getNumCols()); j++) {
size_t idx = i * A.getNumCols() + j;
if (A[i][j] == nullptr
|| num_rows(A[i][j]->getBaseMatrix()) == 0
|| num_cols(A[i][j]->getBaseMatrix()) == 0
|| A[i][j]->getBaseMatrix().nnz() == 0) {
mat.nestMat[idx] = PETSC_NULL;
continue;
}
// create nested matrix from a vector of block matrices
MatCreateNest(PETSC_COMM_SELF, A.getNumRows(), PETSC_NULL, A.getNumCols(), PETSC_NULL, &(mat.nestMat[0]), &mat.matrix);
}else {
mat.nestMat[idx] << *(A[i][j]);
}
}
// create nested matrix from a vector of block matrices
MatCreateNest(PETSC_COMM_SELF, A.getNumRows(), PETSC_NULL, A.getNumCols(), PETSC_NULL, &(mat.nestMat[0]), &mat.matrix);
} else {
bool initMatrix = false;
unsigned nRows(0);
unsigned nEntries(0);
......
AMDiS/src/solver/PetscSolver.cc
View file @ 2aff8c3b
......@@ -63,6 +63,8 @@ namespace AMDiS {
Parameters::get(oem.getName() + "->pc_type", precon);
if (!precon.size())
Parameters::get(oem.getName() + "->left precon", precon);
if (!precon.size())
Parameters::get(oem.getName() + "->right precon", precon);
if (!matSolverPackage && !params.emptyParam[precon]) {
precon = (params.preconMap.find(precon) != params.preconMap.end() ? params.preconMap[precon] : precon);
PetscOptionsInsertString(("-" + kspPrefix + "pc_type " + precon).c_str());
......@@ -138,6 +140,7 @@ namespace AMDiS {
PC pc_;
KSPGetPC(ksp_, &pc_);
PCSetType(pc_, pcType);
PCSetFromOptions(pc_);
}
}
......
AMDiS/src/solver/PetscSolver.h
View file @ 2aff8c3b
......@@ -141,21 +141,23 @@ namespace AMDiS {
return &runner;
}
void setNestedVectors(bool createNestedVector = true)
void setNestedVectors(bool nested = true)
{
vecSol.isNested= createNestedVector;
vecRhs.isNested= createNestedVector;
vecSol.isNested = nested;
vecRhs.isNested = nested;
}
void setNestedMatrix(bool nested=true)
void setNestedMatrix(bool nested = true)
{
petscMat.isNested=nested;
petscMat.isNested=nested;
}
void setNested(bool n)
{
setNestedVectors(n); setNestedMatrix(n);
setNestedVectors(n);
setNestedMatrix(n);
}
protected:
Runner runner;
......@@ -170,10 +172,7 @@ namespace AMDiS {
// transfer matrix and rhs-vector to PETSc data-structures
if (createMatrixData) {
petscMat << A;
if (x.getSize() == 1)
runner.init(A, petscMat.nestMat[0]);
else
runner.init(A, petscMat.matrix);
runner.init(A, petscMat.matrix);
}
vecSol << x;
......@@ -182,10 +181,7 @@ namespace AMDiS {
// solve the linear system using PETSc solvers
t.reset();
if (vecSol.nestVec.size() == 1)
error = runner.solve(petscMat.nestMat[0], vecSol.nestVec[0], vecRhs.nestVec[0]);
else
error = runner.solve(petscMat.matrix, vecSol.vector, vecRhs.vector);
error = runner.solve(petscMat.matrix, vecSol.vector, vecRhs.vector);
// transfer solution from PETSc vector to SystemVector
vecSol.vector >> x;
......
AMDiS/src/solver/itl/details.hpp
View file @ 2aff8c3b
......@@ -31,7 +31,23 @@ namespace itl {
namespace details {
/// Compute the Givens rotation matrix parameters for a and b.
inline void rotmat( double& a, double& b , double& c, double& s)
// template<typename T>
// void rotmat(const T& a, const T& b , T& c, T& s)
// {
// using std::abs; using std::sqrt; using mtl::conj;
//
// const T zero = math::zero(T());
// if (a == zero) {
// c = 0.0;
// s = 1.0;
// } else {
// double temp = abs(a) / sqrt( conj(a)*a + conj(b)*b );
// c = temp;
// s = temp * (b / a);
// }
// }
inline void rotmat(const double& a, const double& b , double& c, double& s)
{
using std::abs; using std::sqrt;
if ( b == 0.0 ) {
......
AMDiS/src/solver/itl/fgmres.hpp
View file @ 2aff8c3b
......@@ -52,28 +52,30 @@ int fgmres_full(const Matrix &A, Vector &x, const Vector &b,
if (size(b) == 0) throw mtl::logic_error("empty rhs vector");
const Scalar zero= math::zero(Scalar()), dbl_tol= 1.e-16, kappa = 10.0;
const Scalar zero= math::zero(Scalar()), breakdown_tol= 1.e-16, kappa = 10.0;
Scalar rho, bnrm2, temp, hr;
Size k, kmax(std::min(size(x), Size(iter.max_iterations() - iter.iterations())));
Vector w(solve(P, b)), r(b - A*x);
Vector w(resource(x)), r(b - A*x);
mtl::matrix::multi_vector<Vector> V(Vector(resource(x), zero), kmax+1);
mtl::matrix::multi_vector<Vector> Z(Vector(resource(x), zero), kmax+1);
mtl::matrix::dense2D<Scalar> H(kmax+1, kmax);
mtl::vector::dense_vector<Scalar> sn(kmax, zero), cs(kmax, zero), s(kmax+1, zero), y(kmax, zero); // replicated in distributed solvers
bnrm2 = two_norm(w);
if (bnrm2 < dbl_tol)
bnrm2 = 1.0;
bnrm2 = two_norm(b);
if (bnrm2 == zero) {
set_to_zero(x);
// b == 0 => solution = 0
return iter.terminate(bnrm2);
}
temp = two_norm(r);
rho= temp * reciprocal(bnrm2);
if (iter.finished(rho))
rho = two_norm(r); // norm of preconditioned residual
if (iter.finished(rho)) // initial guess is good enough solution
return iter;
V.vector(0) = r * reciprocal(temp);
V.vector(0) = r * reciprocal(rho);
H = zero;
s[0] = temp;
s[0] = rho;
// FGMRES iteration
for (k= 0; k < kmax && !iter.finished(rho) ; ++k, ++iter) {
......@@ -104,7 +106,7 @@ int fgmres_full(const Matrix &A, Vector &x, const Vector &b,
}
}
if (H[k+1][k] < dbl_tol)
if (H[k+1][k] < breakdown_tol)
return iter.fail(2, "FGMRES: Singular matrix - nearly hard breakdown");
V.vector(k+1) = w * reciprocal(H[k+1][k]);
......@@ -123,11 +125,11 @@ int fgmres_full(const Matrix &A, Vector &x, const Vector &b,
H[k][k] = cs[k]*H[k][k] + sn[k]*H[k+1][k];
H[k+1][k] = 0.0;
rho = std::abs(s[k+1]) / bnrm2;
rho = std::abs(s[k+1]);
}
// reduce k, to get regular matrix
while (k > 0 && abs(s[k-1]) <= iter.atol()) k--;
// while (k > 0 && abs(s[k-1]) <= iter.atol()) k--;
// iteration is finished -> compute x: solve H*y=g as far as rank of H allows
irange range(k);
......@@ -146,8 +148,8 @@ int fgmres_full(const Matrix &A, Vector &x, const Vector &b,
x += Z.vector(range) * y[range];
r = b - A*x;
return iter.terminate(r);
// r = b - A*x;
return iter.terminate(rho);
}
/// Flexible Generalized Minimal Residual method with restart
......
AMDiS/src/solver/itl/fgmres_householder.hpp
View file @ 2aff8c3b
......@@ -52,7 +52,7 @@ int fgmres_householder_full(const Matrix &A, Vector &x, const Vector &b,
if (size(b) == 0) throw mtl::logic_error("empty rhs vector");
const Scalar zero= math::zero(Scalar()), dbl_tol= 1.e-16;
const Scalar zero= math::zero(Scalar());
Scalar rho, bnrm2, temp, alpha, beta;
Size k, kmax(std::min(size(x), Size(iter.max_iterations() - iter.iterations())));
Vector w(solve(R, b)), r(b - A*x);
......@@ -61,20 +61,19 @@ int fgmres_householder_full(const Matrix &A, Vector &x, const Vector &b,
mtl::vector::dense_vector<Scalar> sn(kmax, zero), cs(kmax, zero), s(kmax+1, zero), y(kmax, zero); // replicated in distributed solvers
mtl::matrix::dense2D<Scalar> H(kmax, kmax);
bnrm2 = two_norm(b);
if (bnrm2 == zero) {
set_to_zero(x);
// b == 0 => solution = 0
return iter.terminate(bnrm2);
}
bnrm2 = two_norm(w);
if (bnrm2 < dbl_tol)
bnrm2 = 1.0;
// TODO: if rhs=0 => solution=0 ??
temp = two_norm(r); // norm of preconditioned residual
rho = temp * reciprocal(bnrm2);
rho = two_norm(r); // norm of preconditioned residual
if (iter.finished(rho)) // initial guess is good enough solution
return iter;
// u = r + sing(r(0))*||r||*e0
beta = signum(r[0])*temp;
beta = signum(r[0])*rho;
w = r;
w[0] += beta;
w *= reciprocal(two_norm(w));
......@@ -140,7 +139,7 @@ int fgmres_householder_full(const Matrix &A, Vector &x, const Vector &b,
irange range(num_rows(H));
H[iall][k] = w[range];
rho = std::abs(s[k+1]) / bnrm2;
rho = std::abs(s[k+1]);
}