Support CPU input for device QuantileDMatrix. (#8136)

- Copy `GHistIndexMatrix` to `Ellpack` when needed.

src/common/hist_util.cuh

@@ -17,6 +17,28 @@
 
 namespace xgboost {
 namespace common {
+namespace cuda {
+/**
+ * copy and paste of the host version, we can't make it a __host__ __device__ function as
+ * the fn might be a host only or device only callable object, which is not allowed by nvcc.
+ */
+template <typename Fn>
+auto __device__ DispatchBinType(BinTypeSize type, Fn&& fn) {
+  switch (type) {
+    case kUint8BinsTypeSize: {
+      return fn(uint8_t{});
+    }
+    case kUint16BinsTypeSize: {
+      return fn(uint16_t{});
+    }
+    case kUint32BinsTypeSize: {
+      return fn(uint32_t{});
+    }
+  }
+  SPAN_CHECK(false);
+  return fn(uint32_t{});
+}
+}  // namespace cuda
 
 namespace detail {
 struct EntryCompareOp {

src/data/device_adapter.cuh

@@ -108,12 +108,12 @@ class CudfAdapter : public detail::SingleBatchDataIter<CudfAdapterBatch> {
     }
 
     device_idx_ = dh::CudaGetPointerDevice(first_column.data);
-    CHECK_NE(device_idx_, -1);
+    CHECK_NE(device_idx_, Context::kCpuId);
     dh::safe_cuda(cudaSetDevice(device_idx_));
     for (auto& json_col : json_columns) {
       auto column = ArrayInterface<1>(get<Object const>(json_col));
       columns.push_back(column);
-      num_rows_ = std::max(num_rows_, size_t(column.Shape(0)));
+      num_rows_ = std::max(num_rows_, column.Shape(0));
       CHECK_EQ(device_idx_, dh::CudaGetPointerDevice(column.data))
           << "All columns should use the same device.";
       CHECK_EQ(num_rows_, column.Shape(0))
@@ -138,7 +138,7 @@ class CudfAdapter : public detail::SingleBatchDataIter<CudfAdapterBatch> {
   CudfAdapterBatch batch_;
   dh::device_vector<ArrayInterface<1>> columns_;
   size_t num_rows_{0};
-  int device_idx_;
+  int32_t device_idx_{Context::kCpuId};
 };
 
 class CupyAdapterBatch : public detail::NoMetaInfo {
@@ -173,7 +173,7 @@ class CupyAdapter : public detail::SingleBatchDataIter<CupyAdapterBatch> {
       return;
     }
     device_idx_ = dh::CudaGetPointerDevice(array_interface_.data);
-    CHECK_NE(device_idx_, -1);
+    CHECK_NE(device_idx_, Context::kCpuId);
   }
   explicit CupyAdapter(std::string cuda_interface_str)
       : CupyAdapter{StringView{cuda_interface_str}} {}
@@ -186,7 +186,7 @@ class CupyAdapter : public detail::SingleBatchDataIter<CupyAdapterBatch> {
  private:
   ArrayInterface<2> array_interface_;
   CupyAdapterBatch batch_;
-  int32_t device_idx_ {-1};
+  int32_t device_idx_ {Context::kCpuId};
 };
 
 // Returns maximum row length

src/data/ellpack_page.cu

@@ -1,14 +1,16 @@
 /*!
- * Copyright 2019-2020 XGBoost contributors
+ * Copyright 2019-2022 XGBoost contributors
  */
-#include <xgboost/data.h>
 #include <thrust/iterator/discard_iterator.h>
 #include <thrust/iterator/transform_output_iterator.h>
+
 #include "../common/categorical.h"
 #include "../common/hist_util.cuh"
 #include "../common/random.h"
 #include "./ellpack_page.cuh"
 #include "device_adapter.cuh"
+#include "gradient_index.h"
+#include "xgboost/data.h"
 
 namespace xgboost {
 
@@ -32,7 +34,7 @@ __global__ void CompressBinEllpackKernel(
     const size_t* __restrict__ row_ptrs,           // row offset of input data
     const Entry* __restrict__ entries,      // One batch of input data
     const float* __restrict__ cuts,         // HistogramCuts::cut_values_
-    const uint32_t* __restrict__ cut_rows,  // HistogramCuts::cut_ptrs_
+    const uint32_t* __restrict__ cut_ptrs,  // HistogramCuts::cut_ptrs_
     common::Span<FeatureType const> feature_types,
     size_t base_row,                        // batch_row_begin
     size_t n_rows,
@@ -50,8 +52,8 @@ __global__ void CompressBinEllpackKernel(
     int feature = entry.index;
     float fvalue = entry.fvalue;
     // {feature_cuts, ncuts} forms the array of cuts of `feature'.
-    const float* feature_cuts = &cuts[cut_rows[feature]];
-    int ncuts = cut_rows[feature + 1] - cut_rows[feature];
+    const float* feature_cuts = &cuts[cut_ptrs[feature]];
+    int ncuts = cut_ptrs[feature + 1] - cut_ptrs[feature];
     bool is_cat = common::IsCat(feature_types, ifeature);
     // Assigning the bin in current entry.
     // S.t.: fvalue < feature_cuts[bin]
@@ -69,7 +71,7 @@ __global__ void CompressBinEllpackKernel(
       bin = ncuts - 1;
     }
     // Add the number of bins in previous features.
-    bin += cut_rows[feature];
+    bin += cut_ptrs[feature];
   }
   // Write to gidx buffer.
   wr.AtomicWriteSymbol(buffer, bin, (irow + base_row) * row_stride + ifeature);
@@ -284,6 +286,70 @@ EllpackPageImpl::EllpackPageImpl(AdapterBatch batch, float missing, int device,
 ELLPACK_BATCH_SPECIALIZE(data::CudfAdapterBatch)
 ELLPACK_BATCH_SPECIALIZE(data::CupyAdapterBatch)
 
+namespace {
+void CopyGHistToEllpack(GHistIndexMatrix const& page, common::Span<size_t const> d_row_ptr,
+                        size_t row_stride, common::CompressedByteT* d_compressed_buffer,
+                        size_t null) {
+  dh::device_vector<uint8_t> data(page.index.begin(), page.index.end());
+  auto d_data = dh::ToSpan(data);
+
+  dh::device_vector<size_t> csc_indptr(page.index.Offset(),
+                                       page.index.Offset() + page.index.OffsetSize());
+  auto d_csc_indptr = dh::ToSpan(csc_indptr);
+
+  auto bin_type = page.index.GetBinTypeSize();
+  common::CompressedBufferWriter writer{page.cut.TotalBins() + 1};  // +1 for null value
+
+  dh::LaunchN(row_stride * page.Size(), [=] __device__(size_t idx) mutable {
+    auto ridx = idx / row_stride;
+    auto ifeature = idx % row_stride;
+
+    auto r_begin = d_row_ptr[ridx];
+    auto r_end = d_row_ptr[ridx + 1];
+    size_t r_size = r_end - r_begin;
+
+    if (ifeature >= r_size) {
+      writer.AtomicWriteSymbol(d_compressed_buffer, null, idx);
+      return;
+    }
+
+    size_t offset = 0;
+    if (!d_csc_indptr.empty()) {
+      // is dense, ifeature is the actual feature index.
+      offset = d_csc_indptr[ifeature];
+    }
+    common::cuda::DispatchBinType(bin_type, [&](auto t) {
+      using T = decltype(t);
+      auto ptr = reinterpret_cast<T const*>(d_data.data());
+      auto bin_idx = ptr[r_begin + ifeature] + offset;
+      writer.AtomicWriteSymbol(d_compressed_buffer, bin_idx, idx);
+    });
+  });
+}
+}  // anonymous namespace
+
+EllpackPageImpl::EllpackPageImpl(Context const* ctx, GHistIndexMatrix const& page,
+                                 common::Span<FeatureType const> ft)
+    : is_dense{page.IsDense()}, base_rowid{page.base_rowid}, n_rows{page.Size()}, cuts_{page.cut} {
+  auto it = common::MakeIndexTransformIter(
+      [&](size_t i) { return page.row_ptr[i + 1] - page.row_ptr[i]; });
+  row_stride = *std::max_element(it, it + page.Size());
+
+  CHECK_GE(ctx->gpu_id, 0);
+  monitor_.Start("InitCompressedData");
+  InitCompressedData(ctx->gpu_id);
+  monitor_.Stop("InitCompressedData");
+
+  // copy gidx
+  common::CompressedByteT* d_compressed_buffer = gidx_buffer.DevicePointer();
+  dh::device_vector<size_t> row_ptr(page.row_ptr);
+  auto d_row_ptr = dh::ToSpan(row_ptr);
+
+  auto accessor = this->GetDeviceAccessor(ctx->gpu_id, ft);
+  auto null = accessor.NullValue();
+  CopyGHistToEllpack(page, d_row_ptr, row_stride, d_compressed_buffer, null);
+}
+
 // A functor that copies the data from one EllpackPage to another.
 struct CopyPage {
   common::CompressedBufferWriter cbw;

src/data/ellpack_page.cuh

@@ -116,6 +116,8 @@ struct EllpackDeviceAccessor {
 };
 
 
+class GHistIndexMatrix;
+
 class EllpackPageImpl {
  public:
   /*!
@@ -154,6 +156,11 @@ class EllpackPageImpl {
                            common::Span<size_t> row_counts_span,
                            common::Span<FeatureType const> feature_types, size_t row_stride,
                            size_t n_rows, common::HistogramCuts const& cuts);
+  /**
+   * \brief Constructor from an existing CPU gradient index.
+   */
+  explicit EllpackPageImpl(Context const* ctx, GHistIndexMatrix const& page,
+                           common::Span<FeatureType const> ft);
 
   /*! \brief Copy the elements of the given ELLPACK page into this page.
    *

src/data/gradient_index.cc

@@ -66,6 +66,7 @@ GHistIndexMatrix::GHistIndexMatrix(MetaInfo const &info, common::HistogramCuts &
       max_num_bins(max_bin_per_feat),
       isDense_{info.num_col_ * info.num_row_ == info.num_nonzero_} {}
 
+
 GHistIndexMatrix::~GHistIndexMatrix() = default;
 
 void GHistIndexMatrix::PushBatch(SparsePage const &batch, common::Span<FeatureType const> ft,

src/data/iterative_dmatrix.cc

@@ -205,7 +205,12 @@ void IterativeDMatrix::InitFromCPU(DataIterHandle iter_handle, float missing,
 
 BatchSet<GHistIndexMatrix> IterativeDMatrix::GetGradientIndex(BatchParam const& param) {
   CheckParam(param);
-  CHECK(ghist_) << "Not initialized with CPU data";
+  CHECK(ghist_) << R"(`QuantileDMatrix` is not initialized with CPU data but used for CPU training.
+Possible solutions:
+- Use `DMatrix` instead.
+- Use CPU input for `QuantileDMatrix`.
+- Run training on GPU.
+)";
   auto begin_iter =
       BatchIterator<GHistIndexMatrix>(new SimpleBatchIteratorImpl<GHistIndexMatrix>(ghist_));
   return BatchSet<GHistIndexMatrix>(begin_iter);

src/data/iterative_dmatrix.cu

@@ -168,7 +168,17 @@ void IterativeDMatrix::InitFromCUDA(DataIterHandle iter_handle, float missing,
 
 BatchSet<EllpackPage> IterativeDMatrix::GetEllpackBatches(BatchParam const& param) {
   CheckParam(param);
-  CHECK(ellpack_) << "Not initialized with GPU data";
+  if (!ellpack_ && !ghist_) {
+    LOG(FATAL) << "`QuantileDMatrix` not initialized.";
+  }
+  if (!ellpack_ && ghist_) {
+    ellpack_.reset(new EllpackPage());
+    this->ctx_.gpu_id = param.gpu_id;
+    this->Info().feature_types.SetDevice(param.gpu_id);
+    *ellpack_->Impl() =
+        EllpackPageImpl(&ctx_, *this->ghist_, this->Info().feature_types.ConstDeviceSpan());
+  }
+  CHECK(ellpack_);
   auto begin_iter = BatchIterator<EllpackPage>(new SimpleBatchIteratorImpl<EllpackPage>(ellpack_));
   return BatchSet<EllpackPage>(begin_iter);
 }

src/data/iterative_dmatrix.h

@@ -22,7 +22,28 @@ class HistogramCuts;
 }
 
 namespace data {
-
+/**
+ * \brief DMatrix type for `QuantileDMatrix`, the naming `IterativeDMatix` is due to its
+ *        construction process.
+ *
+ * `QuantileDMatrix` is an intermediate storage for quantilization results including
+ * quantile cuts and histogram index. Quantilization is designed to be performed on stream
+ * of data (or batches of it). As a result, the `QuantileDMatrix` is also designed to work
+ * with batches of data. During initializaion, it will walk through the data multiple
+ * times iteratively in order to perform quantilization. This design can help us reduce
+ * memory usage significantly by avoiding data concatenation along with removing the CSR
+ * matrix `SparsePage`. However, it has its limitation (can be fixed if needed):
+ *
+ * - It's only supported by hist tree method (both CPU and GPU) since approx requires a
+ *   re-calculation of quantiles for each iteration. We can fix this by retaining a
+ *   reference to the callback if there are feature requests.
+ *
+ * - The CPU format and the GPU format are different, the former uses a CSR + CSC for
+ *   histogram index while the latter uses only Ellpack. This results into a design that
+ *   we can obtain the GPU format from CPU but the other way around is not yet
+ *   supported. We can search the bin value from ellpack to recover the feature index when
+ *   we support copying data from GPU to CPU.
+ */
 class IterativeDMatrix : public DMatrix {
   MetaInfo info_;
   Context ctx_;
@@ -40,7 +61,8 @@ class IterativeDMatrix : public DMatrix {
       LOG(WARNING) << "Inconsistent max_bin between Quantile DMatrix and Booster:" << param.max_bin
                    << " vs. " << batch_param_.max_bin;
     }
-    CHECK(!param.regen) << "Only `hist` and `gpu_hist` tree method can use `QuantileDMatrix`.";
+    CHECK(!param.regen && param.hess.empty())
+        << "Only `hist` and `gpu_hist` tree method can use `QuantileDMatrix`.";
   }
 
   template <typename Page>
@@ -49,7 +71,6 @@ class IterativeDMatrix : public DMatrix {
     return BatchSet<Page>(BatchIterator<Page>(nullptr));
   }
 
- public:
   void InitFromCUDA(DataIterHandle iter, float missing, std::shared_ptr<DMatrix> ref);
   void InitFromCPU(DataIterHandle iter_handle, float missing, std::shared_ptr<DMatrix> ref);
 
@@ -73,8 +94,9 @@ class IterativeDMatrix : public DMatrix {
     batch_param_ = BatchParam{d, max_bin};
     batch_param_.sparse_thresh = 0.2;  // default from TrainParam
 
-    ctx_.UpdateAllowUnknown(Args{{"nthread", std::to_string(nthread)}});
-    if (d == Context::kCpuId) {
+    ctx_.UpdateAllowUnknown(
+        Args{{"nthread", std::to_string(nthread)}, {"gpu_id", std::to_string(d)}});
+    if (ctx_.IsCPU()) {
       this->InitFromCPU(iter_handle, missing, ref);
     } else {
       this->InitFromCUDA(iter_handle, missing, ref);

tests/ci_build/lint_python.py

@@ -121,7 +121,6 @@ def print_summary_map(result_map: Dict[str, Dict[str, int]]) -> int:
                 "python-package/xgboost/sklearn.py",
                 "python-package/xgboost/spark",
                 "python-package/xgboost/federated.py",
-                "python-package/xgboost/spark",
                 # tests
                 "tests/python/test_config.py",
                 "tests/python/test_spark/",

tests/cpp/data/test_ellpack_page.cu

@@ -236,4 +236,45 @@ TEST(EllpackPage, Compact) {
     }
   }
 }
+
+namespace {
+class EllpackPageTest : public testing::TestWithParam<float> {
+ protected:
+  void Run(float sparsity) {
+    // Only testing with small sample size as the cuts might be different between host and
+    // device.
+    size_t n_samples{128}, n_features{13};
+    Context ctx;
+    ctx.gpu_id = 0;
+    auto Xy = RandomDataGenerator{n_samples, n_features, sparsity}.GenerateDMatrix(true);
+    std::unique_ptr<EllpackPageImpl> from_ghist;
+    ASSERT_TRUE(Xy->SingleColBlock());
+    for (auto const& page : Xy->GetBatches<GHistIndexMatrix>(BatchParam{17, 0.6})) {
+      from_ghist.reset(new EllpackPageImpl{&ctx, page, {}});
+    }
+
+    for (auto const& page : Xy->GetBatches<EllpackPage>(BatchParam{0, 17})) {
+      auto from_sparse_page = page.Impl();
+      ASSERT_EQ(from_sparse_page->is_dense, from_ghist->is_dense);
+      ASSERT_EQ(from_sparse_page->base_rowid, 0);
+      ASSERT_EQ(from_sparse_page->base_rowid, from_ghist->base_rowid);
+      ASSERT_EQ(from_sparse_page->n_rows, from_ghist->n_rows);
+      ASSERT_EQ(from_sparse_page->gidx_buffer.Size(), from_ghist->gidx_buffer.Size());
+      auto const& h_gidx_from_sparse = from_sparse_page->gidx_buffer.HostVector();
+      auto const& h_gidx_from_ghist = from_ghist->gidx_buffer.HostVector();
+      ASSERT_EQ(from_sparse_page->NumSymbols(), from_ghist->NumSymbols());
+      common::CompressedIterator<uint32_t> from_ghist_it(h_gidx_from_ghist.data(),
+                                                         from_ghist->NumSymbols());
+      common::CompressedIterator<uint32_t> from_sparse_it(h_gidx_from_sparse.data(),
+                                                          from_sparse_page->NumSymbols());
+      for (size_t i = 0; i < from_ghist->n_rows * from_ghist->row_stride; ++i) {
+        EXPECT_EQ(from_ghist_it[i], from_sparse_it[i]);
+      }
+    }
+  }
+};
+}  // namespace
+
+TEST_P(EllpackPageTest, FromGHistIndex) { this->Run(GetParam()); }
+INSTANTIATE_TEST_SUITE_P(EllpackPage, EllpackPageTest, testing::Values(.0f, .2f, .4f, .8f));
 }  // namespace xgboost