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Merge Pull Request #9241 from brian-kelley/Trilinos/Fix9228
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Automatically Merged using Trilinos Pull Request AutoTester
PR Title: Tpetra: speed up sortAndMerge (#9228)
PR Author: brian-kelley
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trilinos-autotester authored Jun 8, 2021
2 parents 332e870 + c1b5e97 commit 6ab2840
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Showing 3 changed files with 33 additions and 66 deletions.
3 changes: 0 additions & 3 deletions packages/tpetra/core/src/Tpetra_CrsGraph_def.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -5020,7 +5020,6 @@ namespace Tpetra {
using LO = local_ordinal_type;
using GO = global_ordinal_type;
using this_type = CrsGraph<LO, GO, node_type>;
using row_graph_type = RowGraph<LO, GO, node_type>;
const char tfecfFuncName[] = "copyAndPermute: ";
const bool verbose = verbose_;

Expand Down Expand Up @@ -5698,8 +5697,6 @@ namespace Tpetra {
using std::endl;
using crs_graph_type =
CrsGraph<local_ordinal_type, global_ordinal_type, node_type>;
using row_graph_type =
RowGraph<local_ordinal_type, global_ordinal_type, node_type>;
const char tfecfFuncName[] = "packAndPrepare: ";
ProfilingRegion region_papn ("Tpetra::CrsGraph::packAndPrepare");

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6 changes: 3 additions & 3 deletions packages/tpetra/core/src/Tpetra_CrsMatrix_decl.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3794,9 +3794,9 @@ namespace Tpetra {
///
/// \pre The graph is not already storage optimized:
/// <tt>isStorageOptimized() == false</tt>
size_t
mergeRowIndicesAndValues (crs_graph_type& graph,
const RowInfo& rowInfo);
/// \return The new row length, after merging.
static size_t
mergeRowIndicesAndValues (size_t rowLen, local_ordinal_type* cols, impl_scalar_type* vals);

/// \brief Sort and merge duplicate local column indices in all
/// rows on the calling process, along with their corresponding
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90 changes: 30 additions & 60 deletions packages/tpetra/core/src/Tpetra_CrsMatrix_def.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1867,7 +1867,6 @@ namespace Tpetra {
const Teuchos::ArrayView<const Scalar>& values)
{
using std::endl;
typedef impl_scalar_type IST;
const char tfecfFuncName[] = "insertLocalValues: ";

TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC
Expand Down Expand Up @@ -1965,7 +1964,6 @@ namespace Tpetra {
const impl_scalar_type vals[],
const size_t numInputEnt)
{
typedef impl_scalar_type IST;
#ifdef HAVE_TPETRA_DEBUG
const char tfecfFuncName[] = "insertGlobalValuesImpl: ";
const size_t origNumEnt = graph.getNumEntriesInLocalRow (rowInfo.localRow);
Expand Down Expand Up @@ -3284,7 +3282,6 @@ namespace Tpetra {
#endif // HAVE_TPETRA_DEBUG

range_type range (rowinfo.offset1D, rowinfo.offset1D + rowinfo.allocSize);
typedef View<const ST*, device_type, MemoryUnmanaged> subview_type;
// mfh 23 Nov 2015: Don't just create a subview of k_values1D_
// directly, because that first creates a _managed_ subview,
// then returns an unmanaged version of that. That touches the
Expand Down Expand Up @@ -3806,7 +3803,6 @@ CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
scale (const Scalar& alpha)
{
typedef LocalOrdinal LO;
const char tfecfFuncName[] = "scale: ";
const impl_scalar_type theAlpha = static_cast<impl_scalar_type> (alpha);

Expand Down Expand Up @@ -5014,40 +5010,18 @@ CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
}

template <class Scalar, class LocalOrdinal, class GlobalOrdinal, class Node>
size_t
CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
mergeRowIndicesAndValues (crs_graph_type& graph,
const RowInfo& rowInfo)
size_t CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
mergeRowIndicesAndValues (size_t rowLen, LocalOrdinal* cols, impl_scalar_type* vals)
{
#ifdef HAVE_TPETRA_DEBUG
const char tfecfFuncName[] = "mergeRowIndicesAndValues: ";
#endif // HAVE_TPETRA_DEBUG

auto rowValues = this->getValuesViewHostNonConst (rowInfo);
typedef typename std::decay<decltype (rowValues[0]) >::type value_type;
value_type* rowValueIter = rowValues.data ();

auto inds_view = graph.getLocalIndsViewHostNonConst (rowInfo);

impl_scalar_type* rowValueIter = vals;
// beg,end define a half-exclusive interval over which to iterate.
LocalOrdinal* beg = inds_view.data ();
LocalOrdinal* end = inds_view.data () + rowInfo.numEntries;

#ifdef HAVE_TPETRA_DEBUG
TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC
(rowInfo.allocSize != static_cast<size_t> (inds_view.extent (0)) ||
rowInfo.allocSize != static_cast<size_t> (rowValues.extent (0)),
std::runtime_error, "rowInfo.allocSize = " << rowInfo.allocSize
<< " != inds_view.extent(0) = " << inds_view.extent (0)
<< " || rowInfo.allocSize = " << rowInfo.allocSize
<< " != rowValues.extent(0) = " << rowValues.extent (0) << ".");
#endif // HAVE_TPETRA_DEBUG

LocalOrdinal* beg = cols;
LocalOrdinal* end = cols + rowLen;
LocalOrdinal* newend = beg;
if (beg != end) {
LocalOrdinal* cur = beg + 1;
value_type* vcur = rowValueIter + 1;
value_type* vend = rowValueIter;
impl_scalar_type* vcur = rowValueIter + 1;
impl_scalar_type* vend = rowValueIter;
cur = beg+1;
while (cur != end) {
if (*cur != *newend) {
Expand All @@ -5067,10 +5041,7 @@ CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
}
++newend; // one past the last entry, per typical [beg,end) semantics
}
const size_t mergedEntries = newend - beg;
graph.k_numRowEntries_(rowInfo.localRow) = mergedEntries;
const size_t numDups = rowInfo.numEntries - mergedEntries;
return numDups;
return newend - beg;
}

template <class Scalar, class LocalOrdinal, class GlobalOrdinal, class Node>
Expand All @@ -5083,7 +5054,6 @@ CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
typedef typename Kokkos::View<LO*, device_type>::HostMirror::execution_space
host_execution_space;
typedef Kokkos::RangePolicy<host_execution_space, LO> range_type;
//typedef Kokkos::RangePolicy<Kokkos::Serial, LO> range_type;
const char tfecfFuncName[] = "sortAndMergeIndicesAndValues: ";
ProfilingRegion regionSAM ("Tpetra::CrsMatrix::sortAndMergeIndicesAndValues");

Expand All @@ -5103,22 +5073,28 @@ CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
crs_graph_type& graph = * (this->myGraph_);
const LO lclNumRows = static_cast<LO> (this->getNodeNumRows ());
size_t totalNumDups = 0;
// FIXME (mfh 10 May 2017) This may assume CUDA UVM.
Kokkos::parallel_reduce (range_type (0, lclNumRows),
[this, &graph, sorted, merged] (const LO& lclRow, size_t& numDups) {
const RowInfo rowInfo = graph.getRowInfo (lclRow);
if (! sorted) {
auto lclColInds = graph.getLocalIndsViewHostNonConst (rowInfo);
auto vals = this->getValuesViewHostNonConst (rowInfo);

sort2 (lclColInds.data (),
lclColInds.data () + rowInfo.numEntries,
vals.data ());
}
if (! merged) {
numDups += this->mergeRowIndicesAndValues (graph, rowInfo);
}
}, totalNumDups);
{
//Accessing host unpacked (4-array CRS) local matrix.
auto rowBegins_ = graph.rowPtrsUnpacked_host_;
auto rowLengths_ = graph.k_numRowEntries_;
auto vals_ = this->valuesUnpacked_wdv.getHostView(Access::ReadWrite);
auto cols_ = graph.lclIndsUnpacked_wdv.getHostView(Access::ReadWrite);
Kokkos::parallel_reduce ("sortAndMergeIndicesAndValues", range_type (0, lclNumRows),
[=] (const LO lclRow, size_t& numDups) {
size_t rowBegin = rowBegins_(lclRow);
size_t rowLen = rowLengths_(lclRow);
LO* cols = cols_.data() + rowBegin;
impl_scalar_type* vals = vals_.data() + rowBegin;
if (! sorted) {
sort2 (cols, cols + rowLen, vals);
}
if (! merged) {
size_t newRowLength = mergeRowIndicesAndValues (rowLen, cols, vals);
rowLengths_(lclRow) = newRowLength;
numDups += rowLen - newRowLength;
}
}, totalNumDups);
}
if (! sorted) {
graph.indicesAreSorted_ = true; // we just sorted every row
}
Expand Down Expand Up @@ -5895,7 +5871,6 @@ CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
// Currently, the source object must be a RowMatrix with the same
// four template parameters as the target CrsMatrix. We might
// relax this requirement later.
typedef RowMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node> row_matrix_type;
const row_matrix_type* srcRowMat =
dynamic_cast<const row_matrix_type*> (&source);
return (srcRowMat != nullptr);
Expand Down Expand Up @@ -6622,7 +6597,6 @@ CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
std::cerr << os.str ();
}

using row_matrix_type = RowMatrix<Scalar, LO, GO, Node>;
const row_matrix_type* srcRowMat =
dynamic_cast<const row_matrix_type*> (&source);
TEUCHOS_TEST_FOR_EXCEPTION_CLASS_FUNC
Expand Down Expand Up @@ -7034,8 +7008,6 @@ CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
using LO = LocalOrdinal;
using GO = GlobalOrdinal;
using ST = impl_scalar_type;
using HES =
typename View<int*, device_type>::HostMirror::execution_space;
const char tfecfFuncName[] = "packNonStaticNew: ";

const bool verbose = Behavior::verbose("CrsMatrix");
Expand Down Expand Up @@ -7854,8 +7826,6 @@ CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>::
using std::endl;
using LO = local_ordinal_type;
using GO = global_ordinal_type;
using row_matrix_type =
RowMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>;
using crs_matrix_type =
CrsMatrix<Scalar, LocalOrdinal, GlobalOrdinal, Node>;
const char errPfx[] = "Tpetra::CrsMatrix::add: ";
Expand Down

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