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Refactor external memory formats. (#7089)

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* Save base_rowid.
* Return write size.
* Remove unused function.
This commit is contained in:
Jiaming Yuan
2021-07-08 04:04:51 +08:00
committed by GitHub
parent 689eb8f620
commit c766f143ab
5 changed files with 134 additions and 79 deletions
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27
src/data/ellpack_page_raw_format.cu
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@@ -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;
}
};

72
src/data/sparse_page_raw_format.cc
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@@ -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:

13
src/data/sparse_page_writer.h
View File

@@ -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;
};
/*!