From 9f98cf8fe459c088760ab0b0cf7375829f8d0c8e Mon Sep 17 00:00:00 2001
From: Wenqing Wang <wenqing.wang@ufz.de>
Date: Wed, 7 Jan 2015 13:49:32 +0100
Subject: [PATCH] [MaL] Small preparations for PETSc matrix/vector.
Added linear solver time info.
Matrix preallocation type.
Change type of MatSetValues().
Collect finilize assembly calls in one place.
Make PETScVector::viewer() a const method.
---
MathLib/LinAlg/PETSc/PETScLinearSolver.h | 5 +++++
MathLib/LinAlg/PETSc/PETScMatrix.cpp | 3 +++
MathLib/LinAlg/PETSc/PETScMatrix.h | 4 +++-
MathLib/LinAlg/PETSc/PETScTools.cpp | 4 ++++
MathLib/LinAlg/PETSc/PETScVector.cpp | 4 +---
MathLib/LinAlg/PETSc/PETScVector.h | 2 +-
6 files changed, 17 insertions(+), 5 deletions(-)
diff --git a/MathLib/LinAlg/PETSc/PETScLinearSolver.h b/MathLib/LinAlg/PETSc/PETScLinearSolver.h
index 1496df53a59..710194095eb 100644
--- a/MathLib/LinAlg/PETSc/PETScLinearSolver.h
+++ b/MathLib/LinAlg/PETSc/PETScLinearSolver.h
@@ -19,6 +19,8 @@
#include<string>
+#include "logog/include/logog.hpp"
+
#include "petscksp.h"
#include "PETScMatrix.h"
@@ -47,6 +49,9 @@ class PETScLinearSolver
~PETScLinearSolver()
{
+ INFO("info: Time elapsed in PETSc ksp solver for equation: %g s.\n",
+ _elapsed_ctime);
+
KSPDestroy(&_solver);
}
diff --git a/MathLib/LinAlg/PETSc/PETScMatrix.cpp b/MathLib/LinAlg/PETSc/PETScMatrix.cpp
index 9b7d1dec0c4..5fa3c8cca8a 100644
--- a/MathLib/LinAlg/PETSc/PETScMatrix.cpp
+++ b/MathLib/LinAlg/PETSc/PETScMatrix.cpp
@@ -91,8 +91,11 @@ void PETScMatrix::create(const PetscInt d_nz, const PetscInt o_nz)
MatSetFromOptions(_A);
+ MatSetType(_A, MATMPIAIJ);
MatSeqAIJSetPreallocation(_A, d_nz, PETSC_NULL);
MatMPIAIJSetPreallocation(_A, d_nz, PETSC_NULL, o_nz, PETSC_NULL);
+ // If pre-allocation does not work one can use MatSetUp(_A), which is much
+ // slower.
MatGetOwnershipRange(_A, &_start_rank, &_end_rank);
MatGetSize(_A, &_nrows, &_ncols);
diff --git a/MathLib/LinAlg/PETSc/PETScMatrix.h b/MathLib/LinAlg/PETSc/PETScMatrix.h
index b341a19c0ef..ee77b4e106d 100644
--- a/MathLib/LinAlg/PETSc/PETScMatrix.h
+++ b/MathLib/LinAlg/PETSc/PETScMatrix.h
@@ -21,6 +21,8 @@
#include "PETScMatrixOption.h"
#include "PETScVector.h"
+#include "MathLib/LinAlg/RowColumnIndices.h"
+
typedef Mat PETSc_Mat;
namespace MathLib
@@ -242,7 +244,7 @@ void PETScMatrix::add(std::vector<PetscInt> const& row_pos,
const PetscInt nrows = static_cast<PetscInt> (row_pos.size());
const PetscInt ncols = static_cast<PetscInt> (col_pos.size());
- MatSetValues(_A, nrows, &row_pos[0], ncols, &col_pos[0], sub_mat.getEntries(), ADD_VALUES);
+ MatSetValues(_A, nrows, &row_pos[0], ncols, &col_pos[0], &sub_mat(0,0), ADD_VALUES);
};
/*!
diff --git a/MathLib/LinAlg/PETSc/PETScTools.cpp b/MathLib/LinAlg/PETSc/PETScTools.cpp
index 00d5b775562..09beeb20daf 100644
--- a/MathLib/LinAlg/PETSc/PETScTools.cpp
+++ b/MathLib/LinAlg/PETSc/PETScTools.cpp
@@ -23,9 +23,13 @@ void applyKnownSolution(PETScMatrix &A, PETScVector &b, PETScVector &x,
const std::vector<PetscInt> &vec_knownX_id,
const std::vector<PetscScalar> &vec_knownX_x)
{
+ A.finalizeAssembly();
+
A.setRowsColumnsZero(vec_knownX_id);
A.finalizeAssembly();
+ x.finalizeAssembly();
+ b.finalizeAssembly();
if(vec_knownX_id.size() > 0)
{
x.set(vec_knownX_id, vec_knownX_x);
diff --git a/MathLib/LinAlg/PETSc/PETScVector.cpp b/MathLib/LinAlg/PETSc/PETScVector.cpp
index 3f426550086..7669745f118 100644
--- a/MathLib/LinAlg/PETSc/PETScVector.cpp
+++ b/MathLib/LinAlg/PETSc/PETScVector.cpp
@@ -135,14 +135,12 @@ PetscScalar PETScVector::getNorm(MathLib::VecNormType nmtype) const
return norm;
}
-void PETScVector::viewer(const std::string &file_name, const PetscViewerFormat vw_format)
+void PETScVector::viewer(const std::string &file_name, const PetscViewerFormat vw_format) const
{
PetscViewer viewer;
PetscViewerASCIIOpen(PETSC_COMM_WORLD, file_name.c_str(), &viewer);
PetscViewerPushFormat(viewer, vw_format);
- finalizeAssembly();
-
PetscObjectSetName((PetscObject)_v, file_name.c_str());
VecView(_v, viewer);
diff --git a/MathLib/LinAlg/PETSc/PETScVector.h b/MathLib/LinAlg/PETSc/PETScVector.h
index 351a77f51b5..33f6667961d 100644
--- a/MathLib/LinAlg/PETSc/PETScVector.h
+++ b/MathLib/LinAlg/PETSc/PETScVector.h
@@ -231,7 +231,7 @@ class PETScVector
PETSC_VIEWER_DRAW_CONTOUR Views the vector with a contour plot
*/
void viewer(const std::string &file_name,
- const PetscViewerFormat vw_format = PETSC_VIEWER_ASCII_MATLAB );
+ const PetscViewerFormat vw_format = PETSC_VIEWER_ASCII_MATLAB ) const;
private:
PETSc_Vec _v;
--
GitLab