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Sparsity format Reference and OpenMP kernels #350

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merged 8 commits into from
Oct 8, 2019
Merged

Sparsity format Reference and OpenMP kernels #350

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75551c4
Add reference kernels and tests.
pratikvn Sep 12, 2019
9275cd7
Add OpenMP kernels and tests.
pratikvn Sep 12, 2019
03d28d3
Add conversions to Sparsity matrix format from CSR for all execs.
pratikvn Sep 12, 2019
31fcefd
Add a new constructor that automatically converts from the input LinOp.
pratikvn Sep 20, 2019
01e7989
Add ref and omp count diag kernel, tests for rem diag kernel.
pratikvn Sep 30, 2019
8a588b8
Review update
pratikvn Oct 1, 2019
b8bd477
Rename Sparsity to SparsityCsr.
pratikvn Oct 2, 2019
745eb45
Review update
pratikvn Oct 8, 2019
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Add OpenMP kernels and tests.
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@pratikvn
pratikvn committed Sep 30, 2019
commit 9275cd7c22067501f09631b9145aaac19c681331
136 changes: 124 additions & 12 deletions omp/matrix/sparsity_kernels.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ namespace gko {
namespace kernels {
namespace omp {
/**
* @brief The Compressed sparse row matrix format namespace.
* @brief The Sparsity pattern format namespace.
*
* @ingroup sparsity
*/
Expand All @@ -64,8 +64,26 @@ namespace sparsity {
template <typename ValueType, typename IndexType>
void spmv(std::shared_ptr<const OmpExecutor> exec,
const matrix::Sparsity<ValueType, IndexType> *a,
const matrix::Dense<ValueType> *b,
matrix::Dense<ValueType> *c) GKO_NOT_IMPLEMENTED;
const matrix::Dense<ValueType> *b, matrix::Dense<ValueType> *c)
{
auto row_ptrs = a->get_const_row_ptrs();
auto col_idxs = a->get_const_col_idxs();

#pragma omp parallel for
for (size_type row = 0; row < a->get_size()[0]; ++row) {
for (size_type j = 0; j < c->get_size()[1]; ++j) {
c->at(row, j) = zero<ValueType>();
}
for (size_type k = row_ptrs[row];
k < static_cast<size_type>(row_ptrs[row + 1]); ++k) {
auto val = one<ValueType>();
auto col = col_idxs[k];
for (size_type j = 0; j < c->get_size()[1]; ++j) {
c->at(row, j) += val * b->at(col, j);
}
}
}
}

GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(GKO_DECLARE_SPARSITY_SPMV_KERNEL);

Expand All @@ -76,7 +94,28 @@ void advanced_spmv(std::shared_ptr<const OmpExecutor> exec,
const matrix::Sparsity<ValueType, IndexType> *a,
const matrix::Dense<ValueType> *b,
const matrix::Dense<ValueType> *beta,
matrix::Dense<ValueType> *c) GKO_NOT_IMPLEMENTED;
matrix::Dense<ValueType> *c)
{
auto row_ptrs = a->get_const_row_ptrs();
auto col_idxs = a->get_const_col_idxs();
auto valpha = alpha->at(0, 0);
auto vbeta = beta->at(0, 0);

#pragma omp parallel for
for (size_type row = 0; row < a->get_size()[0]; ++row) {
for (size_type j = 0; j < c->get_size()[1]; ++j) {
c->at(row, j) *= vbeta;
}
for (size_type k = row_ptrs[row];
k < static_cast<size_type>(row_ptrs[row + 1]); ++k) {
auto val = one<ValueType>();
auto col = col_idxs[k];
for (size_type j = 0; j < c->get_size()[1]; ++j) {
c->at(row, j) += valpha * val * b->at(col, j);
}
}
}
}

GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
GKO_DECLARE_SPARSITY_ADVANCED_SPMV_KERNEL);
Expand All @@ -96,7 +135,26 @@ template <typename ValueType, typename IndexType>
void remove_diagonal_elements(std::shared_ptr<const OmpExecutor> exec,
matrix::Sparsity<ValueType, IndexType> *matrix,
const IndexType *row_ptrs,
const IndexType *col_idxs) GKO_NOT_IMPLEMENTED;
const IndexType *col_idxs)
{
auto num_rows = matrix->get_size()[0];
auto adj_ptrs = matrix->get_row_ptrs();
auto adj_idxs = matrix->get_col_idxs();
for (auto i = 0; i <= num_rows; ++i) {
adj_ptrs[i] = row_ptrs[i] - i;
}
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std::vector<IndexType> temp_idxs;
for (auto i = 0; i < num_rows; ++i) {
for (auto j = row_ptrs[i]; j < row_ptrs[i + 1]; ++j) {
if (col_idxs[j] != i) {
temp_idxs.push_back(col_idxs[j]);
}
}
}
for (auto i = 0; i < temp_idxs.size(); ++i) {
adj_idxs[i] = temp_idxs[i];
}
}

GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
GKO_DECLARE_SPARSITY_REMOVE_DIAGONAL_ELEMENTS_KERNEL);
Expand All @@ -106,22 +164,47 @@ template <typename IndexType>
inline void convert_sparsity_to_csc(size_type num_rows,
const IndexType *row_ptrs,
const IndexType *col_idxs,
IndexType *row_idxs,
IndexType *col_ptrs) GKO_NOT_IMPLEMENTED;
IndexType *row_idxs, IndexType *col_ptrs)
{
for (size_type row = 0; row < num_rows; ++row) {
for (auto i = row_ptrs[row]; i < row_ptrs[row + 1]; ++i) {
const auto dest_idx = col_ptrs[col_idxs[i]]++;
row_idxs[dest_idx] = row;
}
}
}


template <typename ValueType, typename IndexType>
void transpose_and_transform(std::shared_ptr<const OmpExecutor> exec,
matrix::Sparsity<ValueType, IndexType> *trans,
const matrix::Sparsity<ValueType, IndexType> *orig)
GKO_NOT_IMPLEMENTED;
{
auto trans_row_ptrs = trans->get_row_ptrs();
auto orig_row_ptrs = orig->get_const_row_ptrs();
auto trans_col_idxs = trans->get_col_idxs();
auto orig_col_idxs = orig->get_const_col_idxs();

auto orig_num_cols = orig->get_size()[1];
auto orig_num_rows = orig->get_size()[0];
auto orig_nnz = orig_row_ptrs[orig_num_rows];

trans_row_ptrs[0] = 0;
convert_unsorted_idxs_to_ptrs(orig_col_idxs, orig_nnz, trans_row_ptrs + 1,
orig_num_cols);

convert_sparsity_to_csc(orig_num_rows, orig_row_ptrs, orig_col_idxs,
trans_col_idxs, trans_row_ptrs + 1);
}


template <typename ValueType, typename IndexType>
void transpose(std::shared_ptr<const OmpExecutor> exec,
matrix::Sparsity<ValueType, IndexType> *trans,
const matrix::Sparsity<ValueType, IndexType> *orig)
GKO_NOT_IMPLEMENTED;
{
transpose_and_transform(exec, trans, orig);
}

GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
GKO_DECLARE_SPARSITY_TRANSPOSE_KERNEL);
Expand All @@ -130,7 +213,17 @@ GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
template <typename ValueType, typename IndexType>
void sort_by_column_index(std::shared_ptr<const OmpExecutor> exec,
matrix::Sparsity<ValueType, IndexType> *to_sort)
GKO_NOT_IMPLEMENTED;
{
auto row_ptrs = to_sort->get_row_ptrs();
auto col_idxs = to_sort->get_col_idxs();
const auto number_rows = to_sort->get_size()[0];
#pragma omp parallel for
for (size_type i = 0; i < number_rows; ++i) {
auto start_row_idx = row_ptrs[i];
auto row_nnz = row_ptrs[i + 1] - start_row_idx;
std::sort(col_idxs + start_row_idx, col_idxs + start_row_idx + row_nnz);
}
}

GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
GKO_DECLARE_SPARSITY_SORT_BY_COLUMN_INDEX);
Expand All @@ -139,8 +232,27 @@ GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
template <typename ValueType, typename IndexType>
void is_sorted_by_column_index(
std::shared_ptr<const OmpExecutor> exec,
const matrix::Sparsity<ValueType, IndexType> *to_check,
bool *is_sorted) GKO_NOT_IMPLEMENTED;
const matrix::Sparsity<ValueType, IndexType> *to_check, bool *is_sorted)
{
const auto row_ptrs = to_check->get_const_row_ptrs();
const auto col_idxs = to_check->get_const_col_idxs();
const auto size = to_check->get_size();
bool local_is_sorted = true;
#pragma omp parallel for shared(local_is_sorted)
for (size_type i = 0; i < size[0]; ++i) {
#pragma omp flush(local_is_sorted)
// Skip comparison if any thread detects that it is not sorted
if (local_is_sorted) {
for (auto idx = row_ptrs[i] + 1; idx < row_ptrs[i + 1]; ++idx) {
if (col_idxs[idx - 1] > col_idxs[idx]) {
local_is_sorted = false;
break;
}
}
}
}
*is_sorted = local_is_sorted;
}

GKO_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(
GKO_DECLARE_SPARSITY_IS_SORTED_BY_COLUMN_INDEX);
Expand Down
1 change: 1 addition & 0 deletions omp/test/matrix/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,4 @@ ginkgo_create_test(dense_kernels)
ginkgo_create_test(ell_kernels)
ginkgo_create_test(hybrid_kernels)
ginkgo_create_test(sellp_kernels)
ginkgo_create_test(sparsity_kernels)
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