From 2dacdb31ed327cf1b94a2942278fdfd29d5d64cc Mon Sep 17 00:00:00 2001
From: Wenqing Wang <wenqing.wang@ufz.de>
Date: Mon, 24 Mar 2014 14:07:34 +0100
Subject: [PATCH] Changes with the comments by Nori, Tom and Lars
---
MathLib/LinAlg/Dense/DenseMatrix-impl.h | 4 +--
MathLib/LinAlg/Dense/DenseMatrix.h | 2 +-
MathLib/LinAlg/PETSc/PETScMatrix.cpp | 21 +++++--------
MathLib/LinAlg/PETSc/PETScMatrix.h | 34 ++++++++++-----------
MathLib/LinAlg/PETSc/PETScMatrixOption.h | 25 ++++++++-------
MathLib/LinAlg/PETSc/PETScVector.h | 4 +--
Tests/MathLib/TestGlobalMatrixInterface.cpp | 26 ++++++++--------
scripts/cmake/Find.cmake | 4 +++
scripts/cmake/findPETSC/FindPETSc.cmake | 6 ----
9 files changed, 59 insertions(+), 67 deletions(-)
diff --git a/MathLib/LinAlg/Dense/DenseMatrix-impl.h b/MathLib/LinAlg/Dense/DenseMatrix-impl.h
index 2f3cabc7203..ee0f2ceee19 100644
--- a/MathLib/LinAlg/Dense/DenseMatrix-impl.h
+++ b/MathLib/LinAlg/Dense/DenseMatrix-impl.h
@@ -1,5 +1,5 @@
/**
- * @file DenseMatrix.tpp
+ * @file DenseMatrix-imp.h
* @author Thomas Fischer and Haibing Shao
* @date Jun 10, 2013
*
@@ -54,7 +54,7 @@ DenseMatrix<FP_TYPE, IDX_TYPE>::~DenseMatrix ()
}
template <typename FP_TYPE, typename IDX_TYPE>
-FP_TYPE* DenseMatrix<FP_TYPE, IDX_TYPE>::getData() const
+const FP_TYPE* DenseMatrix<FP_TYPE, IDX_TYPE>::getEntries() const
{
return _data;
}
diff --git a/MathLib/LinAlg/Dense/DenseMatrix.h b/MathLib/LinAlg/Dense/DenseMatrix.h
index 98461d7a633..7aeef330429 100644
--- a/MathLib/LinAlg/Dense/DenseMatrix.h
+++ b/MathLib/LinAlg/Dense/DenseMatrix.h
@@ -55,7 +55,7 @@ public:
/**
* Get the raw data directly
*/
- FP_TYPE *getData () const;
+ const FP_TYPE *getEntries() const;
/**
* Assignment operator, makes a copy of the internal data of the object.
diff --git a/MathLib/LinAlg/PETSc/PETScMatrix.cpp b/MathLib/LinAlg/PETSc/PETScMatrix.cpp
index 2a80d653c07..1d6cbaa6858 100644
--- a/MathLib/LinAlg/PETSc/PETScMatrix.cpp
+++ b/MathLib/LinAlg/PETSc/PETScMatrix.cpp
@@ -18,36 +18,31 @@
namespace MathLib
{
-PETScMatrix::PETScMatrix (const PetscInt size, const PETScMatrixOption mat_opt)
+PETScMatrix::PETScMatrix (const PetscInt size, const PETScMatrixOption &mat_opt)
+ :_size(size), _n_loc_rows(PETSC_DECIDE), _n_loc_cols(mat_opt._n_local_cols)
{
- _size = size;
- _loc_rows = PETSC_DECIDE;
- _loc_cols = mat_opt._local_cols;
-
- if(mat_opt._is_size_local_rows)
+ if(!mat_opt._is_global_size)
{
_size = PETSC_DECIDE;
- _loc_rows = size;
+ _n_loc_rows = size;
}
MatCreate(PETSC_COMM_WORLD, &_A);
- MatSetSizes(_A, _loc_rows, _loc_cols, _size, _size);
+ MatSetSizes(_A, _n_loc_rows, _n_loc_cols, _size, _size);
MatSetFromOptions(_A);
// for a dense matrix: MatSeqAIJSetPreallocation(_A, d_nz, PETSC_NULL);
- MatMPIAIJSetPreallocation(_A, mat_opt._d_nz, PETSC_NULL, mat_opt._o_nz, PETSC_NULL);
+ MatMPIAIJSetPreallocation(_A, mat_opt._d_nnz, PETSC_NULL, mat_opt._o_nnz, PETSC_NULL);
MatGetOwnershipRange(_A, &_start_rank, &_end_rank);
MatGetSize(_A, &_size, PETSC_NULL);
- MatGetLocalSize(_A, &_loc_rows, &_loc_cols);
+ MatGetLocalSize(_A, &_n_loc_rows, &_n_loc_cols);
}
void PETScMatrix::setRowsColumnsZero(std::vector<PetscInt> const& row_pos)
{
- // Each process indicates only rows it owns that are to be zeroed.
- // If it is called, it must be called by all ranks of cores.
-
+ // Each rank (compute core) processes only the rows that belong to the rank itself.
const PetscScalar one = 1.0;
const PetscInt nrows = static_cast<PetscInt> (row_pos.size());
diff --git a/MathLib/LinAlg/PETSc/PETScMatrix.h b/MathLib/LinAlg/PETSc/PETScMatrix.h
index 2500332a552..60ca99208b3 100644
--- a/MathLib/LinAlg/PETSc/PETScMatrix.h
+++ b/MathLib/LinAlg/PETSc/PETScMatrix.h
@@ -27,8 +27,6 @@ namespace MathLib
{
/*!
- \class PETScVector
-
\brief Wrapper class for PETSc matrix routines
*/
class PETScMatrix
@@ -39,7 +37,7 @@ class PETScMatrix
\param size The dimension of the matrix.
\param mat_op The configuration information for creating a matrix
*/
- PETScMatrix(const PetscInt size, const PETScMatrixOption mat_op = PETScMatrixOption() );
+ PETScMatrix(const PetscInt size, const PETScMatrixOption &mat_op = PETScMatrixOption() );
~PETScMatrix()
{
@@ -58,7 +56,7 @@ class PETScMatrix
}
/// Get the dimension
- PetscInt size() const
+ PetscInt getDimension() const
{
return _size;
}
@@ -69,26 +67,26 @@ class PETScMatrix
return _start_rank;
}
- /// Get the last global index of the row in the same rank
+ /// Get the end global index of the rows in the same rank
PetscInt getRangeEnd() const
{
return _end_rank;
}
/// Get the number of local rows
- PetscInt getLocalRows() const
+ PetscInt getNLocalRows() const
{
- return _loc_rows;
+ return _n_loc_rows;
}
/// Get the number of local columns
- PetscInt getLocalColumns() const
+ PetscInt getNLocalColumns() const
{
- return _loc_cols;
+ return _n_loc_cols;
}
/// Get matrix reference
- PETSc_Mat &getData()
+ PETSc_Mat &getRawMatrix()
{
return _A;
}
@@ -100,7 +98,9 @@ class PETScMatrix
}
/*
- \brief Set the specified rows and columns to zero except off-diagonal entries
+ \brief Set the specified rows to zero except off-diagonal entries, i.e.
+ \f$A(k, j) = 0, j!=k, j=1,2,\cdots, n\f$, where \f$k \in \mbox{row\_pos}\f$
+ This fucntion must be called by all rank.
\param row_pos The row indicies of the specified rows.
*/
void setRowsColumnsZero(std::vector<PetscInt> const& row_pos);
@@ -111,13 +111,13 @@ class PETScMatrix
\param vec_r The result vector, e.g. \f$ y \f$
Both of the two arguments must be created prior to be used.
*/
- void multVector(PETScVector &vec, PETScVector &vec_r)
+ void multiVector(const PETScVector &vec, PETScVector &vec_r)
{
MatMult(_A, vec.getData(), vec_r.getData() );
}
/*!
- \brief Insert a single entry with value.
+ \brief Set a single entry with a value.
\param i The row index
\param j The column index
\param value The entry value
@@ -179,12 +179,12 @@ class PETScMatrix
/// PETSc matrix
PETSc_Mat _A;
- /// Dimension
+ /// Dimension of matrix
PetscInt _size;
/// Number of the local rows
- PetscInt _loc_rows;
+ PetscInt _n_loc_rows;
/// Number of the local columns
- PetscInt _loc_cols;
+ PetscInt _n_loc_cols;
/// Starting index in a rank
PetscInt _start_rank;
@@ -208,7 +208,7 @@ 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.getData(), ADD_VALUES);
+ MatSetValues(_A, nrows, &row_pos[0], ncols, &col_pos[0], sub_mat.getEntries(), ADD_VALUES);
};
/*!
diff --git a/MathLib/LinAlg/PETSc/PETScMatrixOption.h b/MathLib/LinAlg/PETSc/PETScMatrixOption.h
index 4ddcb644f01..f9add25c2a6 100644
--- a/MathLib/LinAlg/PETSc/PETScMatrixOption.h
+++ b/MathLib/LinAlg/PETSc/PETScMatrixOption.h
@@ -19,38 +19,37 @@
namespace MathLib
{
/*!
- \struct PETScMatrixOption
\brief This a struct data containing the configuration information to create a PETSc type matrix
*/
struct PETScMatrixOption
{
- PETScMatrixOption() : _is_size_local_rows(false), _local_cols(PETSC_DECIDE),
- _d_nz(10), _o_nz(10)
+ PETScMatrixOption() : _is_global_size(true), _n_local_cols(PETSC_DECIDE),
+ _d_nnz(PETSC_DECIDE), _o_nnz(PETSC_DECIDE)
{ }
/*!
- \brief Flag for the type of the first argument of
- the constructor of class PETScMatrix, size.
- true: the size is the number of local rows,
- false: the size is the number of global rows.
+ \brief Flag for the type of size, which is one of arguments of
+ the constructor of class PETScMatrix
+ true: the size is the number of local rows,
+ false: the size is the number of global rows.
The default is false.
*/
- bool _is_size_local_rows;
+ bool _is_global_size;
/// Number of local columns. The default is PETSC_DECIDE.
- PetscInt _local_cols;
+ PetscInt _n_local_cols;
/*!
\brief Number of nonzeros per row in DIAGONAL portion of local submatrix
- (same value is used for all local rows), the default is 10
+ (same value is used for all local rows), the default is PETSC_DECIDE
*/
- PetscInt _d_nz;
+ PetscInt _d_nnz;
/*!
\brief Number of nonzeros per row in the OFF-DIAGONAL portion of local submatrix
- (same value is used for all local rows), the default is 10
+ (same value is used for all local rows), the default is PETSC_DECIDE
*/
- PetscInt _o_nz;
+ PetscInt _o_nnz;
};
} // end namespace
diff --git a/MathLib/LinAlg/PETSc/PETScVector.h b/MathLib/LinAlg/PETSc/PETScVector.h
index b5a72069fee..c67c3c89374 100644
--- a/MathLib/LinAlg/PETSc/PETScVector.h
+++ b/MathLib/LinAlg/PETSc/PETScVector.h
@@ -39,7 +39,7 @@ class PETScVector
/*!
\brief Constructor
\param vec_size The size of the vector, either global or local
- \param is_global_size The flag of the type of vec_size, i.e. whether it is a global size
+ \param is_global_size The flag of the type of vec_size, i.e. whether it is a global size
or local size. The default is true.
*/
PETScVector(const PetscInt vec_size, const bool is_global_size = true);
@@ -179,7 +179,7 @@ class PETScVector
}
/// Get PETsc vector. Use it only for test purpose
- PETSc_Vec &getData()
+ const PETSc_Vec &getData() const
{
return _v;
}
diff --git a/Tests/MathLib/TestGlobalMatrixInterface.cpp b/Tests/MathLib/TestGlobalMatrixInterface.cpp
index 4a57cbc7cd9..a775af693aa 100644
--- a/Tests/MathLib/TestGlobalMatrixInterface.cpp
+++ b/Tests/MathLib/TestGlobalMatrixInterface.cpp
@@ -42,7 +42,7 @@ void checkGlobalMatrixInterface(T_MATRIX &m)
m.add(0, 0, 1.0);
m.setZero();
- MathLib::DenseMatrix<double, short> local_m(2, 2, 1.0);
+ MathLib::DenseMatrix<double> local_m(2, 2, 1.0);
std::vector<std::size_t> vec_pos(2);
vec_pos[0] = 1;
vec_pos[1] = 3;
@@ -61,16 +61,16 @@ void checkGlobalMatrixInterfaceMPI(T_MATRIX &m, T_VECTOR &v)
MPI_Comm_rank(PETSC_COMM_WORLD, &mrank);
ASSERT_EQ(3u, msize);
- ASSERT_EQ(6u, m.size());
- ASSERT_EQ(m.getRangeEnd()-m.getRangeBegin(), m.getLocalRows());
+ ASSERT_EQ(6u, m.getDimension());
+ ASSERT_EQ(m.getRangeEnd()-m.getRangeBegin(), m.getNLocalRows());
int gathered_cols;
- int local_cols = m.getLocalColumns();
+ int local_cols = m.getNLocalColumns();
MPI_Allreduce(&local_cols, &gathered_cols, 1, MPI_INT, MPI_SUM, PETSC_COMM_WORLD);
ASSERT_EQ(6u, gathered_cols);
// Add entries
- MathLib::DenseMatrix<double, short> loc_m(2);
+ MathLib::DenseMatrix<double> loc_m(2, 2);
loc_m(0, 0) = 1.;
loc_m(0, 1) = 2.;
loc_m(1, 0) = 3.;
@@ -91,7 +91,7 @@ void checkGlobalMatrixInterfaceMPI(T_MATRIX &m, T_VECTOR &v)
v = 1.;
const bool deep_copy = false;
T_VECTOR y(v, deep_copy);
- m.multVector(v, y);
+ m.multiVector(v, y);
ASSERT_EQ(sqrt(3*(3*3 + 7*7)), y.getNorm());
@@ -102,7 +102,7 @@ void checkGlobalMatrixInterfaceMPI(T_MATRIX &m, T_VECTOR &v)
m.add(1, 1, 5.0);
}
MathLib::finalizeMatrixAssembly(m);
- m.multVector(v, y);
+ m.multiVector(v, y);
ASSERT_EQ(sqrt((2*3*3 + 8*8 + 3*7*7)), y.getNorm());
}
@@ -128,10 +128,10 @@ TEST(Math, CheckInterface_LisMatrix)
TEST(Math, CheckInterface_PETScMatrix_Local_Size)
{
MathLib::PETScMatrixOption opt;
- opt._d_nz = 2;
- opt._o_nz = 0;
- opt._is_size_local_rows = true;
- opt._local_cols = 2;
+ opt._d_nnz = 2;
+ opt._o_nnz = 0;
+ opt._is_global_size = false;
+ opt._n_local_cols = 2;
MathLib::PETScMatrix A(2, opt);
const bool is_gloabal_size = false;
@@ -142,8 +142,8 @@ TEST(Math, CheckInterface_PETScMatrix_Local_Size)
TEST(Math, CheckInterface_PETScMatrix_Global_Size)
{
MathLib::PETScMatrixOption opt;
- opt._d_nz = 2;
- opt._o_nz = 0;
+ opt._d_nnz = 2;
+ opt._o_nnz = 0;
MathLib::PETScMatrix A(6, opt);
MathLib::PETScVector x(6);
diff --git a/scripts/cmake/Find.cmake b/scripts/cmake/Find.cmake
index 865941f1ba3..06cf9d7b4dd 100644
--- a/scripts/cmake/Find.cmake
+++ b/scripts/cmake/Find.cmake
@@ -120,6 +120,10 @@ ENDIF()
IF(OGS_USE_PETSC)
MESSAGE (STATUS "Configuring for PETSc" )
+ ##Force CMake to accept a given PETSc configuration in case the failure of MPI tests
+ ##This may cause the compilation broken.
+ SET(PETSC_EXECUTABLE_RUNS YES)
+
SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/scripts/cmake/findPETSC")
FIND_PACKAGE(PETSc REQUIRED)
diff --git a/scripts/cmake/findPETSC/FindPETSc.cmake b/scripts/cmake/findPETSC/FindPETSc.cmake
index 4b4eb3addb2..536e4546cc6 100644
--- a/scripts/cmake/findPETSC/FindPETSc.cmake
+++ b/scripts/cmake/findPETSC/FindPETSc.cmake
@@ -320,12 +320,6 @@ int main(int argc,char *argv[]) {
mark_as_advanced (PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC PETSC_EXECUTABLE_RUNS)
endif ()
-# message (STATUS "dddd---${PETSC_INCLUDES}--${PETSC_LIBRARIES}-- ${petsc_includes_minimal} ")
-# message (STATUS "dddd---${PETSC_EXECUTABLE_RUNS} ggggg ${PETSC_DEFINITIONS}")
-
- set (PETSC_EXECUTABLE_RUNS "YES" CACHE BOOL
-"Can the system successfully run a PETSc executable? This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build. If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
-
include (FindPackageHandleStandardArgs)
find_package_handle_standard_args (PETSc
"PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH."
--
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