Rewrite sparse dmatrix using callbacks. (#7092)

- Reduce dependency on dmlc parsers and provide an interface for users to load data by themselves.
- Remove use of threaded iterator and IO queue.
- Remove `page_size`.
- Make sure the number of pages in memory is bounded.
- Make sure the cache can not be violated.
- Provide an interface for internal algorithms to process data asynchronously.

amalgamation/xgboost-all0.cc

@@ -37,18 +37,14 @@
 #include "../src/data/simple_dmatrix.cc"
 #include "../src/data/sparse_page_raw_format.cc"
 #include "../src/data/ellpack_page.cc"
-#include "../src/data/ellpack_page_source.cc"
 #include "../src/data/gradient_index.cc"
+#include "../src/data/sparse_page_dmatrix.cc"
+#include "../src/data/proxy_dmatrix.cc"
 
 // prediction
 #include "../src/predictor/predictor.cc"
 #include "../src/predictor/cpu_predictor.cc"
 
-#if DMLC_ENABLE_STD_THREAD
-#include "../src/data/sparse_page_dmatrix.cc"
-#include "../src/data/sparse_page_source.cc"
-#endif
-
 // trees
 #include "../src/tree/param.cc"
 #include "../src/tree/tree_model.cc"

include/xgboost/c_api.h

@@ -223,19 +223,31 @@ XGB_DLL int XGDMatrixCreateFromDT(void** data,
  * - XGBCallbackDataIterNext
  * - XGDMatrixCreateFromDataIter
  *
- * Another set is used by Quantile based DMatrix (used by hist algorithm) for reducing
+ * Another set is used by external data iterator. It accept foreign data iterators as
- * memory usage.  Currently only GPU implementation is available.  It accept foreign data
+ * callbacks.  There are 2 different senarios where users might want to pass in callbacks
- * iterators as callbacks and works similar to external memory.  For GPU Hist, the data is
+ * instead of raw data.  First it's the Quantile DMatrix used by GPU Hist. For this case,
- * first compressed by quantile sketching then merged.  This is particular useful for
+ * the data is first compressed by quantile sketching then merged.  This is particular
- * distributed setting as it eliminates 2 copies of data.  1 by a `concat` from external
+ * useful for distributed setting as it eliminates 2 copies of data.  1 by a `concat` from
- * library to make the data into a blob for normal DMatrix initialization, another by the
+ * external library to make the data into a blob for normal DMatrix initialization,
- * internal CSR copy of DMatrix.  Related functions are:
+ * another by the internal CSR copy of DMatrix.  The second use case is external memory
+ * support where users can pass a custom data iterator into XGBoost for loading data in
+ * batches.  There are short notes on each of the use case in respected DMatrix factory
+ * function.
  *
+ * Related functions are:
+ *
+ * # Factory functions
+ * - `XGDMatrixCreateFromCallback` for external memory
+ * - `XGDeviceQuantileDMatrixCreateFromCallback` for quantile DMatrix
+ *
+ * # Proxy that callers can use to pass data to XGBoost
  * - XGProxyDMatrixCreate
  * - XGDMatrixCallbackNext
  * - DataIterResetCallback
  * - XGProxyDMatrixSetDataCudaArrayInterface
  * - XGProxyDMatrixSetDataCudaColumnar
+ * - XGProxyDMatrixSetDataDense
+ * - XGProxyDMatrixSetDataCSR
  * - ... (data setters)
  */
 
@@ -308,17 +320,9 @@ XGB_DLL int XGDMatrixCreateFromDataIter(
     const char* cache_info,
     DMatrixHandle *out);
 
-/*  == Second set of callback functions, used by constructing Quantile based DMatrix. ===
+/**
- *
+ * Second set of callback functions, used by constructing Quantile DMatrix or external
- * Short note for how to use the second set of callback for GPU Hist tree method.
+ * memory DMatrix using custom iterator.
- *
- * Step 0: Define a data iterator with 2 methods `reset`, and `next`.
- * Step 1: Create a DMatrix proxy by `XGProxyDMatrixCreate` and hold the handle.
- * Step 2: Pass the iterator handle, proxy handle and 2 methods into
- *         `XGDeviceQuantileDMatrixCreateFromCallback`.
- * Step 3: Call appropriate data setters in `next` functions.
- *
- * See test_iterative_device_dmatrix.cu or Python interface for examples.
  */
 
 /*!
@@ -344,8 +348,53 @@ XGB_EXTERN_C typedef int XGDMatrixCallbackNext(DataIterHandle iter);  // NOLINT(
  */
 XGB_EXTERN_C typedef void DataIterResetCallback(DataIterHandle handle); // NOLINT(*)
 
+
 /*!
- * \brief Create a device DMatrix with data iterator.
+ * \brief Create an external memory DMatrix with data iterator.
+ *
+ * Short note for how to use second set of callback for external memory data support:
+ *
+ * - Step 0: Define a data iterator with 2 methods `reset`, and `next`.
+ * - Step 1: Create a DMatrix proxy by `XGProxyDMatrixCreate` and hold the handle.
+ * - Step 2: Pass the iterator handle, proxy handle and 2 methods into
+ *           `XGDMatrixCreateFromCallback`, along with other parameters encoded as a JSON object.
+ * - Step 3: Call appropriate data setters in `next` functions.
+ *
+ * For example usage see demo/c-api/external-memory
+ *
+ * \param iter           A handle to external data iterator.
+ * \param proxy          A DMatrix proxy handle created by `XGProxyDMatrixCreate`.
+ * \param reset          Callback function resetting the iterator state.
+ * \param next           Callback function yielding the next batch of data.
+ * \param c_json_config  JSON encoded parameters for DMatrix construction.  Accepted fields are:
+ *
+ *   - missing:      Which value to represent missing value
+ *   - cache_prefix: The path of cache file, caller must initialize all the directories in this path.
+ *   - nthread (optional): Number of threads used for initializing DMatrix.
+ *
+ * \param out      The created external memory DMatrix
+ *
+ * \return 0 when success, -1 when failure happens
+ */
+XGB_DLL int XGDMatrixCreateFromCallback(DataIterHandle iter,
+                                        DMatrixHandle proxy,
+                                        DataIterResetCallback *reset,
+                                        XGDMatrixCallbackNext *next,
+                                        char const* c_json_config,
+                                        DMatrixHandle *out);
+
+/*!
+ * \brief Create a Quantile DMatrix with data iterator.
+ *
+ * Short note for how to use the second set of callback for GPU Hist tree method:
+ *
+ * - Step 0: Define a data iterator with 2 methods `reset`, and `next`.
+ * - Step 1: Create a DMatrix proxy by `XGProxyDMatrixCreate` and hold the handle.
+ * - Step 2: Pass the iterator handle, proxy handle and 2 methods into
+ *           `XGDeviceQuantileDMatrixCreateFromCallback`.
+ * - Step 3: Call appropriate data setters in `next` functions.
+ *
+ * See test_iterative_device_dmatrix.cu or Python interface for examples.
  *
  * \param iter     A handle to external data iterator.
  * \param proxy    A DMatrix proxy handle created by `XGProxyDMatrixCreate`.
@@ -362,6 +411,7 @@ XGB_DLL int XGDeviceQuantileDMatrixCreateFromCallback(
     DataIterHandle iter, DMatrixHandle proxy, DataIterResetCallback *reset,
     XGDMatrixCallbackNext *next, float missing, int nthread, int max_bin,
     DMatrixHandle *out);
+
 /*!
  * \brief Set data on a DMatrix proxy.
  *
@@ -387,6 +437,33 @@ XGProxyDMatrixSetDataCudaArrayInterface(DMatrixHandle handle,
 XGB_DLL int XGProxyDMatrixSetDataCudaColumnar(DMatrixHandle handle,
                                               const char *c_interface_str);
 
+/*!
+ * \brief Set data on a DMatrix proxy.
+ *
+ * \param handle          A DMatrix proxy created by XGProxyDMatrixCreate
+ * \param c_interface_str Null terminated JSON document string representation of array
+ *                        interface.
+ *
+ * \return 0 when success, -1 when failure happens
+ */
+XGB_DLL int XGProxyDMatrixSetDataDense(DMatrixHandle handle,
+                                       char const *c_interface_str);
+
+/*!
+ * \brief Set data on a DMatrix proxy.
+ *
+ * \param handle        A DMatrix proxy created by XGProxyDMatrixCreate
+ * \param indptr        JSON encoded __array_interface__ to row pointer in CSR.
+ * \param indices       JSON encoded __array_interface__ to column indices in CSR.
+ * \param values        JSON encoded __array_interface__ to values in CSR..
+ *
+ * \return 0 when success, -1 when failure happens
+ */
+XGB_DLL int XGProxyDMatrixSetDataCSR(DMatrixHandle handle, char const *indptr,
+                                     char const *indices, char const *data,
+                                     bst_ulong ncol);
+
+
 /*
  * ==========================- End data callback APIs ==========================
  */

include/xgboost/data.h

@@ -171,9 +171,12 @@ class MetaInfo {
    * \param that The other MetaInfo object.
    *
    * \param accumulate_rows Whether rows need to be accumulated in this function.  If
-   *        client code knows number of rows in advance, set this parameter to false.
+   *                        client code knows number of rows in advance, set this
+   *                        parameter to false.
+   * \param check_column Whether the extend method should check the consistency of
+   *                     columns.
    */
-  void Extend(MetaInfo const& that, bool accumulate_rows);
+  void Extend(MetaInfo const& that, bool accumulate_rows, bool check_column);
 
  private:
   /*! \brief argsort of labels */
@@ -211,14 +214,12 @@ struct BatchParam {
   int gpu_id;
   /*! \brief Maximum number of bins per feature for histograms. */
   int max_bin{0};
-  /*! \brief Page size for external memory mode. */
-  size_t gpu_page_size;
   BatchParam() = default;
-  BatchParam(int32_t device, int32_t max_bin, size_t gpu_page_size = 0)
+  BatchParam(int32_t device, int32_t max_bin)
-      : gpu_id{device}, max_bin{max_bin}, gpu_page_size{gpu_page_size} {}
+      : gpu_id{device}, max_bin{max_bin} {}
-  inline bool operator!=(const BatchParam& other) const {
+
-    return gpu_id != other.gpu_id || max_bin != other.max_bin ||
+  bool operator!=(const BatchParam& other) const {
-           gpu_page_size != other.gpu_page_size;
+    return gpu_id != other.gpu_id || max_bin != other.max_bin;
   }
 };
 
@@ -390,11 +391,12 @@ class GHistIndexMatrix;
 template<typename T>
 class BatchIteratorImpl {
  public:
+  using iterator_category = std::forward_iterator_tag;  // NOLINT
   virtual ~BatchIteratorImpl() = default;
-  virtual T& operator*() = 0;
   virtual const T& operator*() const = 0;
-  virtual void operator++() = 0;
+  virtual BatchIteratorImpl& operator++() = 0;
   virtual bool AtEnd() const = 0;
+  virtual std::shared_ptr<T const> Page() const = 0;
 };
 
 template<typename T>
@@ -402,15 +404,12 @@ class BatchIterator {
  public:
   using iterator_category = std::forward_iterator_tag;  // NOLINT
   explicit BatchIterator(BatchIteratorImpl<T>* impl) { impl_.reset(impl); }
+  explicit BatchIterator(std::shared_ptr<BatchIteratorImpl<T>> impl) { impl_ = impl; }
 
-  void operator++() {
+  BatchIterator &operator++() {
     CHECK(impl_ != nullptr);
     ++(*impl_);
-  }
+    return *this;
-
-  T& operator*() {
-    CHECK(impl_ != nullptr);
-    return *(*impl_);
   }
 
   const T& operator*() const {
@@ -428,6 +427,10 @@ class BatchIterator {
     return impl_->AtEnd();
   }
 
+  std::shared_ptr<T const> Page() const {
+    return impl_->Page();
+  }
+
  private:
   std::shared_ptr<BatchIteratorImpl<T>> impl_;
 };
@@ -499,8 +502,7 @@ class DMatrix {
   static DMatrix* Load(const std::string& uri,
                        bool silent,
                        bool load_row_split,
-                       const std::string& file_format = "auto",
+                       const std::string& file_format = "auto");
-                       size_t page_size = kPageSize);
 
   /**
    * \brief Creates a new DMatrix from an external data adapter.
@@ -516,8 +518,7 @@ class DMatrix {
    */
   template <typename AdapterT>
   static DMatrix* Create(AdapterT* adapter, float missing, int nthread,
-                         const std::string& cache_prefix = "",
+                         const std::string& cache_prefix = "");
-                         size_t page_size = kPageSize);
 
   /**
    * \brief Create a new Quantile based DMatrix used for histogram based algorithm.
@@ -545,6 +546,31 @@ class DMatrix {
                          int nthread,
                          int max_bin);
 
+  /**
+   * \brief Create an external memory DMatrix with callbacks.
+   *
+   * \tparam DataIterHandle         External iterator type, defined in C API.
+   * \tparam DMatrixHandle          DMatrix handle, defined in C API.
+   * \tparam DataIterResetCallback  Callback for reset, prototype defined in C API.
+   * \tparam XGDMatrixCallbackNext  Callback for next, prototype defined in C API.
+   *
+   * \param iter    External data iterator
+   * \param proxy   A hanlde to ProxyDMatrix
+   * \param reset   Callback for reset
+   * \param next    Callback for next
+   * \param missing Value that should be treated as missing.
+   * \param nthread number of threads used for initialization.
+   * \param cache   Prefix of cache file path.
+   *
+   * \return A created external memory DMatrix.
+   */
+  template <typename DataIterHandle, typename DMatrixHandle,
+            typename DataIterResetCallback, typename XGDMatrixCallbackNext>
+  static DMatrix *Create(DataIterHandle iter, DMatrixHandle proxy,
+                         DataIterResetCallback *reset,
+                         XGDMatrixCallbackNext *next, float missing,
+                         int32_t nthread, std::string cache);
+
   virtual DMatrix *Slice(common::Span<int32_t const> ridxs) = 0;
   /*! \brief Number of rows per page in external memory.  Approximately 100MB per page for
    *  dataset with 100 features. */

include/xgboost/generic_parameters.h

@@ -29,8 +29,6 @@ struct GenericParameter : public XGBoostParameter<GenericParameter> {
   int gpu_id;
   // fail when gpu_id is invalid
   bool fail_on_invalid_gpu_id {false};
-  // gpu page size in external memory mode, 0 means using the default.
-  size_t gpu_page_size;
   bool validate_parameters {false};
 
   /*!
@@ -66,10 +64,6 @@ struct GenericParameter : public XGBoostParameter<GenericParameter> {
     DMLC_DECLARE_FIELD(fail_on_invalid_gpu_id)
         .set_default(false)
         .describe("Fail with error when gpu_id is invalid.");
-    DMLC_DECLARE_FIELD(gpu_page_size)
-        .set_default(0)
-        .set_lower_bound(0)
-        .describe("GPU page size when running in external memory mode.");
     DMLC_DECLARE_FIELD(validate_parameters)
         .set_default(false)
         .describe("Enable checking whether parameters are used or not.");

src/c_api/c_api.cc

@@ -190,6 +190,35 @@ XGB_DLL int XGDMatrixCreateFromArrayInterface(char const* c_json_strs,
 #endif
 
 // Create from data iterator
+XGB_DLL int XGDMatrixCreateFromCallback(DataIterHandle iter,
+                                        DMatrixHandle proxy,
+                                        DataIterResetCallback *reset,
+                                        XGDMatrixCallbackNext *next,
+                                        char const* c_json_config,
+                                        DMatrixHandle *out) {
+  API_BEGIN();
+  auto config = Json::Load(StringView{c_json_config});
+  float missing = get<Number const>(config["missing"]);
+  std::string cache = get<String const>(config["cache_prefix"]);
+  int32_t n_threads = omp_get_max_threads();
+  if (!IsA<Null>(config["nthread"])) {
+    n_threads = get<Integer const>(config["nthread"]);
+  }
+  *out = new std::shared_ptr<xgboost::DMatrix>{xgboost::DMatrix::Create(
+      iter, proxy, reset, next, missing, n_threads, cache)};
+  API_END();
+}
+
+XGB_DLL int XGDeviceQuantileDMatrixCreateFromCallback(
+    DataIterHandle iter, DMatrixHandle proxy, DataIterResetCallback *reset,
+    XGDMatrixCallbackNext *next, float missing, int nthread,
+    int max_bin, DMatrixHandle *out) {
+  API_BEGIN();
+  *out = new std::shared_ptr<xgboost::DMatrix>{
+    xgboost::DMatrix::Create(iter, proxy, reset, next, missing, nthread, max_bin)};
+  API_END();
+}
+
 XGB_DLL int XGProxyDMatrixCreate(DMatrixHandle* out) {
   API_BEGIN();
   *out = new std::shared_ptr<xgboost::DMatrix>(new xgboost::data::DMatrixProxy);;
@@ -221,15 +250,31 @@ XGB_DLL int XGProxyDMatrixSetDataCudaColumnar(DMatrixHandle handle,
   API_END();
 }
 
-XGB_DLL int XGDeviceQuantileDMatrixCreateFromCallback(
+XGB_DLL int XGProxyDMatrixSetDataDense(DMatrixHandle handle,
-    DataIterHandle iter, DMatrixHandle proxy, DataIterResetCallback *reset,
+                                       char const *c_interface_str) {
-    XGDMatrixCallbackNext *next, float missing, int nthread,
-    int max_bin, DMatrixHandle *out) {
   API_BEGIN();
-  *out = new std::shared_ptr<xgboost::DMatrix>{
+  CHECK_HANDLE();
-    xgboost::DMatrix::Create(iter, proxy, reset, next, missing, nthread, max_bin)};
+  auto p_m = static_cast<std::shared_ptr<xgboost::DMatrix> *>(handle);
+  CHECK(p_m);
+  auto m =   static_cast<xgboost::data::DMatrixProxy*>(p_m->get());
+  CHECK(m) << "Current DMatrix type does not support set data.";
+  m->SetArrayData(c_interface_str);
   API_END();
 }
+
+XGB_DLL int XGProxyDMatrixSetDataCSR(DMatrixHandle handle, char const *indptr,
+                                     char const *indices, char const *data,
+                                     xgboost::bst_ulong ncol) {
+  API_BEGIN();
+  CHECK_HANDLE();
+  auto p_m = static_cast<std::shared_ptr<xgboost::DMatrix> *>(handle);
+  CHECK(p_m);
+  auto m =   static_cast<xgboost::data::DMatrixProxy*>(p_m->get());
+  CHECK(m) << "Current DMatrix type does not support set data.";
+  m->SetCSRData(indptr, indices, data, ncol, true);
+  API_END();
+}
+
 // End Create from data iterator
 
 XGB_DLL int XGDMatrixCreateFromCSREx(const size_t* indptr,

src/common/quantile.cu

@@ -91,7 +91,6 @@ void PruneImpl(int device,
     }
 
     float w = back.rmin - front.rmax;
-    assert(w != 0);
     auto budget = static_cast<float>(d_out.size());
     assert(budget != 0);
     auto q = ((static_cast<float>(idx) * w) / (static_cast<float>(to) - 1.0f) + front.rmax);

src/data/data.cc

@@ -22,11 +22,10 @@
 #include "../common/threading_utils.h"
 #include "../data/adapter.h"
 #include "../data/iterative_device_dmatrix.h"
+#include "file_iterator.h"
 
-#if DMLC_ENABLE_STD_THREAD
 #include "./sparse_page_source.h"
 #include "./sparse_page_dmatrix.h"
-#endif  // DMLC_ENABLE_STD_THREAD
 
 namespace dmlc {
 DMLC_REGISTRY_ENABLE(::xgboost::data::SparsePageFormatReg<::xgboost::SparsePage>);
@@ -500,13 +499,17 @@ void MetaInfo::GetFeatureInfo(const char *field,
   }
 }
 
-void MetaInfo::Extend(MetaInfo const& that, bool accumulate_rows) {
+void MetaInfo::Extend(MetaInfo const& that, bool accumulate_rows, bool check_column) {
   if (accumulate_rows) {
     this->num_row_ += that.num_row_;
   }
   if (this->num_col_ != 0) {
+    if (check_column) {
       CHECK_EQ(this->num_col_, that.num_col_)
           << "Number of columns must be consistent across batches.";
+    } else {
+      this->num_col_ = std::max(this->num_col_, that.num_col_);
+    }
   }
   this->num_col_ = that.num_col_;
 
@@ -630,11 +633,34 @@ DMatrix::~DMatrix() {
   }
 }
 
+DMatrix *TryLoadBinary(std::string fname, bool silent) {
+  int magic;
+  std::unique_ptr<dmlc::Stream> fi(
+      dmlc::Stream::Create(fname.c_str(), "r", true));
+  if (fi != nullptr) {
+    common::PeekableInStream is(fi.get());
+    if (is.PeekRead(&magic, sizeof(magic)) == sizeof(magic)) {
+      if (!DMLC_IO_NO_ENDIAN_SWAP) {
+        dmlc::ByteSwap(&magic, sizeof(magic), 1);
+      }
+      if (magic == data::SimpleDMatrix::kMagic) {
+        DMatrix *dmat = new data::SimpleDMatrix(&is);
+        if (!silent) {
+          LOG(CONSOLE) << dmat->Info().num_row_ << 'x' << dmat->Info().num_col_
+                       << " matrix with " << dmat->Info().num_nonzero_
+                       << " entries loaded from " << fname;
+        }
+        return dmat;
+      }
+    }
+  }
+  return nullptr;
+}
+
 DMatrix* DMatrix::Load(const std::string& uri,
                        bool silent,
                        bool load_row_split,
-                       const std::string& file_format,
+                       const std::string& file_format) {
-                       const size_t page_size) {
   std::string fname, cache_file;
   size_t dlm_pos = uri.find('#');
   if (dlm_pos != std::string::npos) {
@@ -682,34 +708,33 @@ DMatrix* DMatrix::Load(const std::string& uri,
 
   // legacy handling of binary data loading
   if (file_format == "auto" && npart == 1) {
-    int magic;
+    DMatrix *loaded = TryLoadBinary(fname, silent);
-    std::unique_ptr<dmlc::Stream> fi(dmlc::Stream::Create(fname.c_str(), "r", true));
+    if (loaded) {
-    if (fi != nullptr) {
+      return loaded;
-      common::PeekableInStream is(fi.get());
-      if (is.PeekRead(&magic, sizeof(magic)) == sizeof(magic)) {
-        if (!DMLC_IO_NO_ENDIAN_SWAP) {
-          dmlc::ByteSwap(&magic, sizeof(magic), 1);
-        }
-        if (magic == data::SimpleDMatrix::kMagic) {
-          DMatrix* dmat = new data::SimpleDMatrix(&is);
-          if (!silent) {
-            LOG(CONSOLE) << dmat->Info().num_row_ << 'x' << dmat->Info().num_col_ << " matrix with "
-              << dmat->Info().num_nonzero_ << " entries loaded from " << uri;
-          }
-          return dmat;
-        }
-      }
     }
   }
 
-  std::unique_ptr<dmlc::Parser<uint32_t> > parser(
-      dmlc::Parser<uint32_t>::Create(fname.c_str(), partid, npart, file_format.c_str()));
-  data::FileAdapter adapter(parser.get());
   DMatrix* dmat {nullptr};
-
   try {
-    dmat = DMatrix::Create(&adapter, std::numeric_limits<float>::quiet_NaN(), 1,
+    if (cache_file.empty()) {
-                           cache_file, page_size);
+      std::unique_ptr<dmlc::Parser<uint32_t>> parser(
+          dmlc::Parser<uint32_t>::Create(fname.c_str(), partid, npart,
+                                         file_format.c_str()));
+      data::FileAdapter adapter(parser.get());
+      dmat = DMatrix::Create(&adapter, std::numeric_limits<float>::quiet_NaN(),
+                             1, cache_file);
+    } else {
+      data::FileIterator iter{fname, uint32_t(partid), uint32_t(npart),
+                              file_format};
+      dmat = new data::SparsePageDMatrix{
+          &iter,
+          iter.Proxy(),
+          data::fileiter::Reset,
+          data::fileiter::Next,
+          std::numeric_limits<float>::quiet_NaN(),
+          1,
+          cache_file};
+    }
   } catch (dmlc::Error &e) {
     std::vector<std::string> splited = common::Split(fname, '#');
     std::vector<std::string> args = common::Split(splited.front(), '?');
@@ -734,10 +759,6 @@ DMatrix* DMatrix::Load(const std::string& uri,
     LOG(FATAL) << "Encountered parser error:\n" << e.what();
   }
 
-  if (!silent) {
-    LOG(CONSOLE) << dmat->Info().num_row_ << 'x' << dmat->Info().num_col_ << " matrix with "
-                 << dmat->Info().num_nonzero_ << " entries loaded from " << uri;
-  }
   /* sync up number of features after matrix loaded.
    * partitioned data will fail the train/val validation check
    * since partitioned data not knowing the real number of features. */
@@ -769,12 +790,19 @@ DMatrix *DMatrix::Create(DataIterHandle iter, DMatrixHandle proxy,
                          XGDMatrixCallbackNext *next, float missing,
                          int nthread,
                          int max_bin) {
-#if defined(XGBOOST_USE_CUDA)
+  return new data::IterativeDeviceDMatrix(iter, proxy, reset, next, missing,
-  return new data::IterativeDeviceDMatrix(iter, proxy, reset, next, missing, nthread, max_bin);
+                                          nthread, max_bin);
-#else
+}
-  common::AssertGPUSupport();
+
-  return nullptr;
+template <typename DataIterHandle, typename DMatrixHandle,
-#endif
+          typename DataIterResetCallback, typename XGDMatrixCallbackNext>
+DMatrix *DMatrix::Create(DataIterHandle iter, DMatrixHandle proxy,
+                         DataIterResetCallback *reset,
+                         XGDMatrixCallbackNext *next, float missing,
+                         int32_t n_threads,
+                         std::string cache) {
+  return new data::SparsePageDMatrix(iter, proxy, reset, next, missing, n_threads,
+                                     cache);
 }
 
 template DMatrix *DMatrix::Create<DataIterHandle, DMatrixHandle,
@@ -783,49 +811,42 @@ template DMatrix *DMatrix::Create<DataIterHandle, DMatrixHandle,
     XGDMatrixCallbackNext *next, float missing, int nthread,
     int max_bin);
 
+template DMatrix *DMatrix::Create<DataIterHandle, DMatrixHandle,
+                                  DataIterResetCallback, XGDMatrixCallbackNext>(
+    DataIterHandle iter, DMatrixHandle proxy, DataIterResetCallback *reset,
+    XGDMatrixCallbackNext *next, float missing, int32_t n_threads, std::string);
+
 template <typename AdapterT>
 DMatrix* DMatrix::Create(AdapterT* adapter, float missing, int nthread,
-                         const std::string& cache_prefix,  size_t page_size) {
+                         const std::string& cache_prefix) {
-  if (cache_prefix.length() == 0) {
-    // Data split mode is fixed to be row right now.
   return new data::SimpleDMatrix(adapter, missing, nthread);
-  } else {
-#if DMLC_ENABLE_STD_THREAD
-    return new data::SparsePageDMatrix(adapter, missing, nthread, cache_prefix,
-                                       page_size);
-#else
-    LOG(FATAL) << "External memory is not enabled in mingw";
-    return nullptr;
-#endif  // DMLC_ENABLE_STD_THREAD
-  }
 }
 
 template DMatrix* DMatrix::Create<data::DenseAdapter>(
     data::DenseAdapter* adapter, float missing, int nthread,
-    const std::string& cache_prefix, size_t page_size);
+    const std::string& cache_prefix);
 template DMatrix* DMatrix::Create<data::ArrayAdapter>(
     data::ArrayAdapter* adapter, float missing, int nthread,
-    const std::string& cache_prefix, size_t page_size);
+    const std::string& cache_prefix);
 template DMatrix* DMatrix::Create<data::CSRAdapter>(
     data::CSRAdapter* adapter, float missing, int nthread,
-    const std::string& cache_prefix, size_t page_size);
+    const std::string& cache_prefix);
 template DMatrix* DMatrix::Create<data::CSCAdapter>(
     data::CSCAdapter* adapter, float missing, int nthread,
-    const std::string& cache_prefix, size_t page_size);
+    const std::string& cache_prefix);
 template DMatrix* DMatrix::Create<data::DataTableAdapter>(
     data::DataTableAdapter* adapter, float missing, int nthread,
-    const std::string& cache_prefix, size_t page_size);
+    const std::string& cache_prefix);
 template DMatrix* DMatrix::Create<data::FileAdapter>(
     data::FileAdapter* adapter, float missing, int nthread,
-    const std::string& cache_prefix, size_t page_size);
+    const std::string& cache_prefix);
 template DMatrix* DMatrix::Create<data::CSRArrayAdapter>(
     data::CSRArrayAdapter* adapter, float missing, int nthread,
-    const std::string& cache_prefix, size_t page_size);
+    const std::string& cache_prefix);
 template DMatrix *
 DMatrix::Create(data::IteratorAdapter<DataIterHandle, XGBCallbackDataIterNext,
                                       XGBoostBatchCSR> *adapter,
-                float missing, int nthread, const std::string &cache_prefix,
+                float missing, int nthread, const std::string &cache_prefix);
-                size_t page_size);
 
 SparsePage SparsePage::GetTranspose(int num_columns) const {
   SparsePage transpose;
@@ -1044,6 +1065,8 @@ SparsePage::Push(const data::ArrayAdapterBatch& batch, float missing, int nthrea
 template uint64_t
 SparsePage::Push(const data::CSRAdapterBatch& batch, float missing, int nthread);
 template uint64_t
+SparsePage::Push(const data::CSRArrayAdapterBatch& batch, float missing, int nthread);
+template uint64_t
 SparsePage::Push(const data::CSCAdapterBatch& batch, float missing, int nthread);
 template uint64_t
 SparsePage::Push(const data::DataTableAdapterBatch& batch, float missing, int nthread);

src/data/data.cu

@@ -167,7 +167,7 @@ void MetaInfo::SetInfo(const char * c_key, std::string const& interface_str) {
 
 template <typename AdapterT>
 DMatrix* DMatrix::Create(AdapterT* adapter, float missing, int nthread,
-                         const std::string& cache_prefix, size_t page_size) {
+                         const std::string& cache_prefix) {
   CHECK_EQ(cache_prefix.size(), 0)
       << "Device memory construction is not currently supported with external "
          "memory.";
@@ -176,8 +176,8 @@ DMatrix* DMatrix::Create(AdapterT* adapter, float missing, int nthread,
 
 template DMatrix* DMatrix::Create<data::CudfAdapter>(
     data::CudfAdapter* adapter, float missing, int nthread,
-    const std::string& cache_prefix, size_t page_size);
+    const std::string& cache_prefix);
 template DMatrix* DMatrix::Create<data::CupyAdapter>(
     data::CupyAdapter* adapter, float missing, int nthread,
-    const std::string& cache_prefix, size_t page_size);
+    const std::string& cache_prefix);
 }  // namespace xgboost

src/data/ellpack_page.cu

@@ -122,6 +122,7 @@ EllpackPageImpl::EllpackPageImpl(DMatrix* dmat, const BatchParam& param)
   dmat->Info().feature_types.SetDevice(param.gpu_id);
   auto ft = dmat->Info().feature_types.ConstDeviceSpan();
   monitor_.Start("BinningCompression");
+  CHECK(dmat->SingleColBlock());
   for (const auto& batch : dmat->GetBatches<SparsePage>()) {
     CreateHistIndices(param.gpu_id, batch, ft);
   }
@@ -301,9 +302,8 @@ struct CopyPage {
   // The number of elements to skip.
   size_t offset;
 
-  CopyPage(EllpackPageImpl* dst, EllpackPageImpl* src, size_t offset)
+  CopyPage(EllpackPageImpl *dst, EllpackPageImpl const *src, size_t offset)
-      : cbw{dst->NumSymbols()},
+      : cbw{dst->NumSymbols()}, dst_data_d{dst->gidx_buffer.DevicePointer()},
-        dst_data_d{dst->gidx_buffer.DevicePointer()},
         src_iterator_d{src->gidx_buffer.DevicePointer(), src->NumSymbols()},
         offset(offset) {}
 
@@ -314,7 +314,8 @@ struct CopyPage {
 };
 
 // Copy the data from the given EllpackPage to the current page.
-size_t EllpackPageImpl::Copy(int device, EllpackPageImpl* page, size_t offset) {
+size_t EllpackPageImpl::Copy(int device, EllpackPageImpl const *page,
+                             size_t offset) {
   monitor_.Start("Copy");
   size_t num_elements = page->n_rows * page->row_stride;
   CHECK_EQ(row_stride, page->row_stride);
@@ -351,7 +352,7 @@ struct CompactPage {
   size_t base_rowid;
   size_t row_stride;
 
-  CompactPage(EllpackPageImpl* dst, EllpackPageImpl* src,
+  CompactPage(EllpackPageImpl* dst, EllpackPageImpl const* src,
               common::Span<size_t> row_indexes)
       : cbw{dst->NumSymbols()},
         dst_data_d{dst->gidx_buffer.DevicePointer()},
@@ -374,7 +375,7 @@ struct CompactPage {
 };
 
 // Compacts the data from the given EllpackPage into the current page.
-void EllpackPageImpl::Compact(int device, EllpackPageImpl* page,
+void EllpackPageImpl::Compact(int device, EllpackPageImpl const* page,
                               common::Span<size_t> row_indexes) {
   monitor_.Start("Compact");
   CHECK_EQ(row_stride, page->row_stride);
@@ -459,7 +460,7 @@ void EllpackPageImpl::CreateHistIndices(int device,
         gidx_buffer.DevicePointer(), row_ptrs.data().get(),
         entries_d.data().get(), device_accessor.gidx_fvalue_map.data(),
         device_accessor.feature_segments.data(), feature_types,
-        row_batch.base_rowid + batch_row_begin, batch_nrows, row_stride,
+        batch_row_begin, batch_nrows, row_stride,
         null_gidx_value);
   }
 }

src/data/ellpack_page.cuh

@@ -164,7 +164,7 @@ class EllpackPageImpl {
    * @param offset The number of elements to skip before copying.
    * @returns The number of elements copied.
    */
-  size_t Copy(int device, EllpackPageImpl* page, size_t offset);
+  size_t Copy(int device, EllpackPageImpl const *page, size_t offset);
 
   /*! \brief Compact the given ELLPACK page into the current page.
    *
@@ -172,7 +172,7 @@ class EllpackPageImpl {
    * @param page The ELLPACK page to compact from.
    * @param row_indexes Row indexes for the compacted page.
    */
-  void Compact(int device, EllpackPageImpl* page, common::Span<size_t> row_indexes);
+  void Compact(int device, EllpackPageImpl const* page, common::Span<size_t> row_indexes);
 
 
   /*! \return Number of instances in the page. */

src/data/ellpack_page_source.cc

@@ -1,24 +0,0 @@
-/*!
- * Copyright 2019 XGBoost contributors
- */
-#ifndef XGBOOST_USE_CUDA
-#include <dmlc/base.h>
-#if DMLC_ENABLE_STD_THREAD
-
-#include "ellpack_page_source.h"
-#include <xgboost/data.h>
-namespace xgboost {
-namespace data {
-
-EllpackPageSource::EllpackPageSource(DMatrix* dmat,
-                                     const std::string& cache_info,
-                                     const BatchParam& param) noexcept(false) {
-  LOG(FATAL)
-      << "Internal Error: "
-         "XGBoost is not compiled with CUDA but EllpackPageSource is required";
-}
-
-}  // namespace data
-}  // namespace xgboost
-#endif  // DMLC_ENABLE_STD_THREAD
-#endif  // XGBOOST_USE_CUDA

src/data/ellpack_page_source.cu

@@ -1,89 +1,24 @@
 /*!
- * Copyright 2019 XGBoost contributors
+ * Copyright 2019-2021 XGBoost contributors
  */
 #include <memory>
 #include <utility>
 
-#include "../common/hist_util.cuh"
-
 #include "ellpack_page.cuh"
 #include "ellpack_page_source.h"
-#include "sparse_page_source.h"
 
 namespace xgboost {
 namespace data {
-
+void EllpackPageSource::Fetch() {
-// Build the quantile sketch across the whole input data, then use the histogram cuts to compress
+  if (!this->ReadCache()) {
-// each CSR page, and write the accumulated ELLPACK pages to disk.
+    auto const &csr = source_->Page();
-EllpackPageSource::EllpackPageSource(DMatrix* dmat,
+    this->page_.reset(new EllpackPage{});
-                                     const std::string& cache_info,
+    auto *impl = this->page_->Impl();
-                                     const BatchParam& param) noexcept(false) {
+    *impl = EllpackPageImpl(param_.gpu_id, *cuts_, *csr, is_dense_, row_stride_,
-  cache_info_ = ParseCacheInfo(cache_info, kPageType_);
+                            feature_types_);
-  for (auto file : cache_info_.name_shards) {
+    page_->SetBaseRowId(csr->base_rowid);
-    CheckCacheFileExists(file);
+    this->WriteCache();
-  }
-  if (param.gpu_page_size > 0) {
-    page_size_ = param.gpu_page_size;
-  }
-
-  monitor_.Init("ellpack_page_source");
-  dh::safe_cuda(cudaSetDevice(param.gpu_id));
-
-  monitor_.Start("Quantiles");
-  size_t row_stride = GetRowStride(dmat);
-  auto cuts = common::DeviceSketch(param.gpu_id, dmat, param.max_bin);
-  monitor_.Stop("Quantiles");
-
-  monitor_.Start("WriteEllpackPages");
-  WriteEllpackPages(param.gpu_id, dmat, cuts, cache_info, row_stride);
-  monitor_.Stop("WriteEllpackPages");
-
-  external_prefetcher_.reset(
-      new ExternalMemoryPrefetcher<EllpackPage>(cache_info_));
-}
-
-// Compress each CSR page to ELLPACK, and write the accumulated pages to disk.
-void EllpackPageSource::WriteEllpackPages(int device, DMatrix* dmat,
-                                          const common::HistogramCuts& cuts,
-                                          const std::string& cache_info,
-                                          size_t row_stride) const {
-  auto cinfo = ParseCacheInfo(cache_info, kPageType_);
-  const size_t extra_buffer_capacity = 6;
-  SparsePageWriter<EllpackPage> writer(cinfo.name_shards, cinfo.format_shards,
-                                       extra_buffer_capacity);
-  std::shared_ptr<EllpackPage> page;
-  SparsePage temp_host_page;
-  writer.Alloc(&page);
-  auto* impl = page->Impl();
-  auto ft = dmat->Info().feature_types.ConstDeviceSpan();
-
-  size_t bytes_write = 0;
-  double tstart = dmlc::GetTime();
-  for (const auto& batch : dmat->GetBatches<SparsePage>()) {
-    temp_host_page.Push(batch);
-
-    size_t mem_cost_bytes =
-        EllpackPageImpl::MemCostBytes(temp_host_page.Size(), row_stride, cuts);
-    if (mem_cost_bytes >= page_size_) {
-      bytes_write += mem_cost_bytes;
-      *impl = EllpackPageImpl(device, cuts, temp_host_page, dmat->IsDense(),
-                              row_stride, ft);
-      writer.PushWrite(std::move(page));
-      writer.Alloc(&page);
-      impl = page->Impl();
-      temp_host_page.Clear();
-      double tdiff = dmlc::GetTime() - tstart;
-      LOG(INFO) << "Writing " << kPageType_ << " to " << cache_info << " in "
-                << ((bytes_write >> 20UL) / tdiff) << " MB/s, "
-                << (bytes_write >> 20UL) << " written";
   }
 }
-  if (temp_host_page.Size() != 0) {
-    *impl = EllpackPageImpl(device, cuts, temp_host_page, dmat->IsDense(),
-                            row_stride, ft);
-    writer.PushWrite(std::move(page));
-  }
-}
-
 }  // namespace data
 }  // namespace xgboost

src/data/ellpack_page_source.h

@@ -1,5 +1,5 @@
 /*!
- * Copyright 2019 by XGBoost Contributors
+ * Copyright 2019-2021 by XGBoost Contributors
  */
 
 #ifndef XGBOOST_DATA_ELLPACK_PAGE_SOURCE_H_
@@ -8,57 +8,44 @@
 #include <xgboost/data.h>
 #include <memory>
 #include <string>
+#include <utility>
 
-#include "../common/timer.h"
+#include "../common/common.h"
 #include "../common/hist_util.h"
 #include "sparse_page_source.h"
 
 namespace xgboost {
 namespace data {
 
-/*!
+class EllpackPageSource : public PageSourceIncMixIn<EllpackPage> {
- * \brief External memory data source for ELLPACK format.
+  bool is_dense_;
- *
+  size_t row_stride_;
- */
+  BatchParam param_;
-class EllpackPageSource {
+  common::Span<FeatureType const> feature_types_;
+  std::unique_ptr<common::HistogramCuts> cuts_;
+
  public:
-  /*!
+  EllpackPageSource(
-   * \brief Create source from cache files the cache_prefix.
+      float missing, int nthreads, bst_feature_t n_features, size_t n_batches,
-   * \param cache_prefix The prefix of cache we want to solve.
+      std::shared_ptr<Cache> cache, BatchParam param,
-   */
+      std::unique_ptr<common::HistogramCuts> cuts, bool is_dense,
-  explicit EllpackPageSource(DMatrix* dmat,
+      size_t row_stride, common::Span<FeatureType const> feature_types,
-                             const std::string& cache_info,
+      std::shared_ptr<SparsePageSource> source)
-                             const BatchParam& param) noexcept(false);
+      : PageSourceIncMixIn(missing, nthreads, n_features, n_batches, cache),
-
+        is_dense_{is_dense}, row_stride_{row_stride}, param_{param},
-  BatchSet<EllpackPage> GetBatchSet() {
+        feature_types_{feature_types}, cuts_{std::move(cuts)} {
-    auto begin_iter = BatchIterator<EllpackPage>(
+    this->source_ = source;
-        new SparseBatchIteratorImpl<ExternalMemoryPrefetcher<EllpackPage>,
+    this->Fetch();
-                                    EllpackPage>(external_prefetcher_.get()));
-    return BatchSet<EllpackPage>(begin_iter);
   }
 
-  ~EllpackPageSource() {
+  void Fetch() final;
-    external_prefetcher_.reset();
-    for (auto file : cache_info_.name_shards) {
-      TryDeleteCacheFile(file);
-    }
-  }
-
- private:
-  void WriteEllpackPages(int device, DMatrix* dmat,
-                         const common::HistogramCuts& cuts,
-                         const std::string& cache_info,
-                         size_t row_stride) const;
-
-  /*! \brief The page type string for ELLPACK. */
-  const std::string kPageType_{".ellpack.page"};
-
-  size_t page_size_{DMatrix::kPageSize};
-  common::Monitor monitor_;
-  std::unique_ptr<ExternalMemoryPrefetcher<EllpackPage>> external_prefetcher_;
-  CacheInfo cache_info_;
 };
 
+#if !defined(XGBOOST_USE_CUDA)
+inline void EllpackPageSource::Fetch() {
+  common::AssertGPUSupport();
+}
+#endif  // !defined(XGBOOST_USE_CUDA)
 }  // namespace data
 }  // namespace xgboost
 

src/data/file_iterator.h

@@ -0,0 +1,115 @@
+/*!
+ * Copyright 2021 XGBoost contributors
+ */
+#ifndef XGBOOST_DATA_FILE_ITERATOR_H_
+#define XGBOOST_DATA_FILE_ITERATOR_H_
+
+#include <string>
+#include <memory>
+#include <vector>
+#include <utility>
+
+#include "dmlc/data.h"
+#include "xgboost/c_api.h"
+#include "xgboost/json.h"
+#include "array_interface.h"
+
+namespace xgboost {
+namespace data {
+/**
+ * An iterator for implementing external memory support with file inputs.  Users of
+ * external memory are encouraged to define their own file parsers/loaders so this one is
+ * just here for compatibility with old versions of XGBoost and CLI interface.
+ */
+class FileIterator {
+  // uri of input file, encodes parameters about whether it's 1-based index etc.  dmlc
+  // parser will decode these information.
+  std::string uri_;
+  // Equals to rank_id in distributed training, used to split file into parts for each
+  // worker.
+  uint32_t part_idx_;
+  // Equals to total number of workers.
+  uint32_t n_parts_;
+  // Format of the input file, like "libsvm".
+  std::string type_;
+
+  DMatrixHandle proxy_;
+
+  std::unique_ptr<dmlc::Parser<uint32_t>> parser_;
+  // Temporary reference to stage the data.
+  dmlc::RowBlock<uint32_t, float> row_block_;
+  // Storage for the array interface strings.
+  std::string indptr_;
+  std::string values_;
+  std::string indices_;
+
+ public:
+  FileIterator(std::string uri, unsigned part_index, unsigned num_parts,
+               std::string type)
+      : uri_{std::move(uri)}, part_idx_{part_index}, n_parts_{num_parts},
+        type_{std::move(type)} {
+    XGProxyDMatrixCreate(&proxy_);
+  }
+  ~FileIterator() {
+    XGDMatrixFree(proxy_);
+  }
+
+  int Next() {
+    CHECK(parser_);
+    if (parser_->Next()) {
+      row_block_ = parser_->Value();
+
+      indptr_ = MakeArrayInterface(row_block_.offset, row_block_.size + 1);
+      values_ = MakeArrayInterface(row_block_.value,
+                                   row_block_.offset[row_block_.size]);
+      indices_ = MakeArrayInterface(row_block_.index,
+                                    row_block_.offset[row_block_.size]);
+
+      size_t n_columns = *std::max_element(
+          row_block_.index,
+          row_block_.index + row_block_.offset[row_block_.size]);
+      // dmlc parser converts 1-based indexing back to 0-based indexing so we can ignore
+      // this condition and just add 1 to n_columns
+      n_columns += 1;
+
+      XGProxyDMatrixSetDataCSR(proxy_, indptr_.c_str(), indices_.c_str(),
+                               values_.c_str(), n_columns);
+
+      if (row_block_.label) {
+        XGDMatrixSetDenseInfo(proxy_, "label", row_block_.label, row_block_.size, 1);
+      }
+      if (row_block_.qid) {
+        XGDMatrixSetDenseInfo(proxy_, "qid", row_block_.qid, row_block_.size, 1);
+      }
+      if (row_block_.weight) {
+        XGDMatrixSetDenseInfo(proxy_, "weight", row_block_.weight, row_block_.size, 1);
+      }
+      // Continue iteration
+      return true;
+    } else {
+      // Stop iteration
+      return false;
+    }
+  }
+
+  auto Proxy() -> decltype(proxy_) { return proxy_; }
+
+  void Reset() {
+    CHECK(!type_.empty());
+    parser_.reset(dmlc::Parser<uint32_t>::Create(uri_.c_str(), part_idx_,
+                                                 n_parts_, type_.c_str()));
+  }
+};
+
+namespace fileiter {
+inline void Reset(DataIterHandle self) {
+  static_cast<FileIterator*>(self)->Reset();
+}
+
+inline int Next(DataIterHandle self) {
+  return static_cast<FileIterator*>(self)->Next();
+}
+}  // namespace fileiter
+}  // namespace data
+}  // namespace xgboost
+#endif  // XGBOOST_DATA_FILE_ITERATOR_H_

src/data/iterative_device_dmatrix.cu

@@ -143,7 +143,7 @@ void IterativeDeviceDMatrix::Initialize(DataIterHandle iter_handle, float missin
     proxy->Info().num_row_ = num_rows();
     proxy->Info().num_col_ = cols;
     if (batches != 1) {
-      this->info_.Extend(std::move(proxy->Info()), false);
+      this->info_.Extend(std::move(proxy->Info()), false, true);
     }
     n_batches_for_verification++;
   }
@@ -163,7 +163,7 @@ void IterativeDeviceDMatrix::Initialize(DataIterHandle iter_handle, float missin
 BatchSet<EllpackPage> IterativeDeviceDMatrix::GetEllpackBatches(const BatchParam& param) {
   CHECK(page_);
   auto begin_iter =
-      BatchIterator<EllpackPage>(new SimpleBatchIteratorImpl<EllpackPage>(page_.get()));
+      BatchIterator<EllpackPage>(new SimpleBatchIteratorImpl<EllpackPage>(page_));
   return BatchSet<EllpackPage>(begin_iter);
 }
 }  // namespace data

src/data/iterative_device_dmatrix.h

@@ -14,6 +14,7 @@
 #include "xgboost/data.h"
 #include "xgboost/c_api.h"
 #include "proxy_dmatrix.h"
+#include "simple_batch_iterator.h"
 
 namespace xgboost {
 namespace data {
@@ -36,9 +37,10 @@ class IterativeDeviceDMatrix : public DMatrix {
                                   XGDMatrixCallbackNext *next, float missing,
                                   int nthread, int max_bin)
       : proxy_{proxy}, reset_{reset}, next_{next} {
-    batch_param_ = BatchParam{0, max_bin, 0};
+    batch_param_ = BatchParam{0, max_bin};
     this->Initialize(iter, missing, nthread);
   }
+  ~IterativeDeviceDMatrix() override = default;
 
   bool EllpackExists() const override { return true; }
   bool SparsePageExists() const override { return false; }
@@ -74,6 +76,18 @@ class IterativeDeviceDMatrix : public DMatrix {
     return info_;
   }
 };
+
+#if !defined(XGBOOST_USE_CUDA)
+inline void IterativeDeviceDMatrix::Initialize(DataIterHandle iter, float missing, int nthread) {
+  common::AssertGPUSupport();
+}
+inline BatchSet<EllpackPage> IterativeDeviceDMatrix::GetEllpackBatches(const BatchParam& param) {
+  common::AssertGPUSupport();
+  auto begin_iter =
+      BatchIterator<EllpackPage>(new SimpleBatchIteratorImpl<EllpackPage>(page_));
+  return BatchSet<EllpackPage>(BatchIterator<EllpackPage>(begin_iter));
+}
+#endif  // !defined(XGBOOST_USE_CUDA)
 }  // namespace data
 }  // namespace xgboost
 

src/data/proxy_dmatrix.h

@@ -1,5 +1,5 @@
 /*!
- * Copyright 2020 XGBoost contributors
+ * Copyright 2020-2021 XGBoost contributors
  */
 #ifndef XGBOOST_DATA_PROXY_DMATRIX_H_
 #define XGBOOST_DATA_PROXY_DMATRIX_H_

src/data/simple_batch_iterator.h

@@ -1,10 +1,13 @@
 /*!
- * Copyright 2019 XGBoost contributors
+ * Copyright 2019-2021 XGBoost contributors
  */
 #ifndef XGBOOST_DATA_SIMPLE_BATCH_ITERATOR_H_
 #define XGBOOST_DATA_SIMPLE_BATCH_ITERATOR_H_
 
-#include <xgboost/data.h>
+#include <memory>
+#include <utility>
+
+#include "xgboost/data.h"
 
 namespace xgboost {
 namespace data {
@@ -12,20 +15,21 @@ namespace data {
 template<typename T>
 class SimpleBatchIteratorImpl : public BatchIteratorImpl<T> {
  public:
-  explicit SimpleBatchIteratorImpl(T* page) : page_(page) {}
+  explicit SimpleBatchIteratorImpl(std::shared_ptr<T const> page) : page_(std::move(page)) {}
-  T& operator*() override {
-    CHECK(page_ != nullptr);
-    return *page_;
-  }
   const T& operator*() const override {
     CHECK(page_ != nullptr);
     return *page_;
   }
-  void operator++() override { page_ = nullptr; }
+  SimpleBatchIteratorImpl &operator++() override {
+    page_ = nullptr;
+    return *this;
+  }
   bool AtEnd() const override { return page_ == nullptr; }
 
+  std::shared_ptr<T const> Page() const override { return page_; }
+
  private:
-  T* page_{nullptr};
+  std::shared_ptr<T const> page_{nullptr};
 };
 
 }  // namespace data

src/data/simple_dmatrix.cc

@@ -1,5 +1,5 @@
 /*!
- * Copyright 2014~2020 by Contributors
+ * Copyright 2014~2021 by Contributors
  * \file simple_dmatrix.cc
  * \brief the input data structure for gradient boosting
  * \author Tianqi Chen
@@ -27,7 +27,7 @@ const MetaInfo& SimpleDMatrix::Info() const { return info_; }
 
 DMatrix* SimpleDMatrix::Slice(common::Span<int32_t const> ridxs) {
   auto out = new SimpleDMatrix;
-  SparsePage& out_page = out->sparse_page_;
+  SparsePage& out_page = *out->sparse_page_;
   for (auto const &page : this->GetBatches<SparsePage>()) {
     auto batch = page.GetView();
     auto& h_data = out_page.data.HostVector();
@@ -48,17 +48,17 @@ DMatrix* SimpleDMatrix::Slice(common::Span<int32_t const> ridxs) {
 BatchSet<SparsePage> SimpleDMatrix::GetRowBatches() {
   // since csr is the default data structure so `source_` is always available.
   auto begin_iter = BatchIterator<SparsePage>(
-      new SimpleBatchIteratorImpl<SparsePage>(&sparse_page_));
+      new SimpleBatchIteratorImpl<SparsePage>(sparse_page_));
   return BatchSet<SparsePage>(begin_iter);
 }
 
 BatchSet<CSCPage> SimpleDMatrix::GetColumnBatches() {
   // column page doesn't exist, generate it
   if (!column_page_) {
-    column_page_.reset(new CSCPage(sparse_page_.GetTranspose(info_.num_col_)));
+    column_page_.reset(new CSCPage(sparse_page_->GetTranspose(info_.num_col_)));
   }
   auto begin_iter =
-      BatchIterator<CSCPage>(new SimpleBatchIteratorImpl<CSCPage>(column_page_.get()));
+      BatchIterator<CSCPage>(new SimpleBatchIteratorImpl<CSCPage>(column_page_));
   return BatchSet<CSCPage>(begin_iter);
 }
 
@@ -66,11 +66,11 @@ BatchSet<SortedCSCPage> SimpleDMatrix::GetSortedColumnBatches() {
   // Sorted column page doesn't exist, generate it
   if (!sorted_column_page_) {
     sorted_column_page_.reset(
-        new SortedCSCPage(sparse_page_.GetTranspose(info_.num_col_)));
+        new SortedCSCPage(sparse_page_->GetTranspose(info_.num_col_)));
     sorted_column_page_->SortRows();
   }
   auto begin_iter = BatchIterator<SortedCSCPage>(
-      new SimpleBatchIteratorImpl<SortedCSCPage>(sorted_column_page_.get()));
+      new SimpleBatchIteratorImpl<SortedCSCPage>(sorted_column_page_));
   return BatchSet<SortedCSCPage>(begin_iter);
 }
 
@@ -86,7 +86,7 @@ BatchSet<EllpackPage> SimpleDMatrix::GetEllpackBatches(const BatchParam& param)
     batch_param_ = param;
   }
   auto begin_iter =
-      BatchIterator<EllpackPage>(new SimpleBatchIteratorImpl<EllpackPage>(ellpack_page_.get()));
+      BatchIterator<EllpackPage>(new SimpleBatchIteratorImpl<EllpackPage>(ellpack_page_));
   return BatchSet<EllpackPage>(begin_iter);
 }
 
@@ -100,7 +100,7 @@ BatchSet<GHistIndexMatrix> SimpleDMatrix::GetGradientIndex(const BatchParam& par
     batch_param_ = param;
   }
   auto begin_iter = BatchIterator<GHistIndexMatrix>(
-      new SimpleBatchIteratorImpl<GHistIndexMatrix>(gradient_index_.get()));
+      new SimpleBatchIteratorImpl<GHistIndexMatrix>(gradient_index_));
   return BatchSet<GHistIndexMatrix>(begin_iter);
 }
 
@@ -110,8 +110,8 @@ SimpleDMatrix::SimpleDMatrix(AdapterT* adapter, float missing, int nthread) {
   uint64_t default_max = std::numeric_limits<uint64_t>::max();
   uint64_t last_group_id = default_max;
   bst_uint group_size = 0;
-  auto& offset_vec = sparse_page_.offset.HostVector();
+  auto& offset_vec = sparse_page_->offset.HostVector();
-  auto& data_vec = sparse_page_.data.HostVector();
+  auto& data_vec = sparse_page_->data.HostVector();
   uint64_t inferred_num_columns = 0;
   uint64_t total_batch_size = 0;
     // batch_size is either number of rows or cols, depending on data layout
@@ -120,7 +120,7 @@ SimpleDMatrix::SimpleDMatrix(AdapterT* adapter, float missing, int nthread) {
   // Iterate over batches of input data
   while (adapter->Next()) {
     auto& batch = adapter->Value();
-    auto batch_max_columns = sparse_page_.Push(batch, missing, nthread);
+    auto batch_max_columns = sparse_page_->Push(batch, missing, nthread);
     inferred_num_columns = std::max(batch_max_columns, inferred_num_columns);
     total_batch_size += batch.Size();
     // Append meta information if available
@@ -203,8 +203,8 @@ SimpleDMatrix::SimpleDMatrix(dmlc::Stream* in_stream) {
   CHECK(in_stream->Read(&tmagic)) << "invalid input file format";
   CHECK_EQ(tmagic, kMagic) << "invalid format, magic number mismatch";
   info_.LoadBinary(in_stream);
-  in_stream->Read(&sparse_page_.offset.HostVector());
+  in_stream->Read(&sparse_page_->offset.HostVector());
-  in_stream->Read(&sparse_page_.data.HostVector());
+  in_stream->Read(&sparse_page_->data.HostVector());
 }
 
 void SimpleDMatrix::SaveToLocalFile(const std::string& fname) {
@@ -212,8 +212,8 @@ void SimpleDMatrix::SaveToLocalFile(const std::string& fname) {
     int tmagic = kMagic;
     fo->Write(tmagic);
     info_.SaveBinary(fo.get());
-    fo->Write(sparse_page_.offset.HostVector());
+    fo->Write(sparse_page_->offset.HostVector());
-    fo->Write(sparse_page_.data.HostVector());
+    fo->Write(sparse_page_->data.HostVector());
 }
 
 template SimpleDMatrix::SimpleDMatrix(DenseAdapter* adapter, float missing,

src/data/simple_dmatrix.cu

@@ -28,7 +28,7 @@ SimpleDMatrix::SimpleDMatrix(AdapterT* adapter, float missing, int nthread) {
   CHECK(!adapter->Next());
 
   info_.num_nonzero_ = CopyToSparsePage(adapter->Value(), adapter->DeviceIdx(),
-                                        missing, &sparse_page_);
+                                        missing, sparse_page_.get());
   info_.num_col_ = adapter->NumColumns();
   info_.num_row_ = adapter->NumRows();
   // Synchronise worker columns

src/data/simple_dmatrix.h

@@ -1,5 +1,5 @@
 /*!
- * Copyright 2015 by Contributors
+ * Copyright 2015-2021 by Contributors
  * \file simple_dmatrix.h
  * \brief In-memory version of DMatrix.
  * \author Tianqi Chen
@@ -47,11 +47,12 @@ class SimpleDMatrix : public DMatrix {
   BatchSet<GHistIndexMatrix> GetGradientIndex(const BatchParam& param) override;
 
   MetaInfo info_;
-  SparsePage sparse_page_;  // Primary storage type
+  // Primary storage type
-  std::unique_ptr<CSCPage> column_page_;
+  std::shared_ptr<SparsePage> sparse_page_ = std::make_shared<SparsePage>();
-  std::unique_ptr<SortedCSCPage> sorted_column_page_;
+  std::shared_ptr<CSCPage> column_page_;
-  std::unique_ptr<EllpackPage> ellpack_page_;
+  std::shared_ptr<SortedCSCPage> sorted_column_page_;
-  std::unique_ptr<GHistIndexMatrix> gradient_index_;
+  std::shared_ptr<EllpackPage> ellpack_page_;
+  std::shared_ptr<GHistIndexMatrix> gradient_index_;
   BatchParam batch_param_;
 
   bool EllpackExists() const override {

src/data/sparse_page_dmatrix.cc

@@ -1,59 +1,147 @@
 /*!
- * Copyright 2014-2020 by Contributors
+ * Copyright 2014-2021 by Contributors
  * \file sparse_page_dmatrix.cc
  * \brief The external memory version of Page Iterator.
  * \author Tianqi Chen
  */
-#include <dmlc/base.h>
-#include <dmlc/timer.h>
-
-#if DMLC_ENABLE_STD_THREAD
 #include "./sparse_page_dmatrix.h"
-
 #include "./simple_batch_iterator.h"
+#include "gradient_index.h"
 
 namespace xgboost {
 namespace data {
 
-MetaInfo& SparsePageDMatrix::Info() {
+MetaInfo &SparsePageDMatrix::Info() { return info_; }
-  return row_source_->info;
+
+const MetaInfo &SparsePageDMatrix::Info() const { return info_; }
+
+SparsePageDMatrix::SparsePageDMatrix(DataIterHandle iter_handle, DMatrixHandle proxy_handle,
+                                     DataIterResetCallback *reset,
+                                     XGDMatrixCallbackNext *next, float missing,
+                                     int32_t nthreads, std::string cache_prefix)
+    : proxy_{proxy_handle}, iter_{iter_handle}, reset_{reset}, next_{next}, missing_{missing},
+      nthreads_{nthreads}, cache_prefix_{std::move(cache_prefix)} {
+  cache_prefix_ = cache_prefix_.empty() ? "DMatrix" : cache_prefix_;
+  if (rabit::IsDistributed()) {
+    cache_prefix_ += ("-r" + std::to_string(rabit::GetRank()));
+  }
+  DMatrixProxy *proxy = MakeProxy(proxy_);
+  auto iter = DataIterProxy<DataIterResetCallback, XGDMatrixCallbackNext>{
+      iter_, reset_, next_};
+
+  uint32_t n_batches = 0;
+  size_t n_features = 0;
+  size_t n_samples = 0;
+  size_t nnz = 0;
+
+  auto num_rows = [&]() {
+    return HostAdapterDispatch(
+        proxy, [](auto const &value) { return value.NumRows(); });
+  };
+  auto num_cols = [&]() {
+    return HostAdapterDispatch(
+        proxy, [](auto const &value) { return value.NumCols(); });
+  };
+  // the proxy is iterated together with the sparse page source so we can obtain all
+  // information in 1 pass.
+  for (auto const &page : this->GetRowBatchesImpl()) {
+    this->info_.Extend(std::move(proxy->Info()), false, false);
+    n_features = std::max(n_features, num_cols());
+    n_samples += num_rows();
+    nnz += page.data.Size();
+    n_batches++;
   }
 
-const MetaInfo& SparsePageDMatrix::Info() const {
+  iter.Reset();
-  return row_source_->info;
+
+  this->n_batches_ = n_batches;
+  this->info_.num_row_ = n_samples;
+  this->info_.num_col_ = n_features;
+  this->info_.num_nonzero_ = nnz;
+
+  rabit::Allreduce<rabit::op::Max>(&info_.num_col_, 1);
+  CHECK_NE(info_.num_col_, 0);
+}
+
+void SparsePageDMatrix::InitializeSparsePage() {
+  auto id = MakeCache(this, ".row.page", cache_prefix_, &cache_info_);
+  // Don't use proxy DMatrix once this is already initialized, this allows users to
+  // release the iterator and data.
+  if (cache_info_.at(id)->written) {
+    CHECK(sparse_page_source_);
+    sparse_page_source_->Reset();
+    return;
+  }
+
+  auto iter = DataIterProxy<DataIterResetCallback, XGDMatrixCallbackNext>{
+      iter_, reset_, next_};
+  DMatrixProxy *proxy = MakeProxy(proxy_);
+  sparse_page_source_.reset();  // clear before creating new one to prevent conflicts.
+  sparse_page_source_ = std::make_shared<SparsePageSource>(
+      iter, proxy, this->missing_, this->nthreads_, this->info_.num_col_,
+      this->n_batches_, cache_info_.at(id));
+}
+
+BatchSet<SparsePage> SparsePageDMatrix::GetRowBatchesImpl() {
+  this->InitializeSparsePage();
+  auto begin_iter = BatchIterator<SparsePage>(sparse_page_source_);
+  return BatchSet<SparsePage>(BatchIterator<SparsePage>(begin_iter));
 }
 
 BatchSet<SparsePage> SparsePageDMatrix::GetRowBatches() {
-  return row_source_->GetBatchSet();
+  return this->GetRowBatchesImpl();
 }
 
 BatchSet<CSCPage> SparsePageDMatrix::GetColumnBatches() {
-  // Lazily instantiate
+  auto id = MakeCache(this, ".col.page", cache_prefix_, &cache_info_);
+  CHECK_NE(this->Info().num_col_, 0);
+  this->InitializeSparsePage();
   if (!column_source_) {
-    column_source_.reset(new CSCPageSource(this, cache_info_));
+    column_source_ = std::make_shared<CSCPageSource>(
+        this->missing_, this->nthreads_, this->Info().num_col_,
+        this->n_batches_, cache_info_.at(id), sparse_page_source_);
+  } else {
+    column_source_->Reset();
   }
-  return column_source_->GetBatchSet();
+  auto begin_iter = BatchIterator<CSCPage>(column_source_);
+  return BatchSet<CSCPage>(BatchIterator<CSCPage>(begin_iter));
 }
 
 BatchSet<SortedCSCPage> SparsePageDMatrix::GetSortedColumnBatches() {
-  // Lazily instantiate
+  auto id = MakeCache(this, ".sorted.col.page", cache_prefix_, &cache_info_);
+  CHECK_NE(this->Info().num_col_, 0);
+  this->InitializeSparsePage();
   if (!sorted_column_source_) {
-    sorted_column_source_.reset(new SortedCSCPageSource(this, cache_info_));
+    sorted_column_source_ = std::make_shared<SortedCSCPageSource>(
+        this->missing_, this->nthreads_, this->Info().num_col_,
+        this->n_batches_, cache_info_.at(id), sparse_page_source_);
+  } else {
+    sorted_column_source_->Reset();
   }
-  return sorted_column_source_->GetBatchSet();
+  auto begin_iter = BatchIterator<SortedCSCPage>(sorted_column_source_);
+  return BatchSet<SortedCSCPage>(BatchIterator<SortedCSCPage>(begin_iter));
 }
 
-BatchSet<EllpackPage> SparsePageDMatrix::GetEllpackBatches(const BatchParam& param) {
+BatchSet<GHistIndexMatrix> SparsePageDMatrix::GetGradientIndex(const BatchParam& param) {
-  CHECK_GE(param.gpu_id, 0);
   CHECK_GE(param.max_bin, 2);
-  // Lazily instantiate
+  // External memory is not support
-  if (!ellpack_source_ || (batch_param_ != param && param != BatchParam{})) {
+  if (!ghist_index_source_ || (param != batch_param_ && param != BatchParam{})) {
-    ellpack_source_.reset(new EllpackPageSource(this, cache_info_, param));
+    this->InitializeSparsePage();
+    ghist_index_source_.reset(new GHistIndexMatrix{this, param.max_bin});
     batch_param_ = param;
   }
-  return ellpack_source_->GetBatchSet();
+  this->InitializeSparsePage();
+  auto begin_iter = BatchIterator<GHistIndexMatrix>(
+      new SimpleBatchIteratorImpl<GHistIndexMatrix>(ghist_index_source_));
+  return BatchSet<GHistIndexMatrix>(begin_iter);
 }
 
+#if !defined(XGBOOST_USE_CUDA)
+BatchSet<EllpackPage> SparsePageDMatrix::GetEllpackBatches(const BatchParam& param) {
+  common::AssertGPUSupport();
+  auto begin_iter = BatchIterator<EllpackPage>(ellpack_page_source_);
+  return BatchSet<EllpackPage>(BatchIterator<EllpackPage>(begin_iter));
+}
+#endif  // !defined(XGBOOST_USE_CUDA)
 }  // namespace data
 }  // namespace xgboost
-#endif  // DMLC_ENABLE_STD_THREAD

src/data/sparse_page_dmatrix.cu

@@ -0,0 +1,46 @@
+/*!
+ * Copyright 2021 XGBoost contributors
+ */
+#include "sparse_page_source.h"
+#include "../common/hist_util.cuh"
+#include "ellpack_page.cuh"
+#include "sparse_page_dmatrix.h"
+
+namespace xgboost {
+namespace data {
+BatchSet<EllpackPage> SparsePageDMatrix::GetEllpackBatches(const BatchParam& param) {
+  CHECK_GE(param.gpu_id, 0);
+  CHECK_GE(param.max_bin, 2);
+  auto id = MakeCache(this, ".ellpack.page", cache_prefix_, &cache_info_);
+  size_t row_stride = 0;
+  this->InitializeSparsePage();
+  if (!cache_info_.at(id)->written || (batch_param_ != param && param != BatchParam{})) {
+    // reinitialize the cache
+    cache_info_.erase(id);
+    MakeCache(this, ".ellpack.page", cache_prefix_, &cache_info_);
+    std::unique_ptr<common::HistogramCuts> cuts;
+    cuts.reset(new common::HistogramCuts{
+        common::DeviceSketch(param.gpu_id, this, param.max_bin, 0)});
+    this->InitializeSparsePage();  // reset after use.
+
+    row_stride = GetRowStride(this);
+    this->InitializeSparsePage();  // reset after use.
+    CHECK_NE(row_stride, 0);
+    batch_param_ = param;
+
+    auto ft = this->info_.feature_types.ConstDeviceSpan();
+    ellpack_page_source_.reset();  // release resources.
+    ellpack_page_source_.reset(new EllpackPageSource(
+        this->missing_, this->nthreads_, this->Info().num_col_,
+        this->n_batches_, cache_info_.at(id), param, std::move(cuts),
+        this->IsDense(), row_stride, ft, sparse_page_source_));
+  } else {
+    CHECK(sparse_page_source_);
+    ellpack_page_source_->Reset();
+  }
+
+  auto begin_iter = BatchIterator<EllpackPage>(ellpack_page_source_);
+  return BatchSet<EllpackPage>(BatchIterator<EllpackPage>(begin_iter));
+}
+}  // namespace data
+}  // namespace xgboost

src/data/sparse_page_dmatrix.h

@@ -1,5 +1,5 @@
 /*!
- * Copyright 2015 by Contributors
+ * Copyright 2015-2021 by Contributors
  * \file sparse_page_dmatrix.h
  * \brief External-memory version of DMatrix.
  * \author Tianqi Chen
@@ -13,24 +13,88 @@
 #include <string>
 #include <utility>
 #include <vector>
+#include <map>
 
 #include "ellpack_page_source.h"
 #include "sparse_page_source.h"
 
 namespace xgboost {
 namespace data {
-// Used for external memory.
+/**
+ * \brief DMatrix used for external memory.
+ *
+ * The external memory is created for controlling memory usage by splitting up data into
+ * multiple batches.  However that doesn't mean we will actually process exact 1 batch at
+ * a time, which would be terribly slow considering that we have to loop through the
+ * whole dataset for every tree split.  So we use async pre-fetch and let caller to decide
+ * how many batches it wants to process by returning data as shared pointer.  The caller
+ * can use async function to process the data or just stage those batches, making the
+ * decision is out of the scope for sparse page dmatrix.  These 2 optimizations might
+ * defeat the purpose of splitting up dataset since if you load all the batches then the
+ * memory usage is even worse than using a single batch.  Essentially we need to control
+ * how many batches can be in memory at the same time.
+ *
+ * Right now the write to the cache is sequential operation and is blocking, reading from
+ * cache is async but with a hard coded limit of 4 pages as an heuristic.  So by sparse
+ * dmatrix itself there can be only 9 pages in main memory (might be of different types)
+ * at the same time: 1 page pending for write, 4 pre-fetched sparse pages, 4 pre-fetched
+ * dependent pages.  If the caller stops iteration at the middle and start again, then the
+ * number of pages in memory can hit 16 due to pre-fetching, but this should be a bug in
+ * caller's code (XGBoost doesn't discard a large portion of data at the end, there's not
+ * sampling algo that samples only the first portion of data).
+ *
+ * Of course if the caller decides to retain some batches to perform parallel processing,
+ * then we might load all pages in memory, which is also considered as a bug in caller's
+ * code.  So if the algo supports external memory, it must be careful that queue for async
+ * call must have an upper limit.
+ *
+ * Another assumption we make is that the data must be immutable so caller should never
+ * change the data.  Sparse page source returns const page to make sure of that.  If you
+ * want to change the generated page like Ellpack, pass parameter into `GetBatches` to
+ * re-generate them instead of trying to modify the pages in-place.
+ *
+ * A possible optimization is dropping the sparse page once dependent pages like ellpack
+ * are constructed and cached.
+ */
 class SparsePageDMatrix : public DMatrix {
+  MetaInfo info_;
+  BatchParam batch_param_;
+  std::map<std::string, std::shared_ptr<Cache>> cache_info_;
+
+  DMatrixHandle proxy_;
+  DataIterHandle iter_;
+  DataIterResetCallback *reset_;
+  XGDMatrixCallbackNext *next_;
+
+  float missing_;
+  int nthreads_;
+  std::string cache_prefix_;
+  uint32_t n_batches_ {0};
+  // sparse page is the source to other page types, we make a special member function.
+  void InitializeSparsePage();
+  // Non-virtual version that can be used in constructor
+  BatchSet<SparsePage> GetRowBatchesImpl();
+
  public:
-  template <typename AdapterT>
+  explicit SparsePageDMatrix(DataIterHandle iter, DMatrixHandle proxy,
-  explicit SparsePageDMatrix(AdapterT* adapter, float missing, int nthread,
+                             DataIterResetCallback *reset,
-                             const std::string& cache_prefix,
+                             XGDMatrixCallbackNext *next, float missing,
-                             size_t page_size = kPageSize)
+                             int32_t nthreads, std::string cache_prefix);
-      : cache_info_(std::move(cache_prefix)) {
+
-    row_source_.reset(new data::SparsePageSource(adapter, missing, nthread,
+  ~SparsePageDMatrix() override {
-                                                 cache_prefix, page_size));
+    // Clear out all resources before deleting the cache file.
+    sparse_page_source_.reset();
+    ellpack_page_source_.reset();
+    column_source_.reset();
+    sorted_column_source_.reset();
+    ghist_index_source_.reset();
+
+    for (auto const &kv : cache_info_) {
+      CHECK(kv.second);
+      auto n = kv.second->ShardName();
+      TryDeleteCacheFile(n);
+    }
   }
-  ~SparsePageDMatrix() override = default;
 
   MetaInfo& Info() override;
 
@@ -47,30 +111,41 @@ class SparsePageDMatrix : public DMatrix {
   BatchSet<CSCPage> GetColumnBatches() override;
   BatchSet<SortedCSCPage> GetSortedColumnBatches() override;
   BatchSet<EllpackPage> GetEllpackBatches(const BatchParam& param) override;
-  BatchSet<GHistIndexMatrix> GetGradientIndex(const BatchParam&) override {
+  BatchSet<GHistIndexMatrix> GetGradientIndex(const BatchParam&) override;
-    LOG(FATAL) << "Not implemented.";
-    return BatchSet<GHistIndexMatrix>(BatchIterator<GHistIndexMatrix>(nullptr));
-  }
 
   // source data pointers.
-  std::unique_ptr<SparsePageSource> row_source_;
+  std::shared_ptr<SparsePageSource> sparse_page_source_;
-  std::unique_ptr<CSCPageSource> column_source_;
+  std::shared_ptr<EllpackPageSource> ellpack_page_source_;
-  std::unique_ptr<SortedCSCPageSource> sorted_column_source_;
+  std::shared_ptr<CSCPageSource> column_source_;
-  std::unique_ptr<EllpackPageSource> ellpack_source_;
+  std::shared_ptr<SortedCSCPageSource> sorted_column_source_;
-  // saved batch param
+  std::shared_ptr<GHistIndexMatrix> ghist_index_source_;
-  BatchParam batch_param_;
-  // the cache prefix
-  std::string cache_info_;
-  // Store column densities to avoid recalculating
-  std::vector<float> col_density_;
 
   bool EllpackExists() const override {
-    return static_cast<bool>(ellpack_source_);
+    return static_cast<bool>(ellpack_page_source_);
   }
   bool SparsePageExists() const override {
-    return static_cast<bool>(row_source_);
+    return static_cast<bool>(sparse_page_source_);
   }
 };
+
+inline std::string MakeId(std::string prefix, SparsePageDMatrix *ptr) {
+  std::stringstream ss;
+  ss << ptr;
+  return prefix + "-" + ss.str();
+}
+
+inline std::string
+MakeCache(SparsePageDMatrix *ptr, std::string format, std::string prefix,
+          std::map<std::string, std::shared_ptr<Cache>> *out) {
+  auto &cache_info = *out;
+  auto name = MakeId(prefix, ptr);
+  auto id = name + format;
+  auto it = cache_info.find(id);
+  if (it == cache_info.cend()) {
+    cache_info[id].reset(new Cache{false, name, format});
+  }
+  return id;
+}
 }  // namespace data
 }  // namespace xgboost
 #endif  // XGBOOST_DATA_SPARSE_PAGE_DMATRIX_H_

src/data/sparse_page_source.cc

@@ -1,77 +0,0 @@
-/*!
- *  Copyright (c) 2020 by XGBoost Contributors
- */
-#include "sparse_page_source.h"
-
-namespace xgboost {
-namespace data {
-void DataPool::Slice(std::shared_ptr<SparsePage> out, size_t offset,
-                     size_t n_rows, size_t entry_offset) const {
-  auto const &in_offset = pool_.offset.HostVector();
-  auto const &in_data = pool_.data.HostVector();
-  auto &h_offset = out->offset.HostVector();
-  CHECK_LE(offset + n_rows + 1, in_offset.size());
-  h_offset.resize(n_rows + 1, 0);
-  std::transform(in_offset.cbegin() + offset,
-                 in_offset.cbegin() + offset + n_rows + 1, h_offset.begin(),
-                 [=](size_t ptr) { return ptr - entry_offset; });
-
-  auto &h_data = out->data.HostVector();
-  CHECK_GT(h_offset.size(), 0);
-  size_t n_entries = h_offset.back();
-  h_data.resize(n_entries);
-
-  CHECK_EQ(n_entries, in_offset.at(offset + n_rows) - in_offset.at(offset));
-  std::copy_n(in_data.cbegin() + in_offset.at(offset), n_entries,
-              h_data.begin());
-}
-
-void DataPool::SplitWritePage() {
-  size_t total = pool_.Size();
-  size_t offset = 0;
-  size_t entry_offset = 0;
-  do {
-    size_t n_rows = std::min(page_size_, total - offset);
-    std::shared_ptr<SparsePage> out;
-    writer_->Alloc(&out);
-    out->Clear();
-    out->SetBaseRowId(inferred_num_rows_);
-    this->Slice(out, offset, n_rows, entry_offset);
-    inferred_num_rows_ += out->Size();
-    offset += n_rows;
-    entry_offset += out->data.Size();
-    CHECK_NE(out->Size(), 0);
-    writer_->PushWrite(std::move(out));
-  } while (total - offset >= page_size_);
-
-  if (total - offset != 0) {
-    auto out = std::make_shared<SparsePage>();
-    this->Slice(out, offset, total - offset, entry_offset);
-    CHECK_NE(out->Size(), 0);
-    pool_.Clear();
-    pool_.Push(*out);
-  } else {
-    pool_.Clear();
-  }
-}
-size_t DataPool::Finalize() {
-  inferred_num_rows_ += pool_.Size();
-  if (pool_.Size() != 0) {
-    std::shared_ptr<SparsePage> page;
-    this->writer_->Alloc(&page);
-    page->Clear();
-    page->Push(pool_);
-    this->writer_->PushWrite(std::move(page));
-  }
-
-  if (inferred_num_rows_ == 0) {
-    std::shared_ptr<SparsePage> page;
-    this->writer_->Alloc(&page);
-    page->Clear();
-    this->writer_->PushWrite(std::move(page));
-  }
-
-  return inferred_num_rows_;
-}
-}  // namespace data
-}  // namespace xgboost

src/data/sparse_page_source.cu

@@ -0,0 +1,17 @@
+/*!
+ * Copyright 2021 XGBoost contributors
+ */
+#include "sparse_page_source.h"
+#include "proxy_dmatrix.cuh"
+#include "simple_dmatrix.cuh"
+
+namespace xgboost {
+namespace data {
+void DevicePush(DMatrixProxy* proxy, float missing, SparsePage* page) {
+  auto device = proxy->DeviceIdx();
+  Dispatch(proxy, [&](auto const &value) {
+    CopyToSparsePage(value, device, missing, page);
+  });
+}
+}  // namespace data
+}  // namespace xgboost

src/data/sparse_page_source.h

@@ -1,54 +1,18 @@
 /*!
- *  Copyright (c) 2014-2019 by Contributors
+ *  Copyright (c) 2014-2021 by Contributors
- * \file page_csr_source.h
+ * \file sparse_page_source.h
- *  External memory data source, saved with sparse_batch_page binary format.
- * \author Tianqi Chen
- *
- * -------------------------------------------------
- * Random notes on implementation of external memory
- * -------------------------------------------------
- *
- * As of XGBoost 1.3, the general pipeline is:
- *
- * dmlc text file parser --> file adapter --> sparse page source -> data pool -->
- * write to binary cache --> load it back ~~> [ other pages (csc, ellpack, sorted csc) -->
- * write to binary cache ] --> use it in various algorithms.
- *
- *       ~~> means optional
- *
- * The dmlc text file parser returns number of blocks based on available threads, which
- * can make the data partitioning non-deterministic, so here we set up an extra data pool
- * to stage parsed data.  As a result, the number of blocks returned by text parser does
- * not equal to number of blocks in binary cache.
- *
- * Binary cache loading is async by the dmlc threaded iterator, which helps performance,
- * but as this iterator itself is not thread safe, so calling
- * `dmatrix->GetBatches<SparsePage>` is also not thread safe.  Please note that, the
- * threaded iterator is also used inside dmlc text file parser.
- *
- * Memory consumption is difficult to control due to various reasons.  Firstly the text
- * parsing doesn't have a batch size, only a hard coded buffer size is available.
- * Secondly, everything is loaded/written with async queue, with multiple queues running
- * the memory consumption is difficult to measure.
- *
- * The threaded iterator relies heavily on C++ memory model and threading primitive.  The
- * concurrent writer for binary cache is an old copy of moody queue.  We should try to
- * replace them with something more robust.
  */
 #ifndef XGBOOST_DATA_SPARSE_PAGE_SOURCE_H_
 #define XGBOOST_DATA_SPARSE_PAGE_SOURCE_H_
 
-#include <dmlc/threadediter.h>
+#include <algorithm>  // std::min
-#include <dmlc/timer.h>
-
-#include <algorithm>
-#include <limits>
-#include <locale>
-#include <memory>
 #include <string>
 #include <utility>
 #include <vector>
-#include <fstream>
+#include <future>
+#include <thread>
+#include <map>
+#include <memory>
 
 #include "rabit/rabit.h"
 #include "xgboost/base.h"
@@ -56,93 +20,12 @@
 
 #include "adapter.h"
 #include "sparse_page_writer.h"
+#include "proxy_dmatrix.h"
+
 #include "../common/common.h"
-#include <xgboost/data.h>
-
-namespace detail {
-
-// Split a cache info string with delimiter ':'
-// If cache info string contains drive letter (e.g. C:), exclude it before splitting
-inline std::vector<std::string>
-GetCacheShards(const std::string& cache_info) {
-#if (defined _WIN32) || (defined __CYGWIN__)
-  if (cache_info.length() >= 2
-      && std::isalpha(cache_info[0], std::locale::classic())
-      && cache_info[1] == ':') {
-    std::vector<std::string> cache_shards
-      = xgboost::common::Split(cache_info.substr(2), ':');
-    cache_shards[0] = cache_info.substr(0, 2) + cache_shards[0];
-    return cache_shards;
-  }
-#endif  // (defined _WIN32) || (defined __CYGWIN__)
-  return xgboost::common::Split(cache_info, ':');
-}
-
-}  // namespace detail
 
 namespace xgboost {
 namespace data {
-
-template<typename S, typename T>
-class SparseBatchIteratorImpl : public BatchIteratorImpl<T> {
- public:
-  explicit SparseBatchIteratorImpl(S* source) : source_(source) {
-    CHECK(source_ != nullptr);
-    source_->BeforeFirst();
-    source_->Next();
-  }
-  T& operator*() override { return source_->Value(); }
-  const T& operator*() const override { return source_->Value(); }
-  void operator++() override { at_end_ = !source_->Next(); }
-  bool AtEnd() const override { return at_end_; }
-
- private:
-  S* source_{nullptr};
-  bool at_end_{ false };
-};
-
-  /*! \brief magic number used to identify Page */
-  static const int kMagic = 0xffffab02;
-/*!
- * \brief decide the format from cache prefix.
- * \return pair of row format, column format type of the cache prefix.
- */
-inline std::pair<std::string, std::string> DecideFormat(const std::string& cache_prefix) {
-  size_t pos = cache_prefix.rfind(".fmt-");
-
-  if (pos != std::string::npos) {
-    std::string fmt = cache_prefix.substr(pos + 5, cache_prefix.length());
-    size_t cpos = fmt.rfind('-');
-    if (cpos != std::string::npos) {
-      return std::make_pair(fmt.substr(0, cpos), fmt.substr(cpos + 1, fmt.length()));
-    } else {
-      return std::make_pair(fmt, fmt);
-    }
-  } else {
-    std::string raw = "raw";
-    return std::make_pair(raw, raw);
-  }
-}
-
-struct CacheInfo {
-  std::string name_info;
-  std::vector<std::string> format_shards;
-  std::vector<std::string> name_shards;
-};
-
-inline CacheInfo ParseCacheInfo(const std::string& cache_info, const std::string& page_type) {
-  CacheInfo info;
-  std::vector<std::string> cache_shards = ::detail::GetCacheShards(cache_info);
-  CHECK_NE(cache_shards.size(), 0U);
-  // read in the info files.
-  info.name_info = cache_shards[0];
-  for (const std::string& prefix : cache_shards) {
-    info.name_shards.push_back(prefix + page_type);
-    info.format_shards.push_back(DecideFormat(prefix).first);
-  }
-  return info;
-}
-
 inline void TryDeleteCacheFile(const std::string& file) {
   if (std::remove(file.c_str()) != 0) {
     LOG(WARNING) << "Couldn't remove external memory cache file " << file
@@ -150,415 +33,327 @@ inline void TryDeleteCacheFile(const std::string& file) {
   }
 }
 
-inline void CheckCacheFileExists(const std::string& file) {
+struct Cache {
-  std::ifstream f(file.c_str());
+  // whether the write to the cache is complete
-  if (f.good()) {
+  bool written;
-    LOG(FATAL)
+  std::string name;
-        << "Cache file " << file << " exists already;  "
-        << "Is there another DMatrix with the same "
-           "cache prefix?  It can be caused by previously used DMatrix that "
-           "hasn't been collected by language environment garbage collector.  "
-           "Otherwise please remove it manually.";
-  }
-}
-
-/**
- * \brief Given a set of cache files and page type, this object iterates over batches
- * using prefetching for improved performance. Not thread safe.
- *
- * \tparam  PageT Type of the page t.
- */
-template <typename PageT>
-class ExternalMemoryPrefetcher : dmlc::DataIter<PageT> {
- public:
-  explicit ExternalMemoryPrefetcher(const CacheInfo& info) noexcept(false)
-      : base_rowid_(0), page_(nullptr), clock_ptr_(0) {
-    // read in the info files
-    CHECK_NE(info.name_shards.size(), 0U);
-    {
-      std::unique_ptr<dmlc::Stream> finfo(
-          dmlc::Stream::Create(info.name_info.c_str(), "r"));
-      int tmagic;
-      CHECK(finfo->Read(&tmagic));
-      CHECK_EQ(tmagic, kMagic) << "invalid format, magic number mismatch";
-    }
-    files_.resize(info.name_shards.size());
-    formats_.resize(info.name_shards.size());
-    prefetchers_.resize(info.name_shards.size());
-
-    // read in the cache files.
-    for (size_t i = 0; i < info.name_shards.size(); ++i) {
-      std::string name_row = info.name_shards.at(i);
-      files_[i].reset(dmlc::SeekStream::CreateForRead(name_row.c_str()));
-      std::unique_ptr<dmlc::SeekStream>& fi = files_[i];
   std::string format;
-      CHECK(fi->Read(&format)) << "Invalid page format";
+  // offset into binary cache file.
-      formats_[i].reset(CreatePageFormat<PageT>(format));
+  std::vector<size_t> offset;
-      std::unique_ptr<SparsePageFormat<PageT>>& fmt = formats_[i];
+
-      size_t fbegin = fi->Tell();
+  Cache(bool w, std::string n, std::string fmt)
-      prefetchers_[i].reset(new dmlc::ThreadedIter<PageT>(4));
+      : written{w}, name{std::move(n)}, format{std::move(fmt)} {
-      prefetchers_[i]->Init(
+    offset.push_back(0);
-          [&fi, &fmt](PageT** dptr) {
-            if (*dptr == nullptr) {
-              *dptr = new PageT();
-            }
-            return fmt->Read(*dptr, fi.get());
-          },
-          [&fi, fbegin]() { fi->Seek(fbegin); });
-    }
-  }
-  /*! \brief destructor */
-  ~ExternalMemoryPrefetcher() override {
-    delete page_;
   }
 
-  // implement Next
+  static std::string ShardName(std::string name, std::string format) {
-  bool Next() override {
+    CHECK_EQ(format.front(), '.');
-    CHECK(mutex_.try_lock()) << "Multiple threads attempting to use prefetcher";
+    return name + format;
-    // doing clock rotation over shards.
-    if (page_ != nullptr) {
-      size_t n = prefetchers_.size();
-      prefetchers_[(clock_ptr_ + n - 1) % n]->Recycle(&page_);
   }
 
-    if (prefetchers_[clock_ptr_]->Next(&page_)) {
+  std::string ShardName() {
-      page_->SetBaseRowId(base_rowid_);
+    return ShardName(this->name, this->format);
-      base_rowid_ += page_->Size();
+  }
-      // advance clock
+
-      clock_ptr_ = (clock_ptr_ + 1) % prefetchers_.size();
+  // The write is completed.
-      mutex_.unlock();
+  void Commit() {
-      return true;
+    if (!written) {
-    } else {
+      std::partial_sum(offset.begin(), offset.end(), offset.begin());
-      mutex_.unlock();
+      written = true;
+    }
+  }
+};
+
+// Prevents multi-threaded call.
+class TryLockGuard {
+  std::mutex& lock_;
+
+ public:
+  explicit TryLockGuard(std::mutex& lock) : lock_{lock} {  // NOLINT
+    CHECK(lock_.try_lock()) << "Multiple threads attempting to use Sparse DMatrix.";
+  }
+  ~TryLockGuard() {
+    lock_.unlock();
+  }
+};
+
+template <typename S>
+class SparsePageSourceImpl : public BatchIteratorImpl<S> {
+ protected:
+  // Prevents calling this iterator from multiple places(or threads).
+  std::mutex single_threaded_;
+
+  std::shared_ptr<S> page_;
+
+  bool at_end_ {false};
+  float missing_;
+  int nthreads_;
+  bst_feature_t n_features_;
+
+  uint32_t count_{0};
+
+  uint32_t n_batches_ {0};
+
+  std::shared_ptr<Cache> cache_info_;
+  std::unique_ptr<dmlc::Stream> fo_;
+
+  using Ring = std::vector<std::future<std::shared_ptr<S>>>;
+  // A ring storing futures to data.  Since the DMatrix iterator is forward only, so we
+  // can pre-fetch data in a ring.
+  std::unique_ptr<Ring> ring_{new Ring};
+
+  bool ReadCache() {
+    CHECK(!at_end_);
+    if (!cache_info_->written) {
       return false;
     }
+    if (fo_) {
+      fo_.reset();  // flush the data to disk.
+      ring_->resize(n_batches_);
+    }
+    // An heuristic for number of pre-fetched batches.  We can make it part of BatchParam
+    // to let user adjust number of pre-fetched batches when needed.
+    uint32_t constexpr kPreFetch = 4;
+
+    size_t n_prefetch_batches = std::min(kPreFetch, n_batches_);
+    CHECK_GT(n_prefetch_batches, 0) << "total batches:" << n_batches_;
+    size_t fetch_it = count_;
+    for (size_t i = 0; i < n_prefetch_batches; ++i, ++fetch_it) {
+      fetch_it %= n_batches_;  // ring
+      if (ring_->at(fetch_it).valid()) { continue; }
+      auto const *self = this;  // make sure it's const
+      CHECK_LT(fetch_it, cache_info_->offset.size());
+      ring_->at(fetch_it) = std::async(std::launch::async, [fetch_it, self]() {
+        std::unique_ptr<SparsePageFormat<S>> fmt{CreatePageFormat<S>("raw")};
+        auto n = self->cache_info_->ShardName();
+        size_t offset = self->cache_info_->offset.at(fetch_it);
+        std::unique_ptr<dmlc::SeekStream> fi{
+            dmlc::SeekStream::CreateForRead(n.c_str())};
+        fi->Seek(offset);
+        CHECK_EQ(fi->Tell(), offset);
+        auto page = std::make_shared<S>();
+        CHECK(fmt->Read(page.get(), fi.get()));
+        return page;
+      });
+    }
+    CHECK_EQ(std::count_if(ring_->cbegin(), ring_->cend(),
+                           [](auto const &f) { return f.valid(); }),
+             n_prefetch_batches)
+        << "Sparse DMatrix assumes forward iteration.";
+    page_ = (*ring_)[count_].get();
+    return true;
   }
 
-  // implement BeforeFirst
+  void WriteCache() {
-  void BeforeFirst() override {
+    CHECK(!cache_info_->written);
-    CHECK(mutex_.try_lock()) << "Multiple threads attempting to use prefetcher";
+    std::unique_ptr<SparsePageFormat<S>> fmt{CreatePageFormat<S>("raw")};
-    base_rowid_ = 0;
+    if (!fo_) {
-    clock_ptr_ = 0;
+      auto n = cache_info_->ShardName();
-    for (auto& p : prefetchers_) {
+      fo_.reset(dmlc::Stream::Create(n.c_str(), "w"));
-      p->BeforeFirst();
     }
-    mutex_.unlock();
+    auto bytes = fmt->Write(*page_, fo_.get());
+    cache_info_->offset.push_back(bytes);
   }
 
-  // implement Value
+  virtual void Fetch() = 0;
-  PageT& Value() { return *page_; }
-
-  const PageT& Value() const override { return *page_; }
-
- private:
-  std::mutex mutex_;
-  /*! \brief number of rows */
-  size_t base_rowid_;
-  /*! \brief page currently on hold. */
-  PageT* page_;
-  /*! \brief internal clock ptr */
-  size_t clock_ptr_;
-  /*! \brief file pointer to the row blob file. */
-  std::vector<std::unique_ptr<dmlc::SeekStream>> files_;
-  /*! \brief Sparse page format file. */
-  std::vector<std::unique_ptr<SparsePageFormat<PageT>>> formats_;
-  /*! \brief internal prefetcher. */
-  std::vector<std::unique_ptr<dmlc::ThreadedIter<PageT>>> prefetchers_;
-};
-
-
-// A data pool to keep the size of each page balanced and data partitioning to be
-// deterministic.
-class DataPool {
-  size_t inferred_num_rows_;
-  MetaInfo* info_;
-  SparsePage pool_;
-  size_t page_size_;
-  SparsePageWriter<SparsePage> *writer_;
-
-  void Slice(std::shared_ptr<SparsePage> out, size_t offset, size_t n_rows,
-             size_t entry_offset) const;
-  void SplitWritePage();
 
  public:
-  DataPool(MetaInfo *info, size_t page_size,
+  SparsePageSourceImpl(float missing, int nthreads, bst_feature_t n_features,
-           SparsePageWriter<SparsePage> *writer)
+                       uint32_t n_batches, std::shared_ptr<Cache> cache)
-      : inferred_num_rows_{0}, info_{info},
+      : missing_{missing}, nthreads_{nthreads}, n_features_{n_features},
-        page_size_{page_size}, writer_{writer} {}
+        n_batches_{n_batches}, cache_info_{std::move(cache)} {}
 
-  void Push(std::shared_ptr<SparsePage> page) {
+  SparsePageSourceImpl(SparsePageSourceImpl const &that) = delete;
-    info_->num_nonzero_ += page->data.Size();
+
-    pool_.Push(*page);
+  ~SparsePageSourceImpl() override {
-    if (pool_.Size() > page_size_) {
+    for (auto& fu : *ring_) {
-      this->SplitWritePage();
+      if (fu.valid()) {
+        fu.get();
+      }
     }
-    page->Clear();
   }
 
-  size_t Finalize();
+  uint32_t Iter() const { return count_; }
+
+  const S &operator*() const override {
+    CHECK(page_);
+    return *page_;
+  }
+
+  std::shared_ptr<S const> Page() const override {
+    return page_;
+  }
+
+  bool AtEnd() const override {
+    return at_end_;
+  }
+
+  virtual void Reset() {
+    TryLockGuard guard{single_threaded_};
+    at_end_ = false;
+    count_ = 0;
+    this->Fetch();
+  }
 };
 
-class SparsePageSource {
+#if defined(XGBOOST_USE_CUDA)
+void DevicePush(DMatrixProxy* proxy, float missing, SparsePage* page);
+#else
+inline void DevicePush(DMatrixProxy* proxy, float missing, SparsePage* page) {
+  common::AssertGPUSupport();
+}
+#endif
+
+class SparsePageSource : public SparsePageSourceImpl<SparsePage> {
+  DataIterProxy<DataIterResetCallback, XGDMatrixCallbackNext> iter_;
+  DMatrixProxy* proxy_;
+  size_t base_row_id_ {0};
+
+  void Fetch() final {
+    page_ = std::make_shared<SparsePage>();
+    if (!this->ReadCache()) {
+      bool type_error { false };
+      CHECK(proxy_);
+      HostAdapterDispatch(proxy_, [&](auto const &adapter_batch) {
+        page_->Push(adapter_batch, this->missing_, this->nthreads_);
+      }, &type_error);
+      if (type_error) {
+        DevicePush(proxy_, missing_, page_.get());
+      }
+      page_->SetBaseRowId(base_row_id_);
+      base_row_id_ += page_->Size();
+      n_batches_++;
+      this->WriteCache();
+    }
+  }
+
  public:
-  template <typename AdapterT>
+  SparsePageSource(
-  SparsePageSource(AdapterT* adapter, float missing, int nthread,
+      DataIterProxy<DataIterResetCallback, XGDMatrixCallbackNext> iter,
-                   const std::string& cache_info,
+      DMatrixProxy *proxy, float missing, int nthreads,
-                   const size_t page_size = DMatrix::kPageSize) {
+      bst_feature_t n_features, uint32_t n_batches, std::shared_ptr<Cache> cache)
-    const std::string page_type = ".row.page";
+      : SparsePageSourceImpl(missing, nthreads, n_features, n_batches, cache),
-    cache_info_ = ParseCacheInfo(cache_info, page_type);
+        iter_{iter}, proxy_{proxy} {
-
+    if (!cache_info_->written) {
-    // Warn user if old cache files
+      iter_.Reset();
-    CheckCacheFileExists(cache_info_.name_info);
+      iter_.Next();
-    for (auto file : cache_info_.name_shards) {
+    }
-      CheckCacheFileExists(file);
+    this->Fetch();
   }
 
-    {
+  SparsePageSource& operator++() final {
-      SparsePageWriter<SparsePage> writer(cache_info_.name_shards,
+    TryLockGuard guard{single_threaded_};
-                                          cache_info_.format_shards, 6);
+    count_++;
-      DataPool pool(&info, page_size, &writer);
+    if (cache_info_->written) {
-
+      at_end_ = (count_ == n_batches_);
-      std::shared_ptr<SparsePage> page { new SparsePage };
-
-      uint64_t inferred_num_columns = 0;
-      uint64_t inferred_num_rows = 0;
-
-      const uint64_t default_max = std::numeric_limits<uint64_t>::max();
-      uint64_t last_group_id = default_max;
-      bst_uint group_size = 0;
-      std::vector<uint64_t> qids;
-      adapter->BeforeFirst();
-      while (adapter->Next()) {
-        auto& batch = adapter->Value();
-        if (batch.Labels() != nullptr) {
-          auto& labels = info.labels_.HostVector();
-          labels.insert(labels.end(), batch.Labels(),
-                        batch.Labels() + batch.Size());
-        }
-        if (batch.Weights() != nullptr) {
-          auto& weights = info.weights_.HostVector();
-          weights.insert(weights.end(), batch.Weights(),
-                         batch.Weights() + batch.Size());
-        }
-        if (batch.BaseMargin() != nullptr) {
-          auto& base_margin = info.base_margin_.HostVector();
-          base_margin.insert(base_margin.end(), batch.BaseMargin(),
-                             batch.BaseMargin() + batch.Size());
-        }
-        if (batch.Qid() != nullptr) {
-          qids.insert(qids.end(), batch.Qid(), batch.Qid() + batch.Size());
-          // get group
-          for (size_t i = 0; i < batch.Size(); ++i) {
-            const uint64_t cur_group_id = batch.Qid()[i];
-            if (last_group_id == default_max ||
-                last_group_id != cur_group_id) {
-              info.group_ptr_.push_back(group_size);
-            }
-            last_group_id = cur_group_id;
-            ++group_size;
-          }
-        }
-        CHECK_EQ(page->Size(), 0);
-        auto batch_max_columns = page->Push(batch, missing, nthread);
-        inferred_num_columns =
-            std::max(batch_max_columns, inferred_num_columns);
-        inferred_num_rows += page->Size();
-        pool.Push(page);
-        page->SetBaseRowId(inferred_num_rows);
-      }
-
-      if (last_group_id != default_max) {
-        if (group_size > info.group_ptr_.back()) {
-          info.group_ptr_.push_back(group_size);
-        }
-      }
-
-      // Deal with empty rows/columns if necessary
-      if (adapter->NumColumns() == kAdapterUnknownSize) {
-        info.num_col_ = inferred_num_columns;
     } else {
-        info.num_col_ = adapter->NumColumns();
+      at_end_ = !iter_.Next();
     }
-      // Synchronise worker columns
-      rabit::Allreduce<rabit::op::Max>(&info.num_col_, 1);
 
-      if (adapter->NumRows() == kAdapterUnknownSize) {
+    if (at_end_) {
-        info.num_row_ = inferred_num_rows;
+      cache_info_->Commit();
+      if (n_batches_ != 0) {
+        CHECK_EQ(count_, n_batches_);
+      }
+      CHECK_GE(count_, 1);
+      proxy_ = nullptr;
     } else {
-        if (page->offset.HostVector().empty()) {
+      this->Fetch();
-          page->offset.HostVector().emplace_back(0);
+    }
+    return *this;
   }
 
-        while (inferred_num_rows < adapter->NumRows()) {
+  void Reset() override {
-          page->offset.HostVector().emplace_back(
+    if (proxy_) {
-              page->offset.HostVector().back());
+      TryLockGuard guard{single_threaded_};
-          inferred_num_rows++;
+      iter_.Reset();
-        }
-        info.num_row_ = adapter->NumRows();
     }
+    SparsePageSourceImpl::Reset();
 
-      pool.Push(page);
+    TryLockGuard guard{single_threaded_};
-      pool.Finalize();
+    base_row_id_ = 0;
-
-      std::unique_ptr<dmlc::Stream> fo(
-          dmlc::Stream::Create(cache_info_.name_info.c_str(), "w"));
-      int tmagic = kMagic;
-      fo->Write(tmagic);
-      // Either every row has query ID or none at all
-      CHECK(qids.empty() || qids.size() == info.num_row_);
-      info.SaveBinary(fo.get());
   }
-    LOG(INFO) << "SparsePageSource Finished writing to "
-              << cache_info_.name_info;
-
-    external_prefetcher_.reset(
-        new ExternalMemoryPrefetcher<SparsePage>(cache_info_));
-  }
-
-  ~SparsePageSource() {
-    external_prefetcher_.reset();
-    TryDeleteCacheFile(cache_info_.name_info);
-    for (auto file : cache_info_.name_shards) {
-      TryDeleteCacheFile(file);
-    }
-  }
-
-  BatchSet<SparsePage> GetBatchSet() {
-    auto begin_iter = BatchIterator<SparsePage>(
-        new SparseBatchIteratorImpl<ExternalMemoryPrefetcher<SparsePage>,
-                                    SparsePage>(external_prefetcher_.get()));
-    return BatchSet<SparsePage>(begin_iter);
-  }
-  MetaInfo info;
-
- private:
-  std::unique_ptr<ExternalMemoryPrefetcher<SparsePage>> external_prefetcher_;
-  CacheInfo cache_info_;
 };
 
-class CSCPageSource {
+// A mixin for advancing the iterator.
+template <typename S>
+class PageSourceIncMixIn : public SparsePageSourceImpl<S> {
+ protected:
+  std::shared_ptr<SparsePageSource> source_;
+
  public:
-  CSCPageSource(DMatrix* src, const std::string& cache_info,
+  using SparsePageSourceImpl<S>::SparsePageSourceImpl;
-                const size_t page_size = DMatrix::kPageSize) {
+  PageSourceIncMixIn& operator++() final {
-    std::string page_type = ".col.page";
+    TryLockGuard guard{this->single_threaded_};
-    cache_info_ = ParseCacheInfo(cache_info, page_type);
+    ++(*source_);
-    for (auto file : cache_info_.name_shards) {
-      CheckCacheFileExists(file);
-    }
-    {
-      SparsePageWriter<SparsePage> writer(cache_info_.name_shards,
-                                          cache_info_.format_shards, 6);
-      std::shared_ptr<SparsePage> page;
-      writer.Alloc(&page);
-      page->Clear();
 
-      size_t bytes_write = 0;
+    ++this->count_;
-      double tstart = dmlc::GetTime();
+    this->at_end_ = source_->AtEnd();
-      for (auto& batch : src->GetBatches<SparsePage>()) {
-        page->PushCSC(batch.GetTranspose(src->Info().num_col_));
 
-        if (page->MemCostBytes() >= page_size) {
+    if (this->at_end_) {
-          bytes_write += page->MemCostBytes();
+      this->cache_info_->Commit();
-          writer.PushWrite(std::move(page));
+      if (this->n_batches_ != 0) {
-          writer.Alloc(&page);
+        CHECK_EQ(this->count_, this->n_batches_);
-          page->Clear();
-          double tdiff = dmlc::GetTime() - tstart;
-          LOG(INFO) << "Writing to " << cache_info << " in "
-                    << ((bytes_write >> 20UL) / tdiff) << " MB/s, "
-                    << (bytes_write >> 20UL) << " written";
       }
+      CHECK_GE(this->count_, 1);
+    } else {
+      this->Fetch();
     }
-      if (page->data.Size() != 0) {
+    CHECK_EQ(source_->Iter(), this->count_);
-        writer.PushWrite(std::move(page));
+    return *this;
   }
-      LOG(INFO) << "CSCPageSource: Finished writing to "
-                << cache_info_.name_info;
-    }
-    external_prefetcher_.reset(
-        new ExternalMemoryPrefetcher<CSCPage>(cache_info_));
-  }
-
-  ~CSCPageSource() {
-    external_prefetcher_.reset();
-    for (auto file : cache_info_.name_shards) {
-      TryDeleteCacheFile(file);
-    }
-  }
-
-  BatchSet<CSCPage> GetBatchSet() {
-    auto begin_iter = BatchIterator<CSCPage>(
-        new SparseBatchIteratorImpl<ExternalMemoryPrefetcher<CSCPage>, CSCPage>(
-            external_prefetcher_.get()));
-    return BatchSet<CSCPage>(begin_iter);
-  }
-
- private:
-  std::unique_ptr<ExternalMemoryPrefetcher<CSCPage>> external_prefetcher_;
-  CacheInfo cache_info_;
 };
 
-class SortedCSCPageSource {
+class CSCPageSource : public PageSourceIncMixIn<CSCPage> {
+ protected:
+  void Fetch() final {
+    if (!this->ReadCache()) {
+      auto const &csr = source_->Page();
+      this->page_.reset(new CSCPage{});
+      // we might be able to optimize this by merging transpose and pushcsc
+      this->page_->PushCSC(csr->GetTranspose(n_features_));
+      page_->SetBaseRowId(csr->base_rowid);
+      this->WriteCache();
+    }
+  }
+
  public:
-  SortedCSCPageSource(DMatrix* src, const std::string& cache_info,
+  CSCPageSource(
-                      const size_t page_size = DMatrix::kPageSize) {
+      float missing, int nthreads, bst_feature_t n_features, uint32_t n_batches,
-    std::string page_type = ".sorted.col.page";
+      std::shared_ptr<Cache> cache,
-    cache_info_ = ParseCacheInfo(cache_info, page_type);
+      std::shared_ptr<SparsePageSource> source)
-    for (auto file : cache_info_.name_shards) {
+      : PageSourceIncMixIn(missing, nthreads, n_features,
-      CheckCacheFileExists(file);
+                                     n_batches, cache) {
+    this->source_ = source;
+    this->Fetch();
   }
-    {
-      SparsePageWriter<SparsePage> writer(cache_info_.name_shards,
-                                          cache_info_.format_shards, 6);
-      std::shared_ptr<SparsePage> page;
-      writer.Alloc(&page);
-      page->Clear();
-
-      size_t bytes_write = 0;
-      double tstart = dmlc::GetTime();
-      for (auto& batch : src->GetBatches<SparsePage>()) {
-        SparsePage tmp = batch.GetTranspose(src->Info().num_col_);
-        page->PushCSC(tmp);
-        page->SortRows();
-
-        if (page->MemCostBytes() >= page_size) {
-          bytes_write += page->MemCostBytes();
-          writer.PushWrite(std::move(page));
-          writer.Alloc(&page);
-          page->Clear();
-          double tdiff = dmlc::GetTime() - tstart;
-          LOG(INFO) << "Writing to " << cache_info << " in "
-                    << ((bytes_write >> 20UL) / tdiff) << " MB/s, "
-                    << (bytes_write >> 20UL) << " written";
-        }
-      }
-      if (page->data.Size() != 0) {
-        writer.PushWrite(std::move(page));
-      }
-      LOG(INFO) << "SortedCSCPageSource: Finished writing to "
-                << cache_info_.name_info;
-    }
-    external_prefetcher_.reset(
-        new ExternalMemoryPrefetcher<SortedCSCPage>(cache_info_));
-  }
-  ~SortedCSCPageSource() {
-    external_prefetcher_.reset();
-    for (auto file : cache_info_.name_shards) {
-      TryDeleteCacheFile(file);
-    }
-  }
-
-  BatchSet<SortedCSCPage> GetBatchSet() {
-    auto begin_iter = BatchIterator<SortedCSCPage>(
-        new SparseBatchIteratorImpl<ExternalMemoryPrefetcher<SortedCSCPage>,
-                                    SortedCSCPage>(external_prefetcher_.get()));
-    return BatchSet<SortedCSCPage>(begin_iter);
-  }
-
- private:
-  std::unique_ptr<ExternalMemoryPrefetcher<SortedCSCPage>> external_prefetcher_;
-  CacheInfo cache_info_;
 };
 
+class SortedCSCPageSource : public PageSourceIncMixIn<SortedCSCPage> {
+ protected:
+  void Fetch() final {
+    if (!this->ReadCache()) {
+      auto const &csr = this->source_->Page();
+      this->page_.reset(new SortedCSCPage{});
+      // we might be able to optimize this by merging transpose and pushcsc
+      this->page_->PushCSC(csr->GetTranspose(n_features_));
+      CHECK_EQ(this->page_->Size(), n_features_);
+      CHECK_EQ(this->page_->data.Size(), csr->data.Size());
+      this->page_->SortRows();
+      page_->SetBaseRowId(csr->base_rowid);
+      this->WriteCache();
+    }
+  }
+
+ public:
+  SortedCSCPageSource(float missing, int nthreads, bst_feature_t n_features,
+                      uint32_t n_batches, std::shared_ptr<Cache> cache,
+                      std::shared_ptr<SparsePageSource> source)
+      : PageSourceIncMixIn(missing, nthreads, n_features, n_batches, cache) {
+    this->source_ = source;
+    this->Fetch();
+  }
+};
 }  // namespace data
 }  // namespace xgboost
 #endif  // XGBOOST_DATA_SPARSE_PAGE_SOURCE_H_

src/data/sparse_page_writer.h

@@ -63,103 +63,6 @@ inline SparsePageFormat<T>* CreatePageFormat(const std::string& name) {
   return (e->body)();
 }
 
-#if DMLC_ENABLE_STD_THREAD
-/*!
- * \brief A threaded writer to write sparse batch page to sharded files.
- * @tparam T Type of the page.
- */
-template<typename T>
-class SparsePageWriter {
- public:
-  /*!
-   * \brief constructor
-   * \param name_shards name of shard files.
-   * \param format_shards format of each shard.
-   * \param extra_buffer_capacity Extra buffer capacity before block.
-   */
-  explicit SparsePageWriter(const std::vector<std::string>& name_shards,
-                            const std::vector<std::string>& format_shards,
-                            size_t extra_buffer_capacity)
-      : num_free_buffer_(extra_buffer_capacity + name_shards.size()),
-        clock_ptr_(0),
-        workers_(name_shards.size()),
-        qworkers_(name_shards.size()) {
-    CHECK_EQ(name_shards.size(), format_shards.size());
-    // start writer threads
-    for (size_t i = 0; i < name_shards.size(); ++i) {
-      std::string name_shard = name_shards[i];
-      std::string format_shard = format_shards[i];
-      auto* wqueue = &qworkers_[i];
-      workers_[i].reset(new std::thread(
-          [this, name_shard, format_shard, wqueue]() {
-            std::unique_ptr<dmlc::Stream> fo(dmlc::Stream::Create(name_shard.c_str(), "w"));
-            std::unique_ptr<SparsePageFormat<T>> fmt(CreatePageFormat<T>(format_shard));
-            fo->Write(format_shard);
-            std::shared_ptr<T> page;
-            while (wqueue->Pop(&page)) {
-              if (page == nullptr) break;
-              fmt->Write(*page, fo.get());
-              qrecycle_.Push(std::move(page));
-            }
-            fo.reset(nullptr);
-            LOG(INFO) << "SparsePageWriter Finished writing to " << name_shard;
-          }));
-    }
-  }
-
-  /*! \brief destructor, will close the files automatically */
-  ~SparsePageWriter() {
-    for (auto& queue : qworkers_) {
-      // use nullptr to signal termination.
-      std::shared_ptr<T> sig(nullptr);
-      queue.Push(std::move(sig));
-    }
-    for (auto& thread : workers_) {
-      thread->join();
-    }
-  }
-
-  /*!
-   * \brief Push a write job to the writer.
-   * This function won't block,
-   * writing is done by another thread inside writer.
-   * \param page The page to be written
-   */
-  void PushWrite(std::shared_ptr<T>&& page) {
-    qworkers_[clock_ptr_].Push(std::move(page));
-    clock_ptr_ = (clock_ptr_ + 1) % workers_.size();
-  }
-
-  /*!
-   * \brief Allocate a page to store results.
-   *  This function can block when the writer is too slow and buffer pages
-   *  have not yet been recycled.
-   * \param out_page Used to store the allocated pages.
-   */
-  void Alloc(std::shared_ptr<T>* out_page) {
-    CHECK(*out_page == nullptr);
-    if (num_free_buffer_ != 0) {
-      out_page->reset(new T());
-      --num_free_buffer_;
-    } else {
-      CHECK(qrecycle_.Pop(out_page));
-    }
-  }
-
- private:
-  /*! \brief number of allocated pages */
-  size_t num_free_buffer_;
-  /*! \brief clock_pointer */
-  size_t clock_ptr_;
-  /*! \brief writer threads */
-  std::vector<std::unique_ptr<std::thread>> workers_;
-  /*! \brief recycler queue */
-  dmlc::ConcurrentBlockingQueue<std::shared_ptr<T>> qrecycle_;
-  /*! \brief worker threads */
-  std::vector<dmlc::ConcurrentBlockingQueue<std::shared_ptr<T>>> qworkers_;
-};
-#endif  // DMLC_ENABLE_STD_THREAD
-
 /*!
  * \brief Registry entry for sparse page format.
  */

src/tree/gpu_hist/gradient_based_sampler.cu

@@ -131,7 +131,7 @@ class PoissonSampling : public thrust::binary_function<GradientPair, size_t, Gra
       if (rnd_(i) <= p) {
         return gpair / p;
       } else {
-        return GradientPair();
+        return {};
       }
     }
   }
@@ -143,13 +143,13 @@ class PoissonSampling : public thrust::binary_function<GradientPair, size_t, Gra
   CombineGradientPair combine_;
 };
 
-NoSampling::NoSampling(EllpackPageImpl* page) : page_(page) {}
+NoSampling::NoSampling(EllpackPageImpl const* page) : page_(page) {}
 
 GradientBasedSample NoSampling::Sample(common::Span<GradientPair> gpair, DMatrix* dmat) {
   return {dmat->Info().num_row_, page_, gpair};
 }
 
-ExternalMemoryNoSampling::ExternalMemoryNoSampling(EllpackPageImpl* page,
+ExternalMemoryNoSampling::ExternalMemoryNoSampling(EllpackPageImpl const* page,
                                                    size_t n_rows,
                                                    const BatchParam& batch_param)
     : batch_param_(batch_param),
@@ -171,7 +171,7 @@ GradientBasedSample ExternalMemoryNoSampling::Sample(common::Span<GradientPair>
   return {dmat->Info().num_row_, page_.get(), gpair};
 }
 
-UniformSampling::UniformSampling(EllpackPageImpl* page, float subsample)
+UniformSampling::UniformSampling(EllpackPageImpl const* page, float subsample)
     : page_(page), subsample_(subsample) {}
 
 GradientBasedSample UniformSampling::Sample(common::Span<GradientPair> gpair, DMatrix* dmat) {
@@ -183,7 +183,7 @@ GradientBasedSample UniformSampling::Sample(common::Span<GradientPair> gpair, DM
   return {dmat->Info().num_row_, page_, gpair};
 }
 
-ExternalMemoryUniformSampling::ExternalMemoryUniformSampling(EllpackPageImpl* page,
+ExternalMemoryUniformSampling::ExternalMemoryUniformSampling(EllpackPageImpl const* page,
                                                              size_t n_rows,
                                                              const BatchParam& batch_param,
                                                              float subsample)
@@ -231,7 +231,7 @@ GradientBasedSample ExternalMemoryUniformSampling::Sample(common::Span<GradientP
   return {sample_rows, page_.get(), dh::ToSpan(gpair_)};
 }
 
-GradientBasedSampling::GradientBasedSampling(EllpackPageImpl* page,
+GradientBasedSampling::GradientBasedSampling(EllpackPageImpl const* page,
                                              size_t n_rows,
                                              const BatchParam&,
                                              float subsample)
@@ -257,7 +257,7 @@ GradientBasedSample GradientBasedSampling::Sample(common::Span<GradientPair> gpa
 }
 
 ExternalMemoryGradientBasedSampling::ExternalMemoryGradientBasedSampling(
-    EllpackPageImpl* page,
+    EllpackPageImpl const* page,
     size_t n_rows,
     const BatchParam& batch_param,
     float subsample)
@@ -313,7 +313,7 @@ GradientBasedSample ExternalMemoryGradientBasedSampling::Sample(common::Span<Gra
   return {sample_rows, page_.get(), dh::ToSpan(gpair_)};
 }
 
-GradientBasedSampler::GradientBasedSampler(EllpackPageImpl* page,
+GradientBasedSampler::GradientBasedSampler(EllpackPageImpl const* page,
                                            size_t n_rows,
                                            const BatchParam& batch_param,
                                            float subsample,

src/tree/gpu_hist/gradient_based_sampler.cuh

@@ -16,7 +16,7 @@ struct GradientBasedSample {
   /*!\brief Number of sampled rows. */
   size_t sample_rows;
   /*!\brief Sampled rows in ELLPACK format. */
-  EllpackPageImpl* page;
+  EllpackPageImpl const* page;
   /*!\brief Gradient pairs for the sampled rows. */
   common::Span<GradientPair> gpair;
 };
@@ -31,17 +31,17 @@ class SamplingStrategy {
 /*! \brief No sampling in in-memory mode. */
 class NoSampling : public SamplingStrategy {
  public:
-  explicit NoSampling(EllpackPageImpl* page);
+  explicit NoSampling(EllpackPageImpl const* page);
   GradientBasedSample Sample(common::Span<GradientPair> gpair, DMatrix* dmat) override;
 
  private:
-  EllpackPageImpl* page_;
+  EllpackPageImpl const* page_;
 };
 
 /*! \brief No sampling in external memory mode. */
 class ExternalMemoryNoSampling : public SamplingStrategy {
  public:
-  ExternalMemoryNoSampling(EllpackPageImpl* page,
+  ExternalMemoryNoSampling(EllpackPageImpl const* page,
                            size_t n_rows,
                            const BatchParam& batch_param);
   GradientBasedSample Sample(common::Span<GradientPair> gpair, DMatrix* dmat) override;
@@ -55,25 +55,25 @@ class ExternalMemoryNoSampling : public SamplingStrategy {
 /*! \brief Uniform sampling in in-memory mode. */
 class UniformSampling : public SamplingStrategy {
  public:
-  UniformSampling(EllpackPageImpl* page, float subsample);
+  UniformSampling(EllpackPageImpl const* page, float subsample);
   GradientBasedSample Sample(common::Span<GradientPair> gpair, DMatrix* dmat) override;
 
  private:
-  EllpackPageImpl* page_;
+  EllpackPageImpl const* page_;
   float subsample_;
 };
 
 /*! \brief No sampling in external memory mode. */
 class ExternalMemoryUniformSampling : public SamplingStrategy {
  public:
-  ExternalMemoryUniformSampling(EllpackPageImpl* page,
+  ExternalMemoryUniformSampling(EllpackPageImpl const* page,
                                 size_t n_rows,
                                 const BatchParam& batch_param,
                                 float subsample);
   GradientBasedSample Sample(common::Span<GradientPair> gpair, DMatrix* dmat) override;
 
  private:
-  EllpackPageImpl* original_page_;
+  EllpackPageImpl const* original_page_;
   BatchParam batch_param_;
   float subsample_;
   std::unique_ptr<EllpackPageImpl> page_;
@@ -84,14 +84,14 @@ class ExternalMemoryUniformSampling : public SamplingStrategy {
 /*! \brief Gradient-based sampling in in-memory mode.. */
 class GradientBasedSampling : public SamplingStrategy {
  public:
-  GradientBasedSampling(EllpackPageImpl* page,
+  GradientBasedSampling(EllpackPageImpl const* page,
                         size_t n_rows,
                         const BatchParam& batch_param,
                         float subsample);
   GradientBasedSample Sample(common::Span<GradientPair> gpair, DMatrix* dmat) override;
 
  private:
-  EllpackPageImpl* page_;
+  EllpackPageImpl const* page_;
   float subsample_;
   dh::caching_device_vector<float> threshold_;
   dh::caching_device_vector<float> grad_sum_;
@@ -100,14 +100,14 @@ class GradientBasedSampling : public SamplingStrategy {
 /*! \brief Gradient-based sampling in external memory mode.. */
 class ExternalMemoryGradientBasedSampling : public SamplingStrategy {
  public:
-  ExternalMemoryGradientBasedSampling(EllpackPageImpl* page,
+  ExternalMemoryGradientBasedSampling(EllpackPageImpl const* page,
                                       size_t n_rows,
                                       const BatchParam& batch_param,
                                       float subsample);
   GradientBasedSample Sample(common::Span<GradientPair> gpair, DMatrix* dmat) override;
 
  private:
-  EllpackPageImpl* original_page_;
+  EllpackPageImpl const* original_page_;
   BatchParam batch_param_;
   float subsample_;
   dh::caching_device_vector<float> threshold_;
@@ -128,7 +128,7 @@ class ExternalMemoryGradientBasedSampling : public SamplingStrategy {
  */
 class GradientBasedSampler {
  public:
-  GradientBasedSampler(EllpackPageImpl* page,
+  GradientBasedSampler(EllpackPageImpl const* page,
                        size_t n_rows,
                        const BatchParam& batch_param,
                        float subsample,

src/tree/updater_gpu_hist.cu

@@ -163,7 +163,7 @@ class DeviceHistogram {
 template <typename GradientSumT>
 struct GPUHistMakerDevice {
   int device_id;
-  EllpackPageImpl* page;
+  EllpackPageImpl const* page;
   common::Span<FeatureType const> feature_types;
   BatchParam batch_param;
 
@@ -199,7 +199,7 @@ struct GPUHistMakerDevice {
   dh::caching_device_vector<uint32_t> node_categories;
 
   GPUHistMakerDevice(int _device_id,
-                     EllpackPageImpl* _page,
+                     EllpackPageImpl const* _page,
                      common::Span<FeatureType const> _feature_types,
                      bst_uint _n_rows,
                      TrainParam _param,
@@ -488,7 +488,7 @@ struct GPUHistMakerDevice {
     }
   }
 
-  void FinalisePositionInPage(EllpackPageImpl *page,
+  void FinalisePositionInPage(EllpackPageImpl const *page,
                               const common::Span<RegTree::Node> d_nodes,
                               common::Span<FeatureType const> d_feature_types,
                               common::Span<uint32_t const> categories,
@@ -812,7 +812,6 @@ class GPUHistMakerSpecialised {
     BatchParam batch_param{
       device_,
       param_.max_bin,
-      generic_param_->gpu_page_size
     };
     auto page = (*dmat->GetBatches<EllpackPage>(batch_param).begin()).Impl();
     dh::safe_cuda(cudaSetDevice(device_));

tests/cpp/common/test_column_matrix.cc

@@ -125,12 +125,10 @@ TEST(DenseColumnWithMissing, Test) {
 }
 
 void TestGHistIndexMatrixCreation(size_t nthreads) {
-  dmlc::TemporaryDirectory tmpdir;
-  std::string filename = tmpdir.path + "/big.libsvm";
   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, kPageSize, filename) };
+  std::unique_ptr<DMatrix> dmat{ CreateSparsePageDMatrix(kEntries) };
   omp_set_num_threads(nthreads);
   GHistIndexMatrix gmat(dmat.get(), 256);
 }

tests/cpp/common/test_hist_util.h

@@ -83,7 +83,7 @@ inline std::shared_ptr<DMatrix> GetExternalMemoryDMatrixFromData(
   }
   fo.close();
   return std::shared_ptr<DMatrix>(DMatrix::Load(
-      tmp_file + "#" + tmp_file + ".cache", true, false, "auto", page_size));
+      tmp_file + "#" + tmp_file + ".cache", true, false, "auto"));
 }
 
 // Test that elements are approximately equally distributed among bins

tests/cpp/data/test_data.cc

@@ -59,12 +59,9 @@ TEST(SparsePage, PushCSC) {
 }
 
 TEST(SparsePage, PushCSCAfterTranspose) {
-  dmlc::TemporaryDirectory tmpdir;
-  std::string filename = tmpdir.path + "/big.libsvm";
   size_t constexpr kPageSize = 1024, kEntriesPerCol = 3;
   size_t constexpr kEntries = kPageSize * kEntriesPerCol * 2;
-  std::unique_ptr<DMatrix> dmat =
+  std::unique_ptr<DMatrix> dmat = CreateSparsePageDMatrix(kEntries);
-      CreateSparsePageDMatrix(kEntries, 64UL, filename);
   const int ncols = dmat->Info().num_col_;
   SparsePage page; // Consolidated sparse page
   for (const auto &batch : dmat->GetBatches<xgboost::SparsePage>()) {
@@ -76,12 +73,12 @@ TEST(SparsePage, PushCSCAfterTranspose) {
   // Make sure that the final sparse page has the right number of entries
   ASSERT_EQ(kEntries, page.data.Size());
 
-  // The feature value for a feature in each row should be identical, as that is
+  page.SortRows();
-  // how the dmatrix has been created
+  auto v = page.GetView();
-  for (size_t i = 0; i < page.Size(); ++i) {
+  for (size_t i = 0; i < v.Size(); ++i) {
-    auto inst = page.GetView()[i];
+    auto column = v[i];
-    for (size_t j = 1; j < inst.size(); ++j) {
+    for (size_t j = 1; j < column.size(); ++j) {
-      ASSERT_EQ(inst[0].fvalue, inst[j].fvalue);
+      ASSERT_GE(column[j].fvalue, column[j-1].fvalue);
     }
   }
 }

tests/cpp/data/test_ellpack_page.cu

@@ -142,7 +142,7 @@ TEST(EllpackPage, Copy) {
   dmlc::TemporaryDirectory tmpdir;
   std::unique_ptr<DMatrix>
       dmat(CreateSparsePageDMatrixWithRC(kRows, kCols, kPageSize, true, tmpdir));
-  BatchParam param{0, 256, kPageSize};
+  BatchParam param{0, 256};
   auto page = (*dmat->GetBatches<EllpackPage>(param).begin()).Impl();
 
   // Create an empty result page.
@@ -188,7 +188,7 @@ TEST(EllpackPage, Compact) {
   dmlc::TemporaryDirectory tmpdir;
   std::unique_ptr<DMatrix>
       dmat(CreateSparsePageDMatrixWithRC(kRows, kCols, kPageSize, true, tmpdir));
-  BatchParam param{0, 256, kPageSize};
+  BatchParam param{0, 256};
   auto page = (*dmat->GetBatches<EllpackPage>(param).begin()).Impl();
 
   // Create an empty result page.
@@ -212,7 +212,7 @@ TEST(EllpackPage, Compact) {
   std::vector<bst_float> row_result(kCols);
   for (auto& page : dmat->GetBatches<EllpackPage>(param)) {
     auto impl = page.Impl();
-    EXPECT_EQ(impl->base_rowid, current_row);
+    ASSERT_EQ(impl->base_rowid, current_row);
 
     for (size_t i = 0; i < impl->Size(); i++) {
       size_t compacted_row = row_indexes_h[current_row];

tests/cpp/data/test_file_iterator.cc

@@ -0,0 +1,46 @@
+/*!
+ * Copyright 2021 XGBoost contributors
+ */
+#include <gtest/gtest.h>
+#include <dmlc/filesystem.h>
+
+#include <memory>
+
+#include "../../../src/data/file_iterator.h"
+#include "../../../src/data/proxy_dmatrix.h"
+#include "../../../src/data/adapter.h"
+#include "../helpers.h"
+
+namespace xgboost {
+namespace data {
+TEST(FileIterator, Basic) {
+  auto check_n_features = [](FileIterator *iter) {
+    size_t n_features = 0;
+    iter->Reset();
+    while (iter->Next()) {
+      auto proxy = MakeProxy(iter->Proxy());
+      auto csr = dmlc::get<std::shared_ptr<CSRArrayAdapter>>(proxy->Adapter());
+      n_features = std::max(n_features, csr->NumColumns());
+    }
+    ASSERT_EQ(n_features, 5);
+  };
+
+  dmlc::TemporaryDirectory tmpdir;
+  {
+    auto zpath = tmpdir.path + "/0-based.svm";
+    CreateBigTestData(zpath, 3 * 64, true);
+    zpath += "?indexing_mode=0";
+    FileIterator iter{zpath, 0, 1, "libsvm"};
+    check_n_features(&iter);
+  }
+
+  {
+    auto opath = tmpdir.path + "/1-based.svm";
+    CreateBigTestData(opath, 3 * 64, false);
+    opath += "?indexing_mode=1";
+    FileIterator iter{opath, 0, 1, "libsvm"};
+    check_n_features(&iter);
+  }
+}
+}  // namespace data
+}  // namespace xgboost

tests/cpp/data/test_iterative_device_dmatrix.cu

@@ -142,7 +142,7 @@ TEST(IterativeDeviceDMatrix, RowMajorMissing) {
   IterativeDeviceDMatrix m(
       &iter, iter.Proxy(), Reset, Next, std::numeric_limits<float>::quiet_NaN(),
       0, 256);
-  auto &ellpack = *m.GetBatches<EllpackPage>({0, 256, 0}).begin();
+  auto &ellpack = *m.GetBatches<EllpackPage>({0, 256}).begin();
   auto impl = ellpack.Impl();
   common::CompressedIterator<uint32_t> iterator(
       impl->gidx_buffer.HostVector().data(), impl->NumSymbols());

tests/cpp/data/test_metainfo.cc

@@ -260,7 +260,7 @@ TEST(MetaInfo, HostExtend) {
   lhs.SetInfo("group", groups.data(), xgboost::DataType::kUInt32, groups.size());
   rhs.SetInfo("group", groups.data(), xgboost::DataType::kUInt32, groups.size());
 
-  lhs.Extend(rhs, true);
+  lhs.Extend(rhs, true, true);
   ASSERT_EQ(lhs.num_row_, kRows * 2);
   ASSERT_TRUE(lhs.labels_.HostCanRead());
   ASSERT_TRUE(rhs.labels_.HostCanRead());

tests/cpp/data/test_metainfo.cu

@@ -141,7 +141,7 @@ TEST(MetaInfo, DeviceExtend) {
   lhs.num_row_ = kRows;
   rhs.num_row_ = kRows;
 
-  lhs.Extend(rhs, true);
+  lhs.Extend(rhs, true, true);
   ASSERT_EQ(lhs.num_row_, kRows * 2);
   ASSERT_FALSE(lhs.labels_.HostCanRead());
 

tests/cpp/data/test_sparse_page_dmatrix.cc

@@ -6,11 +6,100 @@
 #include <future>
 #include "../../../src/common/io.h"
 #include "../../../src/data/adapter.h"
+#include "../../../src/data/simple_dmatrix.h"
 #include "../../../src/data/sparse_page_dmatrix.h"
+#include "../../../src/data/file_iterator.h"
 #include "../helpers.h"
 
 using namespace xgboost;  // NOLINT
 
+template <typename Page>
+void TestSparseDMatrixLoadFile() {
+  dmlc::TemporaryDirectory tmpdir;
+  auto opath = tmpdir.path + "/1-based.svm";
+  CreateBigTestData(opath, 3 * 64, false);
+  opath += "?indexing_mode=1";
+  data::FileIterator iter{opath, 0, 1, "libsvm"};
+  data::SparsePageDMatrix m{&iter,
+                            iter.Proxy(),
+                            data::fileiter::Reset,
+                            data::fileiter::Next,
+                            std::numeric_limits<float>::quiet_NaN(),
+                            1,
+                            "cache"};
+  ASSERT_EQ(m.Info().num_col_, 5);
+  ASSERT_EQ(m.Info().num_row_, 64);
+
+  std::unique_ptr<dmlc::Parser<uint32_t>> parser(
+      dmlc::Parser<uint32_t>::Create(opath.c_str(), 0, 1, "auto"));
+  auto adapter = data::FileAdapter{parser.get()};
+
+  data::SimpleDMatrix simple{&adapter, std::numeric_limits<float>::quiet_NaN(),
+                             1};
+  Page out;
+  for (auto const& page : m.GetBatches<Page>()) {
+    if (std::is_same<Page, SparsePage>::value) {
+      out.Push(page);
+    } else {
+      out.PushCSC(page);
+    }
+  }
+  ASSERT_EQ(m.Info().num_col_, simple.Info().num_col_);
+  ASSERT_EQ(m.Info().num_row_, simple.Info().num_row_);
+
+  for (auto const& page : simple.GetBatches<Page>()) {
+    ASSERT_EQ(page.offset.HostVector(), out.offset.HostVector());
+    for (size_t i = 0; i < page.data.Size(); ++i) {
+      ASSERT_EQ(page.data.HostVector()[i].fvalue, out.data.HostVector()[i].fvalue);
+    }
+  }
+}
+
+TEST(SparsePageDMatrix, LoadFile) {
+  TestSparseDMatrixLoadFile<SparsePage>();
+  TestSparseDMatrixLoadFile<CSCPage>();
+  TestSparseDMatrixLoadFile<SortedCSCPage>();
+}
+
+// allow caller to retain pages so they can process multiple pages at the same time.
+template <typename Page>
+void TestRetainPage() {
+  auto m = CreateSparsePageDMatrix(10000);
+  auto batches = m->GetBatches<Page>();
+  auto begin = batches.begin();
+  auto end = batches.end();
+
+  std::vector<Page> pages;
+  std::vector<std::shared_ptr<Page const>> iterators;
+  for (auto it = begin; it != end; ++it) {
+    iterators.push_back(it.Page());
+    pages.emplace_back(Page{});
+    if (std::is_same<Page, SparsePage>::value) {
+      pages.back().Push(*it);
+    } else {
+      pages.back().PushCSC(*it);
+    }
+    ASSERT_EQ(pages.back().Size(), (*it).Size());
+  }
+  ASSERT_GE(iterators.size(), 2);
+
+  for (size_t i = 0; i < iterators.size(); ++i) {
+    ASSERT_EQ((*iterators[i]).Size(), pages.at(i).Size());
+    ASSERT_EQ((*iterators[i]).data.HostVector(), pages.at(i).data.HostVector());
+  }
+
+  // make sure it's const and the caller can not modify the content of page.
+  for (auto& page : m->GetBatches<Page>()) {
+    static_assert(std::is_const<std::remove_reference_t<decltype(page)>>::value, "");
+  }
+}
+
+TEST(SparsePageDMatrix, RetainSparsePage) {
+  TestRetainPage<SparsePage>();
+  TestRetainPage<CSCPage>();
+  TestRetainPage<SortedCSCPage>();
+}
+
 TEST(SparsePageDMatrix, MetaInfo) {
   dmlc::TemporaryDirectory tempdir;
   const std::string tmp_file = tempdir.path + "/simple.libsvm";
@@ -19,8 +108,6 @@ TEST(SparsePageDMatrix, MetaInfo) {
 
   xgboost::DMatrix *dmat = xgboost::DMatrix::Load(
       tmp_file + "#" + tmp_file + ".cache", false, false);
-  std::cout << tmp_file << std::endl;
-  EXPECT_TRUE(FileExists(tmp_file + ".cache"));
 
   // Test the metadata that was parsed
   EXPECT_EQ(dmat->Info().num_row_, 8ul);
@@ -32,10 +119,7 @@ TEST(SparsePageDMatrix, MetaInfo) {
 }
 
 TEST(SparsePageDMatrix, RowAccess) {
-  dmlc::TemporaryDirectory tmpdir;
+  std::unique_ptr<xgboost::DMatrix> dmat = xgboost::CreateSparsePageDMatrix(24);
-  std::string filename = tmpdir.path + "/big.libsvm";
-  std::unique_ptr<xgboost::DMatrix> dmat =
-      xgboost::CreateSparsePageDMatrix(24, 4, filename);
 
   // Test the data read into the first row
   auto &batch = *dmat->GetBatches<xgboost::SparsePage>().begin();
@@ -43,7 +127,7 @@ TEST(SparsePageDMatrix, RowAccess) {
   auto first_row = page[0];
   ASSERT_EQ(first_row.size(), 3ul);
   EXPECT_EQ(first_row[2].index, 2u);
-  EXPECT_EQ(first_row[2].fvalue, 20);
+  EXPECT_NEAR(first_row[2].fvalue, 0.986566, 1e-4);
 }
 
 TEST(SparsePageDMatrix, ColAccess) {
@@ -54,55 +138,46 @@ TEST(SparsePageDMatrix, ColAccess) {
       xgboost::DMatrix::Load(tmp_file + "#" + tmp_file + ".cache", true, false);
 
   // Loop over the batches and assert the data is as expected
+  size_t iter = 0;
   for (auto const &col_batch : dmat->GetBatches<xgboost::SortedCSCPage>()) {
     auto col_page = col_batch.GetView();
-    EXPECT_EQ(col_page.Size(), dmat->Info().num_col_);
+    ASSERT_EQ(col_page.Size(), dmat->Info().num_col_);
-    EXPECT_EQ(col_page[1][0].fvalue, 10.0f);
+    if (iter == 1) {
-    EXPECT_EQ(col_page[1].size(), 1);
+      ASSERT_EQ(col_page[0][0].fvalue, 0.f);
+      ASSERT_EQ(col_page[3][0].fvalue, 30.f);
+      ASSERT_EQ(col_page[3][0].index, 1);
+      ASSERT_EQ(col_page[3].size(), 1);
+    } else {
+      ASSERT_EQ(col_page[1][0].fvalue, 10.0f);
+      ASSERT_EQ(col_page[1].size(), 1);
+    }
+    CHECK_LE(col_batch.base_rowid, dmat->Info().num_row_);
+    ++iter;
   }
 
   // Loop over the batches and assert the data is as expected
+  iter = 0;
   for (auto const &col_batch : dmat->GetBatches<xgboost::CSCPage>()) {
     auto col_page = col_batch.GetView();
     EXPECT_EQ(col_page.Size(), dmat->Info().num_col_);
+    if (iter == 0) {
       EXPECT_EQ(col_page[1][0].fvalue, 10.0f);
       EXPECT_EQ(col_page[1].size(), 1);
+    } else {
+      EXPECT_EQ(col_page[3][0].fvalue, 30.f);
+      EXPECT_EQ(col_page[3].size(), 1);
+    }
+    iter++;
   }
-
-  EXPECT_TRUE(FileExists(tmp_file + ".cache"));
-  EXPECT_TRUE(FileExists(tmp_file + ".cache.row.page"));
-  EXPECT_TRUE(FileExists(tmp_file + ".cache.col.page"));
-  EXPECT_TRUE(FileExists(tmp_file + ".cache.sorted.col.page"));
-
   delete dmat;
-
-  EXPECT_FALSE(FileExists(tmp_file + ".cache"));
-  EXPECT_FALSE(FileExists(tmp_file + ".cache.row.page"));
-  EXPECT_FALSE(FileExists(tmp_file + ".cache.col.page"));
-  EXPECT_FALSE(FileExists(tmp_file + ".cache.sorted.col.page"));
-}
-
-TEST(SparsePageDMatrix, ExistingCacheFile) {
-  dmlc::TemporaryDirectory tmpdir;
-  std::string filename = tmpdir.path + "/big.libsvm";
-  size_t constexpr kPageSize = 64, kEntriesPerCol = 3;
-  size_t constexpr kEntries = kPageSize * kEntriesPerCol * 2;
-  std::unique_ptr<xgboost::DMatrix> dmat =
-      xgboost::CreateSparsePageDMatrix(kEntries, kPageSize, filename);
-  EXPECT_ANY_THROW({
-    std::unique_ptr<xgboost::DMatrix> dmat2 =
-        xgboost::CreateSparsePageDMatrix(kEntries, kPageSize, filename);
-  });
 }
 
 TEST(SparsePageDMatrix, ThreadSafetyException) {
-  dmlc::TemporaryDirectory tmpdir;
+  size_t constexpr kEntriesPerCol = 3;
-  std::string filename = tmpdir.path + "/test";
+  size_t constexpr kEntries = 64 * kEntriesPerCol * 2;
-  size_t constexpr kPageSize = 64, kEntriesPerCol = 3;
-  size_t constexpr kEntries = kPageSize * kEntriesPerCol * 2;
 
   std::unique_ptr<xgboost::DMatrix> dmat =
-      xgboost::CreateSparsePageDMatrix(kEntries, kPageSize, filename);
+      xgboost::CreateSparsePageDMatrix(kEntries);
 
   int threads = 1000;
 
@@ -134,13 +209,10 @@ TEST(SparsePageDMatrix, ThreadSafetyException) {
 
 // Multi-batches access
 TEST(SparsePageDMatrix, ColAccessBatches) {
-  dmlc::TemporaryDirectory tmpdir;
-  std::string filename = tmpdir.path + "/big.libsvm";
   size_t constexpr kPageSize = 1024, kEntriesPerCol = 3;
   size_t constexpr kEntries = kPageSize * kEntriesPerCol * 2;
   // Create multiple sparse pages
-  std::unique_ptr<xgboost::DMatrix> dmat{
+  std::unique_ptr<xgboost::DMatrix> dmat{xgboost::CreateSparsePageDMatrix(kEntries)};
-      xgboost::CreateSparsePageDMatrix(kEntries, kPageSize, filename)};
   auto n_threads = omp_get_max_threads();
   omp_set_num_threads(16);
   for (auto const &page : dmat->GetBatches<xgboost::CSCPage>()) {
@@ -149,234 +221,37 @@ TEST(SparsePageDMatrix, ColAccessBatches) {
   omp_set_num_threads(n_threads);
 }
 
-TEST(SparsePageDMatrix, Empty) {
+auto TestSparsePageDMatrixDeterminism(int32_t threads) {
-  dmlc::TemporaryDirectory tempdir;
-  const std::string tmp_file = tempdir.path + "/simple.libsvm";
-  std::vector<float> data{};
-  std::vector<unsigned> feature_idx = {};
-  std::vector<size_t> row_ptr = {};
-
-  {
-    data::CSRAdapter csr_adapter(row_ptr.data(), feature_idx.data(),
-                                 data.data(), 0, 0, 0);
-    data::SparsePageDMatrix dmat(
-        &csr_adapter, std::numeric_limits<float>::quiet_NaN(), 1, tmp_file);
-    EXPECT_EQ(dmat.Info().num_nonzero_, 0);
-    EXPECT_EQ(dmat.Info().num_row_, 0);
-    EXPECT_EQ(dmat.Info().num_col_, 0);
-    for (auto &batch : dmat.GetBatches<SparsePage>()) {
-      EXPECT_EQ(batch.Size(), 0);
-    }
-  }
-
-  {
-    data::DenseAdapter dense_adapter(nullptr, 0, 0);
-    data::SparsePageDMatrix dmat2(
-        &dense_adapter, std::numeric_limits<float>::quiet_NaN(), 1, tmp_file);
-    EXPECT_EQ(dmat2.Info().num_nonzero_, 0);
-    EXPECT_EQ(dmat2.Info().num_row_, 0);
-    EXPECT_EQ(dmat2.Info().num_col_, 0);
-    for (auto &batch : dmat2.GetBatches<SparsePage>()) {
-      EXPECT_EQ(batch.Size(), 0);
-    }
-  }
-  {
-    data::CSCAdapter csc_adapter(nullptr, nullptr, nullptr, 0, 0);
-    data::SparsePageDMatrix dmat3(
-        &csc_adapter, std::numeric_limits<float>::quiet_NaN(), 1, tmp_file);
-    EXPECT_EQ(dmat3.Info().num_nonzero_, 0);
-    EXPECT_EQ(dmat3.Info().num_row_, 0);
-    EXPECT_EQ(dmat3.Info().num_col_, 0);
-    for (auto &batch : dmat3.GetBatches<SparsePage>()) {
-      EXPECT_EQ(batch.Size(), 0);
-    }
-  }
-}
-
-TEST(SparsePageDMatrix, MissingData) {
-  dmlc::TemporaryDirectory tempdir;
-  const std::string tmp_file = tempdir.path + "/simple.libsvm";
-  std::vector<float> data{0.0, std::nanf(""), 1.0};
-  std::vector<unsigned> feature_idx = {0, 1, 0};
-  std::vector<size_t> row_ptr = {0, 2, 3};
-
-  data::CSRAdapter adapter(row_ptr.data(), feature_idx.data(), data.data(), 2,
-                           3, 2);
-  data::SparsePageDMatrix dmat(
-      &adapter, std::numeric_limits<float>::quiet_NaN(), 1, tmp_file);
-  EXPECT_EQ(dmat.Info().num_nonzero_, 2);
-
-  const std::string tmp_file2 = tempdir.path + "/simple2.libsvm";
-  data::SparsePageDMatrix dmat2(&adapter, 1.0, 1, tmp_file2);
-  EXPECT_EQ(dmat2.Info().num_nonzero_, 1);
-}
-
-TEST(SparsePageDMatrix, EmptyRow) {
-  dmlc::TemporaryDirectory tempdir;
-  const std::string tmp_file = tempdir.path + "/simple.libsvm";
-  std::vector<float> data{0.0, 1.0};
-  std::vector<unsigned> feature_idx = {0, 1};
-  std::vector<size_t> row_ptr = {0, 2, 2};
-
-  data::CSRAdapter adapter(row_ptr.data(), feature_idx.data(), data.data(), 2,
-                           2, 2);
-  data::SparsePageDMatrix dmat(
-      &adapter, std::numeric_limits<float>::quiet_NaN(), 1, tmp_file);
-  EXPECT_EQ(dmat.Info().num_nonzero_, 2);
-  EXPECT_EQ(dmat.Info().num_row_, 2);
-  EXPECT_EQ(dmat.Info().num_col_, 2);
-}
-
-TEST(SparsePageDMatrix, FromDense) {
-  dmlc::TemporaryDirectory tempdir;
-  const std::string tmp_file = tempdir.path + "/simple.libsvm";
-  int m = 3;
-  int n = 2;
-  std::vector<float> data = {1, 2, 3, 4, 5, 6};
-  data::DenseAdapter adapter(data.data(), m, n);
-  data::SparsePageDMatrix dmat(
-      &adapter, std::numeric_limits<float>::quiet_NaN(), 1, tmp_file);
-  EXPECT_EQ(dmat.Info().num_col_, 2);
-  EXPECT_EQ(dmat.Info().num_row_, 3);
-  EXPECT_EQ(dmat.Info().num_nonzero_, 6);
-
-  for (auto &batch : dmat.GetBatches<SparsePage>()) {
-    auto page = batch.GetView();
-    for (auto i = 0ull; i < batch.Size(); i++) {
-      auto inst = page[i];
-      for (auto j = 0ull; j < inst.size(); j++) {
-        EXPECT_EQ(inst[j].fvalue, data[i * n + j]);
-        EXPECT_EQ(inst[j].index, j);
-      }
-    }
-  }
-}
-
-TEST(SparsePageDMatrix, FromCSC) {
-  dmlc::TemporaryDirectory tempdir;
-  const std::string tmp_file = tempdir.path + "/simple.libsvm";
-  std::vector<float> data = {1, 3, 2, 4, 5};
-  std::vector<unsigned> row_idx = {0, 1, 0, 1, 2};
-  std::vector<size_t> col_ptr = {0, 2, 5};
-  data::CSCAdapter adapter(col_ptr.data(), row_idx.data(), data.data(), 2, 3);
-  data::SparsePageDMatrix dmat(
-      &adapter, std::numeric_limits<float>::quiet_NaN(), -1, tmp_file);
-  EXPECT_EQ(dmat.Info().num_col_, 2);
-  EXPECT_EQ(dmat.Info().num_row_, 3);
-  EXPECT_EQ(dmat.Info().num_nonzero_, 5);
-
-  auto &batch = *dmat.GetBatches<SparsePage>().begin();
-  auto page = batch.GetView();
-  auto inst = page[0];
-  EXPECT_EQ(inst[0].fvalue, 1);
-  EXPECT_EQ(inst[0].index, 0);
-  EXPECT_EQ(inst[1].fvalue, 2);
-  EXPECT_EQ(inst[1].index, 1);
-
-  inst = page[1];
-  EXPECT_EQ(inst[0].fvalue, 3);
-  EXPECT_EQ(inst[0].index, 0);
-  EXPECT_EQ(inst[1].fvalue, 4);
-  EXPECT_EQ(inst[1].index, 1);
-
-  inst = page[2];
-  EXPECT_EQ(inst[0].fvalue, 5);
-  EXPECT_EQ(inst[0].index, 1);
-}
-
-TEST(SparsePageDMatrix, FromFile) {
-  std::string filename = "test.libsvm";
-  CreateBigTestData(filename, 20);
-  std::unique_ptr<dmlc::Parser<uint32_t>> parser(
-      dmlc::Parser<uint32_t>::Create(filename.c_str(), 0, 1, "auto"));
-  data::FileAdapter adapter(parser.get());
-  dmlc::TemporaryDirectory tempdir;
-  const std::string tmp_file = tempdir.path + "/simple.libsvm";
-
-  data::SparsePageDMatrix dmat(
-      &adapter, std::numeric_limits<float>::quiet_NaN(), -1, tmp_file, 1);
-  ASSERT_EQ(dmat.Info().num_col_, 5);
-
-  for (auto &batch : dmat.GetBatches<SparsePage>()) {
-    std::vector<bst_row_t> expected_offset(batch.Size() + 1);
-    auto page = batch.GetView();
-    int n = -3;
-    std::generate(expected_offset.begin(), expected_offset.end(),
-                  [&n] { return n += 3; });
-    EXPECT_EQ(batch.offset.HostVector(), expected_offset);
-
-    if (batch.base_rowid % 2 == 0) {
-      EXPECT_EQ(page[0][0].index, 0);
-      EXPECT_EQ(page[0][1].index, 1);
-      EXPECT_EQ(page[0][2].index, 2);
-    } else {
-      EXPECT_EQ(page[0][0].index, 0);
-      EXPECT_EQ(page[0][1].index, 3);
-      EXPECT_EQ(page[0][2].index, 4);
-    }
-  }
-}
-
-TEST(SparsePageDMatrix, Large) {
-  std::string filename = "test.libsvm";
-  CreateBigTestData(filename, 1 << 16);
-  std::unique_ptr<dmlc::Parser<uint32_t>> parser(
-      dmlc::Parser<uint32_t>::Create(filename.c_str(), 0, 1, "auto"));
-  data::FileAdapter adapter(parser.get());
-  dmlc::TemporaryDirectory tempdir;
-  const std::string tmp_file = tempdir.path + "/simple.libsvm";
-
-  std::unique_ptr<DMatrix> sparse{new data::SparsePageDMatrix(
-      &adapter, std::numeric_limits<float>::quiet_NaN(), -1, tmp_file, 16)};
-  std::unique_ptr<DMatrix> simple{DMatrix::Load(filename, true, true)};
-
-  std::vector<float> sparse_data;
-  std::vector<size_t> sparse_rptr;
-  std::vector<bst_feature_t> sparse_cids;
-  DMatrixToCSR(sparse.get(), &sparse_data, &sparse_rptr, &sparse_cids);
-
-  std::vector<float> simple_data;
-  std::vector<size_t> simple_rptr;
-  std::vector<bst_feature_t> simple_cids;
-  DMatrixToCSR(simple.get(), &simple_data, &simple_rptr, &simple_cids);
-
-  ASSERT_EQ(sparse_rptr.size(), sparse->Info().num_row_ + 1);
-  ASSERT_EQ(sparse_rptr.size(), simple->Info().num_row_ + 1);
-
-  ASSERT_EQ(sparse_data.size(), simple_data.size());
-  ASSERT_EQ(sparse_data, simple_data);
-  ASSERT_EQ(sparse_rptr.size(), simple_rptr.size());
-  ASSERT_EQ(sparse_rptr, simple_rptr);
-  ASSERT_EQ(sparse_cids, simple_cids);
-}
-
-auto TestSparsePageDMatrixDeterminism(int32_t threads, std::string const& filename) {
   omp_set_num_threads(threads);
   std::vector<float> sparse_data;
   std::vector<size_t> sparse_rptr;
   std::vector<bst_feature_t> sparse_cids;
-
-  std::unique_ptr<dmlc::Parser<uint32_t>> parser(
-      dmlc::Parser<uint32_t>::Create(filename.c_str(), 0, 1, "auto"));
-  data::FileAdapter adapter(parser.get());
   dmlc::TemporaryDirectory tempdir;
-  const std::string tmp_file = tempdir.path + "/simple.libsvm";
+  std::string filename = tempdir.path + "/simple.libsvm";
-  std::unique_ptr<DMatrix> sparse{new data::SparsePageDMatrix(
+  CreateBigTestData(filename, 1 << 16);
-      &adapter, std::numeric_limits<float>::quiet_NaN(), -1, tmp_file, 1 << 8)};
+
+  data::FileIterator iter(filename, 0, 1, "auto");
+  std::unique_ptr<DMatrix> sparse{new data::SparsePageDMatrix{
+      &iter, iter.Proxy(), data::fileiter::Reset, data::fileiter::Next,
+      std::numeric_limits<float>::quiet_NaN(), 1, filename}};
 
   DMatrixToCSR(sparse.get(), &sparse_data, &sparse_rptr, &sparse_cids);
 
-  std::string cache_name = tmp_file + ".row.page";
+  auto cache_name =
+      data::MakeId(filename,
+                   dynamic_cast<data::SparsePageDMatrix *>(sparse.get())) +
+      ".row.page";
   std::string cache = common::LoadSequentialFile(cache_name);
   return cache;
 }
 
 TEST(SparsePageDMatrix, Determinism) {
-  std::string filename = "test.libsvm";
+#if defined(_MSC_VER)
-  CreateBigTestData(filename, 1 << 16);
+  return;
+#endif  // defined(_MSC_VER)
   std::vector<std::string> caches;
   for (size_t i = 1; i < 18; i += 2) {
-    caches.emplace_back(TestSparsePageDMatrixDeterminism(i, filename));
+    caches.emplace_back(TestSparsePageDMatrixDeterminism(i));
   }
 
   for (size_t i = 1; i < caches.size(); ++i) {

tests/cpp/data/test_sparse_page_dmatrix.cu

@@ -4,6 +4,7 @@
 #include "../helpers.h"
 #include "../../../src/common/compressed_iterator.h"
 #include "../../../src/data/ellpack_page.cuh"
+#include "../../../src/data/sparse_page_dmatrix.h"
 
 namespace xgboost {
 
@@ -14,13 +15,22 @@ TEST(SparsePageDMatrix, EllpackPage) {
   DMatrix* dmat = DMatrix::Load(tmp_file + "#" + tmp_file + ".cache", true, false);
 
   // Loop over the batches and assert the data is as expected
-  for (const auto& batch : dmat->GetBatches<EllpackPage>({0, 256, 64})) {
+  size_t n = 0;
-    EXPECT_EQ(batch.Size(), dmat->Info().num_row_);
+  for (const auto& batch : dmat->GetBatches<EllpackPage>({0, 256})) {
+    n += batch.Size();
   }
+  EXPECT_EQ(n, dmat->Info().num_row_);
 
-  EXPECT_TRUE(FileExists(tmp_file + ".cache"));
+  auto path =
-  EXPECT_TRUE(FileExists(tmp_file + ".cache.row.page"));
+      data::MakeId(tmp_file + ".cache",
-  EXPECT_TRUE(FileExists(tmp_file + ".cache.ellpack.page"));
+                   dynamic_cast<data::SparsePageDMatrix *>(dmat)) +
+      ".row.page";
+  EXPECT_TRUE(FileExists(path));
+  path =
+      data::MakeId(tmp_file + ".cache",
+                   dynamic_cast<data::SparsePageDMatrix *>(dmat)) +
+      ".ellpack.page";
+  EXPECT_TRUE(FileExists(path));
 
   delete dmat;
 }
@@ -30,12 +40,12 @@ TEST(SparsePageDMatrix, MultipleEllpackPages) {
   std::string filename = tmpdir.path + "/big.libsvm";
   size_t constexpr kPageSize = 64, kEntriesPerCol = 3;
   size_t constexpr kEntries = kPageSize * kEntriesPerCol * 2;
-  std::unique_ptr<DMatrix> dmat = CreateSparsePageDMatrix(kEntries, kPageSize, filename);
+  std::unique_ptr<DMatrix> dmat = CreateSparsePageDMatrix(kEntries, filename);
 
   // Loop over the batches and count the records
   int64_t batch_count = 0;
   int64_t row_count = 0;
-  for (const auto& batch : dmat->GetBatches<EllpackPage>({0, 256, 7UL})) {
+  for (const auto& batch : dmat->GetBatches<EllpackPage>({0, 256})) {
     EXPECT_LT(batch.Size(), dmat->Info().num_row_);
     batch_count++;
     row_count += batch.Size();
@@ -43,7 +53,36 @@ TEST(SparsePageDMatrix, MultipleEllpackPages) {
   EXPECT_GE(batch_count, 2);
   EXPECT_EQ(row_count, dmat->Info().num_row_);
 
-  EXPECT_TRUE(FileExists(filename + ".cache.ellpack.page"));
+  auto path =
+      data::MakeId(filename,
+                   dynamic_cast<data::SparsePageDMatrix *>(dmat.get())) +
+      ".ellpack.page";
+}
+
+TEST(SparsePageDMatrix, RetainEllpackPage) {
+  auto m = CreateSparsePageDMatrix(10000);
+  auto batches = m->GetBatches<EllpackPage>({0, 32});
+  auto begin = batches.begin();
+  auto end = batches.end();
+
+  std::vector<HostDeviceVector<common::CompressedByteT>> gidx_buffers;
+  std::vector<std::shared_ptr<EllpackPage const>> iterators;
+  for (auto it = begin; it != end; ++it) {
+    iterators.push_back(it.Page());
+    gidx_buffers.emplace_back(HostDeviceVector<common::CompressedByteT>{});
+    gidx_buffers.back().Resize((*it).Impl()->gidx_buffer.Size());
+    gidx_buffers.back().Copy((*it).Impl()->gidx_buffer);
+  }
+  ASSERT_GE(iterators.size(), 2);
+
+  for (size_t i = 0; i < iterators.size(); ++i) {
+    ASSERT_EQ((*iterators[i]).Impl()->gidx_buffer.HostVector(), gidx_buffers.at(i).HostVector());
+  }
+
+  // make sure it's const and the caller can not modify the content of page.
+  for (auto& page : m->GetBatches<EllpackPage>({0, 32})) {
+    static_assert(std::is_const<std::remove_reference_t<decltype(page)>>::value, "");
+  }
 }
 
 TEST(SparsePageDMatrix, EllpackPageContent) {
@@ -59,7 +98,7 @@ TEST(SparsePageDMatrix, EllpackPageContent) {
   std::unique_ptr<DMatrix>
       dmat_ext(CreateSparsePageDMatrixWithRC(kRows, kCols, kPageSize, true, tmpdir));
 
-  BatchParam param{0, 2, 0};
+  BatchParam param{0, 2};
   auto impl = (*dmat->GetBatches<EllpackPage>(param).begin()).Impl();
   EXPECT_EQ(impl->base_rowid, 0);
   EXPECT_EQ(impl->n_rows, kRows);
@@ -67,7 +106,17 @@ TEST(SparsePageDMatrix, EllpackPageContent) {
   EXPECT_EQ(impl->row_stride, 2);
   EXPECT_EQ(impl->Cuts().TotalBins(), 4);
 
-  auto impl_ext = (*dmat_ext->GetBatches<EllpackPage>(param).begin()).Impl();
+  std::unique_ptr<EllpackPageImpl> impl_ext;
+  size_t offset = 0;
+  for (auto& batch : dmat_ext->GetBatches<EllpackPage>(param)) {
+    if (!impl_ext) {
+      impl_ext.reset(new EllpackPageImpl(
+          batch.Impl()->gidx_buffer.DeviceIdx(), batch.Impl()->Cuts(),
+          batch.Impl()->is_dense, batch.Impl()->row_stride, kRows));
+    }
+    auto n_elems = impl_ext->Copy(0, batch.Impl(), offset);
+    offset += n_elems;
+  }
   EXPECT_EQ(impl_ext->base_rowid, 0);
   EXPECT_EQ(impl_ext->n_rows, kRows);
   EXPECT_FALSE(impl_ext->is_dense);
@@ -109,7 +158,7 @@ TEST(SparsePageDMatrix, MultipleEllpackPageContent) {
   std::unique_ptr<DMatrix>
       dmat_ext(CreateSparsePageDMatrixWithRC(kRows, kCols, kPageSize, true, tmpdir));
 
-  BatchParam param{0, kMaxBins, kPageSize};
+  BatchParam param{0, kMaxBins};
   auto impl = (*dmat->GetBatches<EllpackPage>(param).begin()).Impl();
   EXPECT_EQ(impl->base_rowid, 0);
   EXPECT_EQ(impl->n_rows, kRows);
@@ -150,7 +199,7 @@ TEST(SparsePageDMatrix, EllpackPageMultipleLoops) {
   std::unique_ptr<DMatrix>
       dmat_ext(CreateSparsePageDMatrixWithRC(kRows, kCols, kPageSize, true, tmpdir));
 
-  BatchParam param{0, kMaxBins, kPageSize};
+  BatchParam param{0, kMaxBins};
 
   size_t current_row = 0;
   for (auto& page : dmat_ext->GetBatches<EllpackPage>(param)) {

tests/cpp/gbm/test_gbtree.cc

@@ -155,7 +155,8 @@ TEST(GBTree, ChoosePredictor) {
   ASSERT_TRUE(data.HostCanWrite());
 
   // pull data into device.
-  data = HostDeviceVector<Entry>(data.HostVector(), 0);
+  data.HostVector();
+  data.SetDevice(0);
   data.DeviceSpan();
   ASSERT_FALSE(data.HostCanWrite());
 

tests/cpp/helpers.cc

@@ -18,6 +18,7 @@
 #include "xgboost/c_api.h"
 #include "../../src/data/adapter.h"
 #include "../../src/data/simple_dmatrix.h"
+#include "../../src/data/sparse_page_dmatrix.h"
 #include "../../src/gbm/gbtree_model.h"
 #include "xgboost/predictor.h"
 
@@ -45,12 +46,25 @@ void CreateSimpleTestData(const std::string& filename) {
   CreateBigTestData(filename, 6);
 }
 
-void CreateBigTestData(const std::string& filename, size_t n_entries) {
+void CreateBigTestData(const std::string& filename, size_t n_entries, bool zero_based) {
   std::ofstream fo(filename.c_str());
   const size_t entries_per_row = 3;
+  std::string odd_row;
+  if (zero_based) {
+    odd_row = " 0:0 3:30 4:40\n";
+  } else {
+    odd_row = " 1:0 4:30 5:40\n";
+  }
+  std::string even_row;
+  if (zero_based) {
+    even_row = " 0:0 1:10 2:20\n";
+  } else {
+    even_row = " 1:0 2:10 3:20\n";
+  }
+
   size_t n_rows = (n_entries + entries_per_row - 1) / entries_per_row;
   for (size_t i = 0; i < n_rows; ++i) {
-    const char* row = i % 2 == 0 ? " 0:0 1:10 2:20\n" : " 0:0 3:30 4:40\n";
+    auto row = i % 2 == 0 ? even_row : odd_row;
     fo << i << row;
   }
 }
@@ -348,13 +362,20 @@ GetDMatrixFromData(const std::vector<float> &x, int num_rows, int num_columns){
       &adapter, std::numeric_limits<float>::quiet_NaN(), 1));
 }
 
-std::unique_ptr<DMatrix> CreateSparsePageDMatrix(
+std::unique_ptr<DMatrix> CreateSparsePageDMatrix(size_t n_entries,
-    size_t n_entries, size_t page_size, std::string tmp_file) {
+                                                 std::string prefix) {
-  // Create sufficiently large data to make two row pages
+  size_t n_columns = 3;
-  CreateBigTestData(tmp_file, n_entries);
+  size_t n_rows = n_entries / n_columns;
-  std::unique_ptr<DMatrix> dmat { DMatrix::Load(
+  ArrayIterForTest iter(0, n_rows, n_columns, 2);
-      tmp_file + "#" + tmp_file + ".cache", true, false, "auto", page_size)};
+
-  EXPECT_TRUE(FileExists(tmp_file + ".cache.row.page"));
+  std::unique_ptr<DMatrix> dmat{DMatrix::Create(
+      static_cast<DataIterHandle>(&iter), iter.Proxy(), Reset, Next,
+      std::numeric_limits<float>::quiet_NaN(), 1, prefix)};
+  auto row_page_path =
+      data::MakeId(prefix,
+                   dynamic_cast<data::SparsePageDMatrix *>(dmat.get())) +
+      ".row.page";
+  EXPECT_TRUE(FileExists(row_page_path)) << row_page_path;
 
   // Loop over the batches and count the records
   int64_t batch_count = 0;
@@ -368,7 +389,6 @@ std::unique_ptr<DMatrix> CreateSparsePageDMatrix(
   return dmat;
 }
 
-
 std::unique_ptr<DMatrix> CreateSparsePageDMatrixWithRC(
     size_t n_rows, size_t n_cols, size_t page_size, bool deterministic,
     const dmlc::TemporaryDirectory& tempdir) {
@@ -432,7 +452,7 @@ std::unique_ptr<DMatrix> CreateSparsePageDMatrixWithRC(
     uri += "#" + tmp_file + ".cache";
   }
   std::unique_ptr<DMatrix> dmat(
-      DMatrix::Load(uri, true, false, "auto", page_size));
+      DMatrix::Load(uri, true, false, "auto"));
   return dmat;
 }
 
@@ -481,6 +501,28 @@ std::unique_ptr<GradientBooster> CreateTrainedGBM(
   return gbm;
 }
 
+ArrayIterForTest::ArrayIterForTest(float sparsity, size_t rows, size_t cols,
+                                   size_t batches) : rows_{rows}, cols_{cols}, n_batches_{batches} {
+  XGProxyDMatrixCreate(&proxy_);
+  rng_.reset(new RandomDataGenerator{rows_, cols_, sparsity});
+  std::tie(batches_, interface_) =
+      rng_->GenerateArrayInterfaceBatch(&data_, n_batches_);
+}
+
+ArrayIterForTest::~ArrayIterForTest() { XGDMatrixFree(proxy_); }
+
+int ArrayIterForTest::Next() {
+  if (iter_ == n_batches_) {
+    return 0;
+  }
+  XGProxyDMatrixSetDataDense(proxy_, batches_[iter_].c_str());
+  iter_++;
+  return 1;
+}
+
+size_t constexpr ArrayIterForTest::kRows;
+size_t constexpr ArrayIterForTest::kCols;
+
 void DMatrixToCSR(DMatrix *dmat, std::vector<float> *p_data,
                   std::vector<size_t> *p_row_ptr,
                   std::vector<bst_feature_t> *p_cids) {

tests/cpp/helpers.cu

@@ -8,16 +8,16 @@ namespace xgboost {
 
 CudaArrayIterForTest::CudaArrayIterForTest(float sparsity, size_t rows,
                                            size_t cols, size_t batches)
-    : rows_{rows}, cols_{cols}, n_batches_{batches} {
+    : ArrayIterForTest{sparsity, rows, cols, batches} {
-  XGProxyDMatrixCreate(&proxy_);
-  rng_.reset(new RandomDataGenerator{rows_, cols_, sparsity});
   rng_->Device(0);
   std::tie(batches_, interface_) =
       rng_->GenerateArrayInterfaceBatch(&data_, n_batches_);
   this->Reset();
 }
 
-CudaArrayIterForTest::~CudaArrayIterForTest() { XGDMatrixFree(proxy_); }
+size_t constexpr CudaArrayIterForTest::kRows;
+size_t constexpr CudaArrayIterForTest::kCols;
+size_t constexpr CudaArrayIterForTest::kBatches;
 
 int CudaArrayIterForTest::Next() {
   if (iter_ == n_batches_) {
@@ -28,8 +28,6 @@ int CudaArrayIterForTest::Next() {
   return 1;
 }
 
-size_t constexpr CudaArrayIterForTest::kRows;
-size_t constexpr CudaArrayIterForTest::kCols;
 
 std::shared_ptr<DMatrix> RandomDataGenerator::GenerateDeviceDMatrix(bool with_label,
                                                                     bool float_label,

tests/cpp/helpers.h

@@ -55,7 +55,9 @@ int64_t GetFileSize(const std::string& filename);
 
 void CreateSimpleTestData(const std::string& filename);
 
-void CreateBigTestData(const std::string& filename, size_t n_entries);
+// Create a libsvm format file with 3 entries per-row. `zero_based` specifies whether it's
+// 0-based indexing.
+void CreateBigTestData(const std::string& filename, size_t n_entries, bool zero_based = true);
 
 void CheckObjFunction(std::unique_ptr<xgboost::ObjFunction> const& obj,
                       std::vector<xgboost::bst_float> preds,
@@ -300,8 +302,7 @@ GenerateRandomCategoricalSingleColumn(int n, size_t num_categories) {
 std::shared_ptr<DMatrix> GetDMatrixFromData(const std::vector<float> &x,
                                             int num_rows, int num_columns);
 
-std::unique_ptr<DMatrix> CreateSparsePageDMatrix(
+std::unique_ptr<DMatrix> CreateSparsePageDMatrix(size_t n_entries, std::string prefix = "cache");
-    size_t n_entries, size_t page_size, std::string tmp_file);
 
 /**
  * \fn std::unique_ptr<DMatrix> CreateSparsePageDMatrixWithRC(size_t n_rows, size_t n_cols,
@@ -356,7 +357,8 @@ inline HostDeviceVector<GradientPair> GenerateRandomGradients(const size_t n_row
 
 typedef void *DMatrixHandle;  // NOLINT(*);
 
-class CudaArrayIterForTest {
+class ArrayIterForTest {
+ protected:
   HostDeviceVector<float> data_;
   size_t iter_ {0};
   DMatrixHandle proxy_;
@@ -373,20 +375,32 @@ class CudaArrayIterForTest {
   size_t static constexpr kBatches { 100 };
   size_t static constexpr kCols { 13 };
 
-  explicit CudaArrayIterForTest(float sparsity, size_t rows = kRows,
-                                size_t cols = kCols, size_t batches = kBatches);
-  ~CudaArrayIterForTest();
-
   std::string AsArray() const {
     return interface_;
   }
 
-  int Next();
+  virtual int Next();
-  void Reset() {
+  virtual void Reset() {
     iter_ = 0;
   }
   size_t Iter() const { return iter_; }
   auto Proxy() -> decltype(proxy_) { return proxy_; }
+
+  explicit ArrayIterForTest(float sparsity, size_t rows = kRows,
+                            size_t cols = kCols, size_t batches = kBatches);
+  virtual ~ArrayIterForTest();
+};
+
+class CudaArrayIterForTest : public ArrayIterForTest {
+ public:
+  size_t static constexpr kRows{1000};
+  size_t static constexpr kBatches{100};
+  size_t static constexpr kCols{13};
+
+  explicit CudaArrayIterForTest(float sparsity, size_t rows = kRows,
+                                size_t cols = kCols, size_t batches = kBatches);
+  int Next() override;
+  ~CudaArrayIterForTest() override = default;
 };
 
 void DMatrixToCSR(DMatrix *dmat, std::vector<float> *p_data,
@@ -396,11 +410,11 @@ void DMatrixToCSR(DMatrix *dmat, std::vector<float> *p_data,
 typedef void *DataIterHandle;  // NOLINT(*)
 
 inline void Reset(DataIterHandle self) {
-  static_cast<CudaArrayIterForTest*>(self)->Reset();
+  static_cast<ArrayIterForTest*>(self)->Reset();
 }
 
 inline int Next(DataIterHandle self) {
-  return static_cast<CudaArrayIterForTest*>(self)->Next();
+  return static_cast<ArrayIterForTest*>(self)->Next();
 }
 
 class RMMAllocator;

tests/cpp/predictor/test_cpu_predictor.cc

@@ -92,13 +92,10 @@ TEST(CpuPredictor, IterationRange) {
 }
 
 TEST(CpuPredictor, ExternalMemory) {
-  dmlc::TemporaryDirectory tmpdir;
-  std::string filename = tmpdir.path + "/big.libsvm";
-
   size_t constexpr kPageSize = 64, kEntriesPerCol = 3;
   size_t constexpr kEntries = kPageSize * kEntriesPerCol * 2;
 
-  std::unique_ptr<DMatrix> dmat = CreateSparsePageDMatrix(kEntries, kPageSize, filename);
+  std::unique_ptr<DMatrix> dmat = CreateSparsePageDMatrix(kEntries);
   auto lparam = CreateEmptyGenericParam(GPUIDX);
 
   std::unique_ptr<Predictor> cpu_predictor =

tests/cpp/predictor/test_gpu_predictor.cu

@@ -102,13 +102,10 @@ TEST(GPUPredictor, ExternalMemoryTest) {
 
   gbm::GBTreeModel model = CreateTestModel(&param, n_classes);
   std::vector<std::unique_ptr<DMatrix>> dmats;
-  dmlc::TemporaryDirectory tmpdir;
+
-  std::string file0 = tmpdir.path + "/big_0.libsvm";
+  dmats.push_back(CreateSparsePageDMatrix(400));
-  std::string file1 = tmpdir.path + "/big_1.libsvm";
+  dmats.push_back(CreateSparsePageDMatrix(800));
-  std::string file2 = tmpdir.path + "/big_2.libsvm";
+  dmats.push_back(CreateSparsePageDMatrix(8000));
-  dmats.push_back(CreateSparsePageDMatrix(400, 64UL, file0));
-  dmats.push_back(CreateSparsePageDMatrix(800, 128UL, file1));
-  dmats.push_back(CreateSparsePageDMatrix(8000, 1024UL, file2));
 
   for (const auto& dmat: dmats) {
     dmat->Info().base_margin_.Resize(dmat->Info().num_row_ * n_classes, 0.5);

tests/cpp/test_learner.cc

@@ -98,8 +98,7 @@ TEST(Learner, SLOW_CheckMultiBatch) {  // NOLINT
   const std::string tmp_file = tempdir.path + "/big.libsvm";
   CreateBigTestData(tmp_file, 50000);
   std::shared_ptr<DMatrix> dmat(xgboost::DMatrix::Load(
-      tmp_file + "#" + tmp_file + ".cache", true, false, "auto", 100));
+      tmp_file + "#" + tmp_file + ".cache", true, false, "auto"));
-  EXPECT_TRUE(FileExists(tmp_file + ".cache.row.page"));
   EXPECT_FALSE(dmat->SingleColBlock());
   size_t num_row = dmat->Info().num_row_;
   std::vector<bst_float> labels(num_row);

tests/cpp/tree/gpu_hist/test_gradient_based_sampler.cu

@@ -27,7 +27,7 @@ void VerifySampling(size_t page_size,
   }
   gpair.SetDevice(0);
 
-  BatchParam param{0, 256, page_size};
+  BatchParam param{0, 256};
   auto page = (*dmat->GetBatches<EllpackPage>(param).begin()).Impl();
   if (page_size != 0) {
     EXPECT_NE(page->n_rows, kRows);
@@ -82,7 +82,7 @@ TEST(GradientBasedSampler, NoSamplingExternalMemory) {
   auto gpair = GenerateRandomGradients(kRows);
   gpair.SetDevice(0);
 
-  BatchParam param{0, 256, kPageSize};
+  BatchParam param{0, 256};
   auto page = (*dmat->GetBatches<EllpackPage>(param).begin()).Impl();
   EXPECT_NE(page->n_rows, kRows);
 

tests/cpp/tree/gpu_hist/test_histogram.cu

@@ -15,7 +15,7 @@ void TestDeterministicHistogram(bool is_dense, int shm_size) {
 
   float sparsity = is_dense ? 0.0f : 0.5f;
   auto matrix = RandomDataGenerator(kRows, kCols, sparsity).GenerateDMatrix();
-  BatchParam batch_param{0, static_cast<int32_t>(kBins), 0};
+  BatchParam batch_param{0, static_cast<int32_t>(kBins)};
 
   for (auto const& batch : matrix->GetBatches<EllpackPage>(batch_param)) {
     auto* page = batch.Impl();
@@ -116,7 +116,7 @@ void TestGPUHistogramCategorical(size_t num_categories) {
   auto x = GenerateRandomCategoricalSingleColumn(kRows, num_categories);
   auto cat_m = GetDMatrixFromData(x, kRows, 1);
   cat_m->Info().feature_types.HostVector().push_back(FeatureType::kCategorical);
-  BatchParam batch_param{0, static_cast<int32_t>(kBins), 0};
+  BatchParam batch_param{0, static_cast<int32_t>(kBins)};
   tree::RowPartitioner row_partitioner(0, kRows);
   auto ridx = row_partitioner.GetRows(0);
   dh::device_vector<GradientPairPrecise> cat_hist(num_categories);

tests/cpp/tree/test_gpu_hist.cu

@@ -152,7 +152,6 @@ TEST(GpuHist, ApplySplit) {
   BatchParam bparam;
   bparam.gpu_id = 0;
   bparam.max_bin = 3;
-  bparam.gpu_page_size = 0;
 
   for (auto& ellpack : m->GetBatches<EllpackPage>(bparam)){
     auto impl = ellpack.Impl();
@@ -291,9 +290,13 @@ void TestHistogramIndexImpl() {
   // Extract the device maker from the histogram makers and from that its compressed
   // histogram index
   const auto &maker = hist_maker.maker;
+  auto grad = GenerateRandomGradients(kNRows);
+  grad.SetDevice(0);
+  maker->Reset(&grad, hist_maker_dmat.get(), kNCols);
   std::vector<common::CompressedByteT> h_gidx_buffer(maker->page->gidx_buffer.HostVector());
 
   const auto &maker_ext = hist_maker_ext.maker;
+  maker_ext->Reset(&grad, hist_maker_ext_dmat.get(), kNCols);
   std::vector<common::CompressedByteT> h_gidx_buffer_ext(maker_ext->page->gidx_buffer.HostVector());
 
   ASSERT_EQ(maker->page->Cuts().TotalBins(), maker_ext->page->Cuts().TotalBins());
@@ -365,7 +368,7 @@ void UpdateTree(HostDeviceVector<GradientPair>* gpair, DMatrix* dmat,
     // Loop over the batches and count the records
     int64_t batch_count = 0;
     int64_t row_count = 0;
-    for (const auto& batch : dmat->GetBatches<EllpackPage>({0, max_bin, gpu_page_size})) {
+    for (const auto& batch : dmat->GetBatches<EllpackPage>({0, max_bin})) {
       EXPECT_LT(batch.Size(), dmat->Info().num_row_);
       batch_count++;
       row_count += batch.Size();
@@ -386,7 +389,6 @@ void UpdateTree(HostDeviceVector<GradientPair>* gpair, DMatrix* dmat,
 
   tree::GPUHistMakerSpecialised<GradientPairPrecise> hist_maker;
   GenericParameter generic_param(CreateEmptyGenericParam(0));
-  generic_param.gpu_page_size = gpu_page_size;
   hist_maker.Configure(args, &generic_param);
 
   hist_maker.Update(gpair, dmat, {tree});