Refactor for GHistIndex.

src/common/hist_util.h

@@ -125,26 +125,25 @@ class HistogramCuts {
   /**
    * \brief Search the bin index for numerical feature.
    */
-  bst_bin_t SearchBin(Entry const& e) const {
-    return SearchBin(e.fvalue, e.index);
-  }
+  bst_bin_t SearchBin(Entry const& e) const { return SearchBin(e.fvalue, e.index); }
 
   /**
    * \brief Search the bin index for categorical feature.
    */
-  bst_bin_t SearchCatBin(Entry const &e) const {
+  bst_bin_t SearchCatBin(float value, bst_feature_t fidx) const {
     auto const &ptrs = this->Ptrs();
     auto const &vals = this->Values();
-    auto end = ptrs.at(e.index + 1) + vals.cbegin();
-    auto beg = ptrs[e.index] + vals.cbegin();
+    auto end = ptrs.at(fidx + 1) + vals.cbegin();
+    auto beg = ptrs[fidx] + vals.cbegin();
     // Truncates the value in case it's not perfectly rounded.
-    auto v  = static_cast<float>(common::AsCat(e.fvalue));
+    auto v  = static_cast<float>(common::AsCat(value));
     auto bin_idx = std::lower_bound(beg, end, v) - vals.cbegin();
-    if (bin_idx == ptrs.at(e.index + 1)) {
+    if (bin_idx == ptrs.at(fidx + 1)) {
       bin_idx -= 1;
     }
     return bin_idx;
   }
+  bst_bin_t SearchCatBin(Entry const& e) const { return SearchCatBin(e.fvalue, e.index); }
 };
 
 /**

src/data/gradient_index.cc

@@ -17,27 +17,59 @@ namespace xgboost {
 
 GHistIndexMatrix::GHistIndexMatrix() : columns_{std::make_unique<common::ColumnMatrix>()} {}
 
-GHistIndexMatrix::GHistIndexMatrix(DMatrix *x, int32_t max_bin, double sparse_thresh,
-                                   bool sorted_sketch, int32_t n_threads,
+GHistIndexMatrix::GHistIndexMatrix(DMatrix *p_fmat, bst_bin_t max_bins_per_feat,
+                                   double sparse_thresh, bool sorted_sketch, int32_t n_threads,
                                    common::Span<float> hess) {
-  this->Init(x, max_bin, sparse_thresh, sorted_sketch, n_threads, hess);
+  CHECK(p_fmat->SingleColBlock());
+  // We use sorted sketching for approx tree method since it's more efficient in
+  // computation time (but higher memory usage).
+  cut = common::SketchOnDMatrix(p_fmat, max_bins_per_feat, n_threads, sorted_sketch, hess);
+
+  max_num_bins = max_bins_per_feat;
+  const uint32_t nbins = cut.Ptrs().back();
+  hit_count.resize(nbins, 0);
+  hit_count_tloc_.resize(n_threads * nbins, 0);
+
+  size_t new_size = 1;
+  for (const auto &batch : p_fmat->GetBatches<SparsePage>()) {
+    new_size += batch.Size();
+  }
+
+  row_ptr.resize(new_size);
+  row_ptr[0] = 0;
+
+  const bool isDense = p_fmat->IsDense();
+  this->isDense_ = isDense;
+  auto ft = p_fmat->Info().feature_types.ConstHostSpan();
+
+  for (const auto &batch : p_fmat->GetBatches<SparsePage>()) {
+    this->PushBatch(batch, ft, nbins, n_threads);
+  }
+  this->columns_ = std::make_unique<common::ColumnMatrix>();
+
+  // hessian is empty when hist tree method is used or when dataset is empty
+  if (hess.empty() && !std::isnan(sparse_thresh)) {
+    // hist
+    CHECK(!sorted_sketch);
+    for (auto const &page : p_fmat->GetBatches<SparsePage>()) {
+      this->columns_->Init(page, *this, sparse_thresh, n_threads);
+    }
+  }
 }
 
 GHistIndexMatrix::~GHistIndexMatrix() = default;
 
-void GHistIndexMatrix::PushBatch(SparsePage const &batch,
-                                 common::Span<FeatureType const> ft,
-                                 size_t rbegin, size_t prev_sum, uint32_t nbins,
-                                 int32_t n_threads) {
+void GHistIndexMatrix::PushBatch(SparsePage const &batch, common::Span<FeatureType const> ft,
+                                 bst_bin_t n_total_bins, int32_t n_threads) {
   auto page = batch.GetView();
   auto it = common::MakeIndexTransformIter([&](size_t ridx) { return page[ridx].size(); });
-  common::PartialSum(n_threads, it, it + page.Size(), prev_sum, row_ptr.begin() + rbegin);
+  common::PartialSum(n_threads, it, it + page.Size(), static_cast<size_t>(0), row_ptr.begin());
   // The number of threads is pegged to the batch size. If the OMP block is parallelized
   // on anything other than the batch/block size, it should be reassigned
   const size_t batch_threads =
       std::max(static_cast<size_t>(1), std::min(batch.Size(), static_cast<size_t>(n_threads)));
 
-  const size_t n_index = row_ptr[rbegin + batch.Size()];  // number of entries in this page
+  const size_t n_index = row_ptr[batch.Size()];  // number of entries in this page
   ResizeIndex(n_index, isDense_);
 
   CHECK_GT(cut.Values().size(), 0U);
@@ -47,90 +79,37 @@ void GHistIndexMatrix::PushBatch(SparsePage const &batch,
   }
   uint32_t const *offsets = index.Offset();
 
+  auto n_bins_total = cut.TotalBins();
+  auto is_valid = [](auto) { return true; };  // SparsePage always contains valid entries
+  data::SparsePageAdapterBatch adapter_batch{page};
   if (isDense_) {
     // Inside the lambda functions, bin_idx is the index for cut value across all
     // features. By subtracting it with starting pointer of each feature, we can reduce
     // it to smaller value and compress it to smaller types.
-    common::BinTypeSize curent_bin_size = index.GetBinTypeSize();
-    if (curent_bin_size == common::kUint8BinsTypeSize) {
-      common::Span<uint8_t> index_data_span = {index.data<uint8_t>(), n_index};
-      SetIndexData(index_data_span, ft, batch_threads, batch, rbegin, nbins,
-                   [offsets](auto bin_idx, auto fidx) {
-                     return static_cast<uint8_t>(bin_idx - offsets[fidx]);
-                   });
-    } else if (curent_bin_size == common::kUint16BinsTypeSize) {
-      common::Span<uint16_t> index_data_span = {index.data<uint16_t>(), n_index};
-      SetIndexData(index_data_span, ft, batch_threads, batch, rbegin, nbins,
-                   [offsets](auto bin_idx, auto fidx) {
-                     return static_cast<uint16_t>(bin_idx - offsets[fidx]);
-                   });
-    } else {
-      CHECK_EQ(curent_bin_size, common::kUint32BinsTypeSize);
-      common::Span<uint32_t> index_data_span = {index.data<uint32_t>(), n_index};
-      SetIndexData(index_data_span, ft, batch_threads, batch, rbegin, nbins,
-                   [offsets](auto bin_idx, auto fidx) {
-                     return static_cast<uint32_t>(bin_idx - offsets[fidx]);
-                   });
-    }
+    common::DispatchBinType(index.GetBinTypeSize(), [&](auto dtype) {
+      using T = decltype(dtype);
+      common::Span<T> index_data_span = {index.data<T>(), index.Size()};
+      SetIndexData(
+          index_data_span, ft, batch_threads, adapter_batch, is_valid, n_bins_total,
+          [offsets](auto bin_idx, auto fidx) { return static_cast<T>(bin_idx - offsets[fidx]); });
+    });
   } else {
     /* For sparse DMatrix we have to store index of feature for each bin
        in index field to chose right offset. So offset is nullptr and index is
        not reduced */
     common::Span<uint32_t> index_data_span = {index.data<uint32_t>(), n_index};
-    SetIndexData(index_data_span, ft, batch_threads, batch, rbegin, nbins,
+    SetIndexData(index_data_span, ft, batch_threads, adapter_batch, is_valid, n_bins_total,
                  [](auto idx, auto) { return idx; });
   }
 
-  common::ParallelFor(nbins, n_threads, [&](bst_omp_uint idx) {
+  common::ParallelFor(n_total_bins, n_threads, [&](bst_omp_uint idx) {
     for (int32_t tid = 0; tid < n_threads; ++tid) {
-      hit_count[idx] += hit_count_tloc_[tid * nbins + idx];
-      hit_count_tloc_[tid * nbins + idx] = 0;  // reset for next batch
+      hit_count[idx] += hit_count_tloc_[tid * n_total_bins + idx];
+      hit_count_tloc_[tid * n_total_bins + idx] = 0;  // reset for next batch
     }
   });
 }
 
-void GHistIndexMatrix::Init(DMatrix *p_fmat, int max_bins, double sparse_thresh, bool sorted_sketch,
-                            int32_t n_threads, common::Span<float> hess) {
-  // We use sorted sketching for approx tree method since it's more efficient in
-  // computation time (but higher memory usage).
-  cut = common::SketchOnDMatrix(p_fmat, max_bins, n_threads, sorted_sketch, hess);
-
-  max_num_bins = max_bins;
-  const uint32_t nbins = cut.Ptrs().back();
-  hit_count.resize(nbins, 0);
-  hit_count_tloc_.resize(n_threads * nbins, 0);
-
-  size_t new_size = 1;
-  for (const auto &batch : p_fmat->GetBatches<SparsePage>()) {
-    new_size += batch.Size();
-  }
-
-  row_ptr.resize(new_size);
-  row_ptr[0] = 0;
-
-  size_t rbegin = 0;
-  size_t prev_sum = 0;
-  const bool isDense = p_fmat->IsDense();
-  this->isDense_ = isDense;
-  auto ft = p_fmat->Info().feature_types.ConstHostSpan();
-
-  for (const auto &batch : p_fmat->GetBatches<SparsePage>()) {
-    this->PushBatch(batch, ft, rbegin, prev_sum, nbins, n_threads);
-    prev_sum = row_ptr[rbegin + batch.Size()];
-    rbegin += batch.Size();
-  }
-  this->columns_ = std::make_unique<common::ColumnMatrix>();
-
-  // hessian is empty when hist tree method is used or when dataset is empty
-  if (hess.empty() && !std::isnan(sparse_thresh)) {
-    // hist
-    CHECK(!sorted_sketch);
-    for (auto const &page : p_fmat->GetBatches<SparsePage>()) {
-      this->columns_->Init(page, *this, sparse_thresh, n_threads);
-    }
-  }
-}
-
 void GHistIndexMatrix::Init(SparsePage const &batch, common::Span<FeatureType const> ft,
                             common::HistogramCuts const &cuts, int32_t max_bins_per_feat,
                             bool isDense, double sparse_thresh, int32_t n_threads) {
@@ -148,10 +127,7 @@ void GHistIndexMatrix::Init(SparsePage const &batch, common::Span<FeatureType co
   hit_count.resize(nbins, 0);
   hit_count_tloc_.resize(n_threads * nbins, 0);
 
-  size_t rbegin = 0;
-  size_t prev_sum = 0;
-
-  this->PushBatch(batch, ft, rbegin, prev_sum, nbins, n_threads);
+  this->PushBatch(batch, ft, nbins, n_threads);
   this->columns_ = std::make_unique<common::ColumnMatrix>();
   if (!std::isnan(sparse_thresh)) {
     this->columns_->Init(batch, *this, sparse_thresh, n_threads);

src/data/gradient_index.h

@@ -10,6 +10,7 @@
 #include "../common/categorical.h"
 #include "../common/hist_util.h"
 #include "../common/threading_utils.h"
+#include "adapter.h"
 #include "xgboost/base.h"
 #include "xgboost/data.h"
 
@@ -32,8 +33,38 @@ class GHistIndexMatrix {
    * \param rbegin The beginning row index of current page. (total rows in previous pages)
    * \param prev_sum Total number of entries in previous pages.
    */
-  void PushBatch(SparsePage const& batch, common::Span<FeatureType const> ft, size_t rbegin,
-                 size_t prev_sum, uint32_t nbins, int32_t n_threads);
+  void PushBatch(SparsePage const& batch, common::Span<FeatureType const> ft,
+                 bst_bin_t n_total_bins, int32_t n_threads);
+
+  template <typename Batch, typename BinIdxType, typename GetOffset, typename IsValid>
+  void SetIndexData(common::Span<BinIdxType> index_data_span, common::Span<FeatureType const> ft,
+                    size_t batch_threads, Batch const& batch, IsValid&& is_valid, size_t nbins,
+                    GetOffset&& get_offset) {
+    auto batch_size = batch.Size();
+    BinIdxType* index_data = index_data_span.data();
+    auto const& ptrs = cut.Ptrs();
+    auto const& values = cut.Values();
+    common::ParallelFor(batch_size, batch_threads, [&](size_t i) {
+      auto line = batch.GetLine(i);
+      size_t ibegin = row_ptr[i];  // index of first entry for current block
+      size_t k = 0;
+      auto tid = omp_get_thread_num();
+      for (size_t j = 0; j < line.Size(); ++j) {
+        data::COOTuple elem = line.GetElement(j);
+        if (is_valid(elem)) {
+          bst_bin_t bin_idx{-1};
+          if (common::IsCat(ft, elem.column_idx)) {
+            bin_idx = cut.SearchCatBin(elem.value, elem.column_idx);
+          } else {
+            bin_idx = cut.SearchBin(elem.value, elem.column_idx, ptrs, values);
+          }
+          index_data[ibegin + k] = get_offset(bin_idx, j);
+          ++hit_count_tloc_[tid * nbins + bin_idx];
+          ++k;
+        }
+      }
+    });
+  }
 
  public:
   /*! \brief row pointer to rows by element position */
@@ -50,52 +81,15 @@ class GHistIndexMatrix {
   size_t base_rowid{0};
 
   GHistIndexMatrix();
-  GHistIndexMatrix(DMatrix* x, int32_t max_bin, double sparse_thresh, bool sorted_sketch,
-                   int32_t n_threads, common::Span<float> hess = {});
+  GHistIndexMatrix(DMatrix* x, bst_bin_t max_bins_per_feat, double sparse_thresh,
+                   bool sorted_sketch, int32_t n_threads, common::Span<float> hess = {});
   ~GHistIndexMatrix();
 
-  // Create a global histogram matrix, given cut
-  void Init(DMatrix* p_fmat, int max_bins, double sparse_thresh, bool sorted_sketch,
-            int32_t n_threads, common::Span<float> hess);
+  // Create a global histogram matrix, given cut. Used by external memory
   void Init(SparsePage const& page, common::Span<FeatureType const> ft,
             common::HistogramCuts const& cuts, int32_t max_bins_per_feat, bool is_dense,
             double sparse_thresh, int32_t n_threads);
 
-  // specific method for sparse data as no possibility to reduce allocated memory
-  template <typename BinIdxType, typename GetOffset>
-  void SetIndexData(common::Span<BinIdxType> index_data_span,
-                    common::Span<FeatureType const> ft,
-                    size_t batch_threads, const SparsePage &batch,
-                    size_t rbegin, size_t nbins, GetOffset get_offset) {
-    const xgboost::Entry *data_ptr = batch.data.HostVector().data();
-    const std::vector<bst_row_t> &offset_vec = batch.offset.HostVector();
-    const size_t batch_size = batch.Size();
-    CHECK_LT(batch_size, offset_vec.size());
-    BinIdxType* index_data = index_data_span.data();
-    auto const& ptrs = cut.Ptrs();
-    auto const& values = cut.Values();
-    common::ParallelFor(batch_size, batch_threads, [&](omp_ulong ridx) {
-      const int tid = omp_get_thread_num();
-      size_t ibegin = row_ptr[rbegin + ridx];    // index of first entry for current block
-      size_t iend = row_ptr[rbegin + ridx + 1];  // first entry for next block
-      const size_t size = offset_vec[ridx + 1] - offset_vec[ridx];
-      SparsePage::Inst inst = {data_ptr + offset_vec[ridx], size};
-      CHECK_EQ(ibegin + inst.size(), iend);
-      for (bst_uint j = 0; j < inst.size(); ++j) {
-        auto e = inst[j];
-        if (common::IsCat(ft, e.index)) {
-          bst_bin_t bin_idx = cut.SearchCatBin(e);
-          index_data[ibegin + j] = get_offset(bin_idx, j);
-          ++hit_count_tloc_[tid * nbins + bin_idx];
-        } else {
-          bst_bin_t bin_idx = cut.SearchBin(e.fvalue, e.index, ptrs, values);
-          index_data[ibegin + j] = get_offset(bin_idx, j);
-          ++hit_count_tloc_[tid * nbins + bin_idx];
-        }
-      }
-    });
-  }
-
   void ResizeIndex(const size_t n_index, const bool isDense);
 
   void GetFeatureCounts(size_t* counts) const {

tests/cpp/common/test_column_matrix.cc

@@ -107,22 +107,5 @@ TEST(DenseColumnWithMissing, Test) {
     });
   }
 }
-
-void TestGHistIndexMatrixCreation(size_t nthreads) {
-  size_t constexpr kPageSize = 1024, kEntriesPerCol = 3;
-  size_t constexpr kEntries = kPageSize * kEntriesPerCol * 2;
-  /* This should create multiple sparse pages */
-  std::unique_ptr<DMatrix> dmat{CreateSparsePageDMatrix(kEntries)};
-  GHistIndexMatrix gmat(dmat.get(), 256, 0.5f, false, common::OmpGetNumThreads(nthreads));
-}
-
-TEST(HistIndexCreationWithExternalMemory, Test) {
-  // Vary the number of threads to make sure that the last batch
-  // is distributed properly to the available number of threads
-  // in the thread pool
-  TestGHistIndexMatrixCreation(20);
-  TestGHistIndexMatrixCreation(30);
-  TestGHistIndexMatrixCreation(40);
-}
 }  // namespace common
 }  // namespace xgboost

tests/cpp/data/test_gradient_index.cc

@@ -44,9 +44,7 @@ TEST(GradientIndex, FromCategoricalBasic) {
   h_ft.resize(kCols, FeatureType::kCategorical);
 
   BatchParam p(max_bins, 0.8);
-  GHistIndexMatrix gidx;
-
-  gidx.Init(m.get(), max_bins, p.sparse_thresh, false, common::OmpGetNumThreads(0), {});
+  GHistIndexMatrix gidx(m.get(), max_bins, p.sparse_thresh, false, common::OmpGetNumThreads(0), {});
 
   auto x_copy = x;
   std::sort(x_copy.begin(), x_copy.end());

tests/cpp/tree/hist/test_histogram.cc

@@ -413,10 +413,16 @@ void TestHistogramExternalMemory(BatchParam batch_param, bool is_approx) {
 
     single_build.Reset(total_bins, batch_param, common::OmpGetNumThreads(0), 1, false);
     SparsePage concat;
-    GHistIndexMatrix gmat;
     std::vector<float> hess(m->Info().num_row_, 1.0f);
-    gmat.Init(m.get(), batch_param.max_bin, std::numeric_limits<double>::quiet_NaN(), false,
-              common::OmpGetNumThreads(0), hess);
+    for (auto const& page : m->GetBatches<SparsePage>()) {
+      concat.Push(page);
+    }
+
+    auto cut = common::SketchOnDMatrix(m.get(), batch_param.max_bin, common::OmpGetNumThreads(0),
+                                       false, hess);
+    GHistIndexMatrix gmat;
+    gmat.Init(concat, {}, cut, batch_param.max_bin, false, std::numeric_limits<double>::quiet_NaN(),
+              common::OmpGetNumThreads(0));
     single_build.BuildHist(0, gmat, &tree, row_set_collection, nodes, {}, h_gpair);
     single_page = single_build.Histogram()[0];
   }