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Matrix assembly data #644

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merged 5 commits into from
Oct 23, 2020
Merged

Matrix assembly data #644

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5a80512
add DENSE_ prefix to some kernel DECLARE_ macros
upsj Oct 18, 2020
2fde034
Add matrix_assembly_data with option of adding to matrix entries
fritzgoebel Sep 21, 2020
366460e
add matrix assembly data to matrix formats
upsj Oct 17, 2020
4a07ea4
review updates
upsj Oct 23, 2020
0447469
use pair for symbolic non-zero location
upsj Oct 23, 2020
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29 changes: 15 additions & 14 deletions core/device_hooks/common_kernels.inc.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -208,42 +208,43 @@ GKO_INSTANTIATE_FOR_EACH_VALUE_TYPE(
GKO_DECLARE_DENSE_CALCULATE_TOTAL_COLS_KERNEL);

template <typename ValueType>
GKO_DECLARE_TRANSPOSE_KERNEL(ValueType)
GKO_DECLARE_DENSE_TRANSPOSE_KERNEL(ValueType)
GKO_NOT_COMPILED(GKO_HOOK_MODULE);
GKO_INSTANTIATE_FOR_EACH_VALUE_TYPE(GKO_DECLARE_TRANSPOSE_KERNEL);
GKO_INSTANTIATE_FOR_EACH_VALUE_TYPE(GKO_DECLARE_DENSE_TRANSPOSE_KERNEL);

template <typename ValueType>
GKO_DECLARE_CONJ_TRANSPOSE_KERNEL(ValueType)
GKO_DECLARE_DENSE_CONJ_TRANSPOSE_KERNEL(ValueType)
GKO_NOT_COMPILED(GKO_HOOK_MODULE);
GKO_INSTANTIATE_FOR_EACH_VALUE_TYPE(GKO_DECLARE_CONJ_TRANSPOSE_KERNEL);
GKO_INSTANTIATE_FOR_EACH_VALUE_TYPE(GKO_DECLARE_DENSE_CONJ_TRANSPOSE_KERNEL);

template <typename ValueType, typename IndexType>
GKO_DECLARE_ROW_PERMUTE_KERNEL(ValueType, IndexType)
GKO_DECLARE_DENSE_ROW_PERMUTE_KERNEL(ValueType, IndexType)
GKO_NOT_COMPILED(GKO_HOOK_MODULE);
GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(GKO_DECLARE_ROW_PERMUTE_KERNEL);
GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
GKO_DECLARE_DENSE_ROW_PERMUTE_KERNEL);

template <typename ValueType, typename IndexType>
GKO_DECLARE_COLUMN_PERMUTE_KERNEL(ValueType, IndexType)
GKO_DECLARE_DENSE_COLUMN_PERMUTE_KERNEL(ValueType, IndexType)
GKO_NOT_COMPILED(GKO_HOOK_MODULE);
GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
GKO_DECLARE_COLUMN_PERMUTE_KERNEL);
GKO_DECLARE_DENSE_COLUMN_PERMUTE_KERNEL);

template <typename ValueType, typename IndexType>
GKO_DECLARE_INVERSE_ROW_PERMUTE_KERNEL(ValueType, IndexType)
GKO_DECLARE_DENSE_INV_ROW_PERMUTE_KERNEL(ValueType, IndexType)
GKO_NOT_COMPILED(GKO_HOOK_MODULE);
GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
GKO_DECLARE_INVERSE_ROW_PERMUTE_KERNEL);
GKO_DECLARE_DENSE_INV_ROW_PERMUTE_KERNEL);

template <typename ValueType, typename IndexType>
GKO_DECLARE_INVERSE_COLUMN_PERMUTE_KERNEL(ValueType, IndexType)
GKO_DECLARE_DENSE_INV_COLUMN_PERMUTE_KERNEL(ValueType, IndexType)
GKO_NOT_COMPILED(GKO_HOOK_MODULE);
GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
GKO_DECLARE_INVERSE_COLUMN_PERMUTE_KERNEL);
GKO_DECLARE_DENSE_INV_COLUMN_PERMUTE_KERNEL);

template <typename ValueType>
GKO_DECLARE_EXTRACT_DIAGONAL_KERNEL(ValueType)
GKO_DECLARE_DENSE_EXTRACT_DIAGONAL_KERNEL(ValueType)
GKO_NOT_COMPILED(GKO_HOOK_MODULE);
GKO_INSTANTIATE_FOR_EACH_VALUE_TYPE(GKO_DECLARE_EXTRACT_DIAGONAL_KERNEL);
GKO_INSTANTIATE_FOR_EACH_VALUE_TYPE(GKO_DECLARE_DENSE_EXTRACT_DIAGONAL_KERNEL);

template <typename ValueType>
GKO_DECLARE_INPLACE_ABSOLUTE_DENSE_KERNEL(ValueType)
Expand Down
28 changes: 14 additions & 14 deletions core/matrix/dense_kernels.hpp
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Expand Up @@ -133,41 +133,41 @@ namespace kernels {
size_type *result, size_type stride_factor, \
size_type slice_size)

#define GKO_DECLARE_TRANSPOSE_KERNEL(_type) \
#define GKO_DECLARE_DENSE_TRANSPOSE_KERNEL(_type) \
void transpose(std::shared_ptr<const DefaultExecutor> exec, \
const matrix::Dense<_type> *orig, \
matrix::Dense<_type> *trans)

#define GKO_DECLARE_CONJ_TRANSPOSE_KERNEL(_type) \
#define GKO_DECLARE_DENSE_CONJ_TRANSPOSE_KERNEL(_type) \
void conj_transpose(std::shared_ptr<const DefaultExecutor> exec, \
const matrix::Dense<_type> *orig, \
matrix::Dense<_type> *trans)

#define GKO_DECLARE_ROW_PERMUTE_KERNEL(_vtype, _itype) \
#define GKO_DECLARE_DENSE_ROW_PERMUTE_KERNEL(_vtype, _itype) \
void row_permute(std::shared_ptr<const DefaultExecutor> exec, \
const Array<_itype> *permutation_indices, \
const matrix::Dense<_vtype> *orig, \
matrix::Dense<_vtype> *row_permuted)

#define GKO_DECLARE_COLUMN_PERMUTE_KERNEL(_vtype, _itype) \
#define GKO_DECLARE_DENSE_COLUMN_PERMUTE_KERNEL(_vtype, _itype) \
void column_permute(std::shared_ptr<const DefaultExecutor> exec, \
const Array<_itype> *permutation_indices, \
const matrix::Dense<_vtype> *orig, \
matrix::Dense<_vtype> *column_permuted)

#define GKO_DECLARE_INVERSE_ROW_PERMUTE_KERNEL(_vtype, _itype) \
#define GKO_DECLARE_DENSE_INV_ROW_PERMUTE_KERNEL(_vtype, _itype) \
void inverse_row_permute(std::shared_ptr<const DefaultExecutor> exec, \
const Array<_itype> *permutation_indices, \
const matrix::Dense<_vtype> *orig, \
matrix::Dense<_vtype> *row_permuted)

#define GKO_DECLARE_INVERSE_COLUMN_PERMUTE_KERNEL(_vtype, _itype) \
#define GKO_DECLARE_DENSE_INV_COLUMN_PERMUTE_KERNEL(_vtype, _itype) \
void inverse_column_permute(std::shared_ptr<const DefaultExecutor> exec, \
const Array<_itype> *permutation_indices, \
const matrix::Dense<_vtype> *orig, \
matrix::Dense<_vtype> *column_permuted)

#define GKO_DECLARE_EXTRACT_DIAGONAL_KERNEL(_vtype) \
#define GKO_DECLARE_DENSE_EXTRACT_DIAGONAL_KERNEL(_vtype) \
void extract_diagonal(std::shared_ptr<const DefaultExecutor> exec, \
const matrix::Dense<_vtype> *orig, \
matrix::Diagonal<_vtype> *diag)
Expand Down Expand Up @@ -219,19 +219,19 @@ namespace kernels {
template <typename ValueType> \
GKO_DECLARE_DENSE_CALCULATE_TOTAL_COLS_KERNEL(ValueType); \
template <typename ValueType> \
GKO_DECLARE_TRANSPOSE_KERNEL(ValueType); \
GKO_DECLARE_DENSE_TRANSPOSE_KERNEL(ValueType); \
template <typename ValueType> \
GKO_DECLARE_CONJ_TRANSPOSE_KERNEL(ValueType); \
GKO_DECLARE_DENSE_CONJ_TRANSPOSE_KERNEL(ValueType); \
template <typename ValueType, typename IndexType> \
GKO_DECLARE_ROW_PERMUTE_KERNEL(ValueType, IndexType); \
GKO_DECLARE_DENSE_ROW_PERMUTE_KERNEL(ValueType, IndexType); \
template <typename ValueType, typename IndexType> \
GKO_DECLARE_COLUMN_PERMUTE_KERNEL(ValueType, IndexType); \
GKO_DECLARE_DENSE_COLUMN_PERMUTE_KERNEL(ValueType, IndexType); \
template <typename ValueType, typename IndexType> \
GKO_DECLARE_INVERSE_ROW_PERMUTE_KERNEL(ValueType, IndexType); \
GKO_DECLARE_DENSE_INV_ROW_PERMUTE_KERNEL(ValueType, IndexType); \
template <typename ValueType, typename IndexType> \
GKO_DECLARE_INVERSE_COLUMN_PERMUTE_KERNEL(ValueType, IndexType); \
GKO_DECLARE_DENSE_INV_COLUMN_PERMUTE_KERNEL(ValueType, IndexType); \
template <typename ValueType> \
GKO_DECLARE_EXTRACT_DIAGONAL_KERNEL(ValueType); \
GKO_DECLARE_DENSE_EXTRACT_DIAGONAL_KERNEL(ValueType); \
template <typename ValueType> \
GKO_DECLARE_INPLACE_ABSOLUTE_DENSE_KERNEL(ValueType); \
template <typename ValueType> \
Expand Down
1 change: 1 addition & 0 deletions core/test/base/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ ginkgo_create_test(executor)
ginkgo_create_test(iterator_factory)
ginkgo_create_test(lin_op)
ginkgo_create_test(math)
ginkgo_create_test(matrix_assembly_data)
ginkgo_create_test(matrix_data)
ginkgo_create_test(mtx_io)
ginkgo_create_test(perturbation)
Expand Down
129 changes: 129 additions & 0 deletions core/test/base/matrix_assembly_data.cpp
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@@ -0,0 +1,129 @@
/*******************************<GINKGO LICENSE>******************************
Copyright (c) 2017-2020, the Ginkgo authors
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:

1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
******************************<GINKGO LICENSE>*******************************/

#include <ginkgo/core/base/matrix_assembly_data.hpp>


#include <gtest/gtest.h>


namespace {


TEST(MatrixAssemblyData, InitializesWithZeros)
{
gko::matrix_assembly_data<double, int> m(gko::dim<2>{3, 5});

ASSERT_EQ(m.get_size(), gko::dim<2>(3, 5));
ASSERT_EQ(m.get_num_stored_elements(), 0);
ASSERT_EQ(m.get_value(0, 0), 0.0);
ASSERT_FALSE(m.contains(0, 0));
}


TEST(MatrixAssemblyData, InsertsValuesWithoutAdding)
{
gko::matrix_assembly_data<double, int> m(gko::dim<2>{3, 5});

m.add_value(0, 0, 1.3);
m.add_value(2, 3, 2.2);
m.add_value(1, 4, 1.1);
m.add_value(1, 2, 3.6);

ASSERT_EQ(m.get_size(), gko::dim<2>(3, 5));
ASSERT_EQ(m.get_num_stored_elements(), 4);
ASSERT_EQ(m.get_value(0, 0), 1.3);
ASSERT_EQ(m.get_value(2, 3), 2.2);
ASSERT_EQ(m.get_value(1, 4), 1.1);
ASSERT_EQ(m.get_value(1, 2), 3.6);
ASSERT_TRUE(m.contains(0, 0));
}


TEST(MatrixAssemblyData, InsertsValuesWithAdding)
{
gko::matrix_assembly_data<double, int> m(gko::dim<2>{3, 5});

m.add_value(0, 0, 1.3);
m.add_value(2, 3, 2.2);
m.add_value(1, 4, 1.1);
m.add_value(1, 2, 3.6);
m.add_value(1, 4, 9.1);
m.add_value(2, 3, 1.3);

ASSERT_EQ(m.get_size(), gko::dim<2>(3, 5));
ASSERT_EQ(m.get_num_stored_elements(), 4);
ASSERT_EQ(m.get_value(0, 0), 1.3);
ASSERT_EQ(m.get_value(2, 3), 3.5);
ASSERT_EQ(m.get_value(1, 4), 10.2);
ASSERT_EQ(m.get_value(1, 2), 3.6);
}


TEST(MatrixAssemblyData, OverwritesValuesWhenNotAdding)
{
gko::matrix_assembly_data<double, int> m(gko::dim<2>{3, 5});

m.set_value(0, 0, 1.3);
m.set_value(2, 3, 2.2);
m.set_value(1, 4, 1.1);
m.set_value(1, 2, 3.6);
m.set_value(1, 4, 9.1);
m.set_value(2, 3, 1.4);

ASSERT_EQ(m.get_size(), gko::dim<2>(3, 5));
ASSERT_EQ(m.get_num_stored_elements(), 4);
ASSERT_EQ(m.get_value(0, 0), 1.3);
ASSERT_EQ(m.get_value(2, 3), 1.4);
ASSERT_EQ(m.get_value(1, 4), 9.1);
ASSERT_EQ(m.get_value(1, 2), 3.6);
}


TEST(MatrixAssemblyData, GetsSortedData)
{
gko::matrix_assembly_data<double, int> m(gko::dim<2>{3, 5});
std::vector<gko::matrix_data<double, int>::nonzero_type> reference{
{0, 0, 1.3}, {1, 2, 3.6}, {1, 4, 1.1}, {2, 3, 2.2}};
m.set_value(0, 0, 1.3);
m.set_value(2, 3, 2.2);
m.set_value(1, 4, 1.1);
m.set_value(1, 2, 3.6);

auto sorted = m.get_ordered_data();

ASSERT_EQ(sorted.size, m.get_size());
ASSERT_EQ(sorted.nonzeros, reference);
}


} // namespace
20 changes: 20 additions & 0 deletions core/test/matrix/coo.cpp
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Expand Up @@ -211,6 +211,26 @@ TYPED_TEST(Coo, CanBeReadFromMatrixData)
}


TYPED_TEST(Coo, CanBeReadFromMatrixAssemblyData)
{
using Mtx = typename TestFixture::Mtx;
using value_type = typename TestFixture::value_type;
using index_type = typename TestFixture::index_type;
auto m = Mtx::create(this->exec);
gko::matrix_assembly_data<value_type, index_type> data(gko::dim<2>{2, 3});
data.set_value(0, 0, 1.0);
data.set_value(0, 1, 3.0);
data.set_value(0, 2, 2.0);
data.set_value(1, 0, 0.0);
data.set_value(1, 1, 5.0);
data.set_value(1, 2, 0.0);

m->read(data);

this->assert_equal_to_original_mtx(m.get());
}


TYPED_TEST(Coo, GeneratesCorrectMatrixData)
{
using Mtx = typename TestFixture::Mtx;
Expand Down
21 changes: 21 additions & 0 deletions core/test/matrix/csr.cpp
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Expand Up @@ -221,6 +221,27 @@ TYPED_TEST(Csr, CanBeReadFromMatrixData)
}


TYPED_TEST(Csr, CanBeReadFromMatrixAssemblyData)
{
using Mtx = typename TestFixture::Mtx;
using value_type = typename TestFixture::value_type;
using index_type = typename TestFixture::index_type;
auto m = Mtx::create(this->exec,
std::make_shared<typename Mtx::load_balance>(2));
gko::matrix_assembly_data<value_type, index_type> data(gko::dim<2>{2, 3});
data.set_value(0, 0, 1.0);
data.set_value(0, 1, 3.0);
data.set_value(0, 2, 2.0);
data.set_value(1, 0, 0.0);
data.set_value(1, 1, 5.0);
data.set_value(1, 2, 0.0);

m->read(data);

this->assert_equal_to_original_mtx(m.get());
}


TYPED_TEST(Csr, GeneratesCorrectMatrixData)
{
using value_type = typename TestFixture::value_type;
Expand Down
25 changes: 25 additions & 0 deletions core/test/matrix/dense.cpp
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Expand Up @@ -278,6 +278,31 @@ TYPED_TEST(Dense, GeneratesCorrectMatrixData)
}


TYPED_TEST(Dense, CanBeReadFromMatrixAssemblyData)
{
using value_type = typename TestFixture::value_type;
auto m = gko::matrix::Dense<TypeParam>::create(this->exec);
gko::matrix_assembly_data<TypeParam> data(gko::dim<2>{2, 3});
data.set_value(0, 0, 1.0);
data.set_value(0, 1, 3.0);
data.set_value(0, 2, 2.0);
data.set_value(1, 0, 0.0);
data.set_value(1, 1, 5.0);
data.set_value(1, 2, 0.0);

m->read(data);

ASSERT_EQ(m->get_size(), gko::dim<2>(2, 3));
ASSERT_EQ(m->get_num_stored_elements(), 6);
EXPECT_EQ(m->at(0, 0), value_type{1.0});
EXPECT_EQ(m->at(1, 0), value_type{0.0});
EXPECT_EQ(m->at(0, 1), value_type{3.0});
EXPECT_EQ(m->at(1, 1), value_type{5.0});
EXPECT_EQ(m->at(0, 2), value_type{2.0});
ASSERT_EQ(m->at(1, 2), value_type{0.0});
}


TYPED_TEST(Dense, CanCreateSubmatrix)
{
using value_type = typename TestFixture::value_type;
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20 changes: 20 additions & 0 deletions core/test/matrix/ell.cpp
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Expand Up @@ -231,4 +231,24 @@ TYPED_TEST(Ell, GeneratesCorrectMatrixData)
}


TYPED_TEST(Ell, CanBeReadFromMatrixAssemblyData)
{
using Mtx = typename TestFixture::Mtx;
using value_type = typename TestFixture::value_type;
using index_type = typename TestFixture::index_type;
auto m = Mtx::create(this->exec);
gko::matrix_assembly_data<value_type, index_type> data(gko::dim<2>{2, 3});
data.set_value(0, 0, 1.0);
data.set_value(0, 1, 3.0);
data.set_value(0, 2, 2.0);
data.set_value(1, 0, 0.0);
data.set_value(1, 1, 5.0);
data.set_value(1, 2, 0.0);

m->read(data);

this->assert_equal_to_original_mtx(m.get());
}


} // namespace
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