Refactor external memory formats. (#7089)

* Save base_rowid.
* Return write size.
* Remove unused function.

src/data/ellpack_page_raw_format.cu

@@ -1,7 +1,6 @@
 /*!
- * Copyright 2019 XGBoost contributors
+ * Copyright 2019-2021 XGBoost contributors
  */
-
 #include <xgboost/data.h>
 #include <dmlc/registry.h>
 
@@ -13,6 +12,7 @@ namespace data {
 
 DMLC_REGISTRY_FILE_TAG(ellpack_page_raw_format);
 
+
 class EllpackPageRawFormat : public SparsePageFormat<EllpackPage> {
  public:
   bool Read(EllpackPage* page, dmlc::SeekStream* fi) override {
@@ -23,29 +23,34 @@ class EllpackPageRawFormat : public SparsePageFormat<EllpackPage> {
     fi->Read(&impl->n_rows);
     fi->Read(&impl->is_dense);
     fi->Read(&impl->row_stride);
-    if (!fi->Read(&impl->gidx_buffer.HostVector())) {
+    fi->Read(&impl->gidx_buffer.HostVector());
+    if (!fi->Read(&impl->base_rowid)) {
       return false;
     }
     return true;
   }
 
-  bool Read(EllpackPage* page,
-            dmlc::SeekStream* fi,
-            const std::vector<bst_uint>& sorted_index_set) override {
-    LOG(FATAL) << "Not implemented";
-    return false;
-  }
-
-  void Write(const EllpackPage& page, dmlc::Stream* fo) override {
+  size_t Write(const EllpackPage& page, dmlc::Stream* fo) override {
+    size_t bytes = 0;
     auto* impl = page.Impl();
     fo->Write(impl->Cuts().cut_values_.ConstHostVector());
+    bytes += impl->Cuts().cut_values_.ConstHostSpan().size_bytes() + sizeof(uint64_t);
     fo->Write(impl->Cuts().cut_ptrs_.ConstHostVector());
+    bytes += impl->Cuts().cut_ptrs_.ConstHostSpan().size_bytes() + sizeof(uint64_t);
     fo->Write(impl->Cuts().min_vals_.ConstHostVector());
+    bytes += impl->Cuts().min_vals_.ConstHostSpan().size_bytes() + sizeof(uint64_t);
     fo->Write(impl->n_rows);
+    bytes += sizeof(impl->n_rows);
     fo->Write(impl->is_dense);
+    bytes += sizeof(impl->is_dense);
     fo->Write(impl->row_stride);
+    bytes += sizeof(impl->row_stride);
     CHECK(!impl->gidx_buffer.ConstHostVector().empty());
     fo->Write(impl->gidx_buffer.HostVector());
+    bytes += impl->gidx_buffer.ConstHostSpan().size_bytes() + sizeof(uint64_t);
+    fo->Write(impl->base_rowid);
+    bytes += sizeof(impl->base_rowid);
+    return bytes;
   }
 };
 

src/data/sparse_page_raw_format.cc

@@ -1,10 +1,12 @@
 /*!
- * Copyright (c) 2015 by Contributors
+ * Copyright (c) 2015-2021 by Contributors
  * \file sparse_page_raw_format.cc
  *  Raw binary format of sparse page.
  */
 #include <xgboost/data.h>
 #include <dmlc/registry.h>
+
+#include "xgboost/logging.h"
 #include "./sparse_page_writer.h"
 
 namespace xgboost {
@@ -17,78 +19,36 @@ class SparsePageRawFormat : public SparsePageFormat<T> {
  public:
   bool Read(T* page, dmlc::SeekStream* fi) override {
     auto& offset_vec = page->offset.HostVector();
-    if (!fi->Read(&offset_vec)) return false;
+    if (!fi->Read(&offset_vec)) {
+      return false;
+    }
     auto& data_vec = page->data.HostVector();
     CHECK_NE(page->offset.Size(), 0U) << "Invalid SparsePage file";
     data_vec.resize(offset_vec.back());
     if (page->data.Size() != 0) {
-      CHECK_EQ(fi->Read(dmlc::BeginPtr(data_vec),
-                        (page->data).Size() * sizeof(Entry)),
-               (page->data).Size() * sizeof(Entry))
+      size_t n_bytes = fi->Read(dmlc::BeginPtr(data_vec),
+                                (page->data).Size() * sizeof(Entry));
+      CHECK_EQ(n_bytes, (page->data).Size() * sizeof(Entry))
           << "Invalid SparsePage file";
     }
+    fi->Read(&page->base_rowid, sizeof(page->base_rowid));
     return true;
   }
 
-  bool Read(T* page,
-            dmlc::SeekStream* fi,
-            const std::vector<bst_uint>& sorted_index_set) override {
-    if (!fi->Read(&disk_offset_)) return false;
-    auto& offset_vec = page->offset.HostVector();
-    auto& data_vec = page->data.HostVector();
-    // setup the offset
-    offset_vec.clear();
-    offset_vec.push_back(0);
-    for (unsigned int fid : sorted_index_set) {
-      CHECK_LT(fid + 1, disk_offset_.size());
-      size_t size = disk_offset_[fid + 1] - disk_offset_[fid];
-      offset_vec.push_back(offset_vec.back() + size);
-    }
-    data_vec.resize(offset_vec.back());
-    // read in the data
-    size_t begin = fi->Tell();
-    size_t curr_offset = 0;
-    for (size_t i = 0; i < sorted_index_set.size();) {
-      bst_uint fid = sorted_index_set[i];
-      if (disk_offset_[fid] != curr_offset) {
-        CHECK_GT(disk_offset_[fid], curr_offset);
-        fi->Seek(begin + disk_offset_[fid] * sizeof(Entry));
-        curr_offset = disk_offset_[fid];
-      }
-      size_t j, size_to_read = 0;
-      for (j = i; j < sorted_index_set.size(); ++j) {
-        if (disk_offset_[sorted_index_set[j]] == disk_offset_[fid] + size_to_read) {
-          size_to_read += offset_vec[j + 1] - offset_vec[j];
-        } else {
-          break;
-        }
-      }
-
-      if (size_to_read != 0) {
-        CHECK_EQ(fi->Read(dmlc::BeginPtr(data_vec) + offset_vec[i],
-                          size_to_read * sizeof(Entry)),
-                 size_to_read * sizeof(Entry))
-            << "Invalid SparsePage file";
-        curr_offset += size_to_read;
-      }
-      i = j;
-    }
-    // seek to end of record
-    if (curr_offset != disk_offset_.back()) {
-      fi->Seek(begin + disk_offset_.back() * sizeof(Entry));
-    }
-    return true;
-  }
-
-  void Write(const T& page, dmlc::Stream* fo) override {
+  size_t Write(const T& page, dmlc::Stream* fo) override {
     const auto& offset_vec = page.offset.HostVector();
     const auto& data_vec = page.data.HostVector();
     CHECK(page.offset.Size() != 0 && offset_vec[0] == 0);
     CHECK_EQ(offset_vec.back(), page.data.Size());
     fo->Write(offset_vec);
+    auto bytes = page.MemCostBytes();
+    bytes += sizeof(uint64_t);
     if (page.data.Size() != 0) {
       fo->Write(dmlc::BeginPtr(data_vec), page.data.Size() * sizeof(Entry));
     }
+    fo->Write(&page.base_rowid, sizeof(page.base_rowid));
+    bytes += sizeof(page.base_rowid);
+    return bytes;
   }
 
  private:

src/data/sparse_page_writer.h

@@ -42,22 +42,11 @@ class SparsePageFormat {
    * \return true of the loading as successful, false if end of file was reached
    */
   virtual bool Read(T* page, dmlc::SeekStream* fi) = 0;
-
-  /*!
-   * \brief read only the segments we are interested in, advance fi to end of the block.
-   * \param page The page to load the data into.
-   * \param fi the input stream of the file
-   * \param sorted_index_set sorted index of segments we are interested in
-   * \return true of the loading as successful, false if end of file was reached
-   */
-  virtual bool Read(T* page,
-                    dmlc::SeekStream* fi,
-                    const std::vector<bst_uint>& sorted_index_set) = 0;
   /*!
    * \brief save the data to fo, when a page was written.
    * \param fo output stream
    */
-  virtual void Write(const T& page, dmlc::Stream* fo) = 0;
+  virtual size_t Write(const T& page, dmlc::Stream* fo) = 0;
 };
 
 /*!

tests/cpp/data/test_ellpack_page_raw_format.cu

@@ -0,0 +1,45 @@
+/*!
+ * Copyright 2021 XGBoost contributors
+ */
+#include <gtest/gtest.h>
+#include <dmlc/filesystem.h>
+#include <xgboost/data.h>
+
+#include "../../../src/data/sparse_page_source.h"
+#include "../../../src/data/ellpack_page.cuh"
+
+#include "../helpers.h"
+
+namespace xgboost {
+namespace data {
+TEST(EllpackPageRawFormat, IO) {
+  std::unique_ptr<SparsePageFormat<EllpackPage>> format{CreatePageFormat<EllpackPage>("raw")};
+
+  auto m = RandomDataGenerator{100, 14, 0.5}.GenerateDMatrix();
+  dmlc::TemporaryDirectory tmpdir;
+  std::string path = tmpdir.path + "/ellpack.page";
+
+  {
+    std::unique_ptr<dmlc::Stream> fo{dmlc::Stream::Create(path.c_str(), "w")};
+    for (auto const &ellpack : m->GetBatches<EllpackPage>({0, 256})) {
+      format->Write(ellpack, fo.get());
+    }
+  }
+
+  EllpackPage page;
+  std::unique_ptr<dmlc::SeekStream> fi{dmlc::SeekStream::CreateForRead(path.c_str())};
+  format->Read(&page, fi.get());
+
+  for (auto const &ellpack : m->GetBatches<EllpackPage>({0, 256})) {
+    auto loaded = page.Impl();
+    auto orig = ellpack.Impl();
+    ASSERT_EQ(loaded->Cuts().Ptrs(), orig->Cuts().Ptrs());
+    ASSERT_EQ(loaded->Cuts().MinValues(), orig->Cuts().MinValues());
+    ASSERT_EQ(loaded->Cuts().Values(), orig->Cuts().Values());
+    ASSERT_EQ(loaded->base_rowid, orig->base_rowid);
+    ASSERT_EQ(loaded->row_stride, orig->row_stride);
+    ASSERT_EQ(loaded->gidx_buffer.HostVector(), orig->gidx_buffer.HostVector());
+  }
+}
+}  // namespace data
+}  // namespace xgboost

tests/cpp/data/test_sparse_page_raw_format.cc

@@ -0,0 +1,56 @@
+/*!
+ * Copyright 2021 XGBoost contributors
+ */
+#include <gtest/gtest.h>
+#include <dmlc/filesystem.h>
+#include <xgboost/data.h>
+
+#include "../../../src/data/sparse_page_source.h"
+#include "../helpers.h"
+
+namespace xgboost {
+namespace data {
+template <typename S> void TestSparsePageRawFormat() {
+  std::unique_ptr<SparsePageFormat<S>> format{CreatePageFormat<S>("raw")};
+
+  auto m = RandomDataGenerator{100, 14, 0.5}.GenerateDMatrix();
+  ASSERT_TRUE(m->SingleColBlock());
+  dmlc::TemporaryDirectory tmpdir;
+  std::string path = tmpdir.path + "/sparse.page";
+  S orig;
+  {
+    // block code to flush the stream
+    std::unique_ptr<dmlc::Stream> fo{dmlc::Stream::Create(path.c_str(), "w")};
+    for (auto const &page : m->GetBatches<S>()) {
+      orig.Push(page);
+      format->Write(page, fo.get());
+    }
+  }
+
+  S page;
+  std::unique_ptr<dmlc::SeekStream> fi{dmlc::SeekStream::CreateForRead(path.c_str())};
+  format->Read(&page, fi.get());
+  for (size_t i = 0; i < orig.data.Size(); ++i) {
+    ASSERT_EQ(page.data.HostVector()[i].fvalue,
+              orig.data.HostVector()[i].fvalue);
+    ASSERT_EQ(page.data.HostVector()[i].index, orig.data.HostVector()[i].index);
+  }
+  for (size_t i = 0; i < orig.offset.Size(); ++i) {
+    ASSERT_EQ(page.offset.HostVector()[i], orig.offset.HostVector()[i]);
+  }
+  ASSERT_EQ(page.base_rowid, orig.base_rowid);
+}
+
+TEST(SparsePageRawFormat, SparsePage) {
+  TestSparsePageRawFormat<SparsePage>();
+}
+
+TEST(SparsePageRawFormat, CSCPage) {
+  TestSparsePageRawFormat<CSCPage>();
+}
+
+TEST(SparsePageRawFormat, SortedCSCPage) {
+  TestSparsePageRawFormat<SortedCSCPage>();
+}
+}  // namespace data
+}  // namespace xgboost