9700776597
* Initial support for cudf integration. * Add two C APIs for consuming data and metainfo. * Add CopyFrom for SimpleCSRSource as a generic function to consume the data. * Add FromDeviceColumnar for consuming device data. * Add new MetaInfo::SetInfo for consuming label, weight etc.
435 lines
16 KiB
C++
435 lines
16 KiB
C++
/*!
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* Copyright 2015-2019 by Contributors
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* \file data.cc
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*/
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#include <xgboost/data.h>
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#include <xgboost/logging.h>
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#include <dmlc/registry.h>
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#include <cstring>
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#include "./sparse_page_writer.h"
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#include "./simple_dmatrix.h"
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#include "./simple_csr_source.h"
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#include "../common/io.h"
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#if DMLC_ENABLE_STD_THREAD
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#include "./sparse_page_source.h"
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#include "./sparse_page_dmatrix.h"
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#endif // DMLC_ENABLE_STD_THREAD
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namespace dmlc {
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DMLC_REGISTRY_ENABLE(::xgboost::data::SparsePageFormatReg);
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} // namespace dmlc
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namespace xgboost {
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// implementation of inline functions
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void MetaInfo::Clear() {
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num_row_ = num_col_ = num_nonzero_ = 0;
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labels_.HostVector().clear();
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root_index_.clear();
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group_ptr_.clear();
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weights_.HostVector().clear();
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base_margin_.HostVector().clear();
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}
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void MetaInfo::SaveBinary(dmlc::Stream *fo) const {
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int32_t version = kVersion;
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fo->Write(&version, sizeof(version));
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fo->Write(&num_row_, sizeof(num_row_));
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fo->Write(&num_col_, sizeof(num_col_));
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fo->Write(&num_nonzero_, sizeof(num_nonzero_));
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fo->Write(labels_.HostVector());
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fo->Write(group_ptr_);
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fo->Write(weights_.HostVector());
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fo->Write(root_index_);
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fo->Write(base_margin_.HostVector());
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}
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void MetaInfo::LoadBinary(dmlc::Stream *fi) {
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int version;
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CHECK(fi->Read(&version, sizeof(version)) == sizeof(version)) << "MetaInfo: invalid version";
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CHECK(version >= 1 && version <= kVersion) << "MetaInfo: unsupported file version";
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CHECK(fi->Read(&num_row_, sizeof(num_row_)) == sizeof(num_row_)) << "MetaInfo: invalid format";
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CHECK(fi->Read(&num_col_, sizeof(num_col_)) == sizeof(num_col_)) << "MetaInfo: invalid format";
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CHECK(fi->Read(&num_nonzero_, sizeof(num_nonzero_)) == sizeof(num_nonzero_))
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<< "MetaInfo: invalid format";
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CHECK(fi->Read(&labels_.HostVector())) << "MetaInfo: invalid format";
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CHECK(fi->Read(&group_ptr_)) << "MetaInfo: invalid format";
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if (version == kVersionWithQid) {
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std::vector<uint64_t> qids;
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CHECK(fi->Read(&qids)) << "MetaInfo: invalid format";
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}
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CHECK(fi->Read(&weights_.HostVector())) << "MetaInfo: invalid format";
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CHECK(fi->Read(&root_index_)) << "MetaInfo: invalid format";
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CHECK(fi->Read(&base_margin_.HostVector())) << "MetaInfo: invalid format";
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}
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// try to load group information from file, if exists
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inline bool MetaTryLoadGroup(const std::string& fname,
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std::vector<unsigned>* group) {
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std::unique_ptr<dmlc::Stream> fi(dmlc::Stream::Create(fname.c_str(), "r", true));
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if (fi == nullptr) return false;
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dmlc::istream is(fi.get());
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group->clear();
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group->push_back(0);
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unsigned nline = 0;
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while (is >> nline) {
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group->push_back(group->back() + nline);
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}
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return true;
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}
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// try to load weight information from file, if exists
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inline bool MetaTryLoadFloatInfo(const std::string& fname,
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std::vector<bst_float>* data) {
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std::unique_ptr<dmlc::Stream> fi(dmlc::Stream::Create(fname.c_str(), "r", true));
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if (fi == nullptr) return false;
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dmlc::istream is(fi.get());
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data->clear();
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bst_float value;
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while (is >> value) {
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data->push_back(value);
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}
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return true;
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}
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// macro to dispatch according to specified pointer types
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#define DISPATCH_CONST_PTR(dtype, old_ptr, cast_ptr, proc) \
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switch (dtype) { \
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case kFloat32: { \
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auto cast_ptr = reinterpret_cast<const float*>(old_ptr); proc; break; \
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} \
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case kDouble: { \
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auto cast_ptr = reinterpret_cast<const double*>(old_ptr); proc; break; \
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} \
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case kUInt32: { \
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auto cast_ptr = reinterpret_cast<const uint32_t*>(old_ptr); proc; break; \
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} \
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case kUInt64: { \
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auto cast_ptr = reinterpret_cast<const uint64_t*>(old_ptr); proc; break; \
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} \
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default: LOG(FATAL) << "Unknown data type" << dtype; \
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} \
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void MetaInfo::SetInfo(const char* key, const void* dptr, DataType dtype, size_t num) {
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if (!std::strcmp(key, "root_index")) {
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root_index_.resize(num);
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DISPATCH_CONST_PTR(dtype, dptr, cast_dptr,
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std::copy(cast_dptr, cast_dptr + num, root_index_.begin()));
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} else if (!std::strcmp(key, "label")) {
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auto& labels = labels_.HostVector();
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labels.resize(num);
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DISPATCH_CONST_PTR(dtype, dptr, cast_dptr,
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std::copy(cast_dptr, cast_dptr + num, labels.begin()));
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} else if (!std::strcmp(key, "weight")) {
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auto& weights = weights_.HostVector();
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weights.resize(num);
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DISPATCH_CONST_PTR(dtype, dptr, cast_dptr,
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std::copy(cast_dptr, cast_dptr + num, weights.begin()));
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} else if (!std::strcmp(key, "base_margin")) {
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auto& base_margin = base_margin_.HostVector();
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base_margin.resize(num);
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DISPATCH_CONST_PTR(dtype, dptr, cast_dptr,
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std::copy(cast_dptr, cast_dptr + num, base_margin.begin()));
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} else if (!std::strcmp(key, "group")) {
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group_ptr_.resize(num + 1);
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DISPATCH_CONST_PTR(dtype, dptr, cast_dptr,
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std::copy(cast_dptr, cast_dptr + num, group_ptr_.begin() + 1));
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group_ptr_[0] = 0;
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for (size_t i = 1; i < group_ptr_.size(); ++i) {
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group_ptr_[i] = group_ptr_[i - 1] + group_ptr_[i];
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}
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} else {
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LOG(FATAL) << "Unknown metainfo: " << key;
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}
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}
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#if !defined(XGBOOST_USE_CUDA)
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void MetaInfo::SetInfo(const char * c_key, std::string const& interface_str) {
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LOG(FATAL) << "XGBoost version is not compiled with GPU support";
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}
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#endif // !defined(XGBOOST_USE_CUDA)
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DMatrix* DMatrix::Load(const std::string& uri,
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bool silent,
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bool load_row_split,
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const std::string& file_format,
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const size_t page_size) {
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std::string fname, cache_file;
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size_t dlm_pos = uri.find('#');
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if (dlm_pos != std::string::npos) {
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cache_file = uri.substr(dlm_pos + 1, uri.length());
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fname = uri.substr(0, dlm_pos);
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CHECK_EQ(cache_file.find('#'), std::string::npos)
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<< "Only one `#` is allowed in file path for cache file specification.";
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if (load_row_split) {
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std::ostringstream os;
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std::vector<std::string> cache_shards = common::Split(cache_file, ':');
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for (size_t i = 0; i < cache_shards.size(); ++i) {
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size_t pos = cache_shards[i].rfind('.');
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if (pos == std::string::npos) {
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os << cache_shards[i]
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<< ".r" << rabit::GetRank()
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<< "-" << rabit::GetWorldSize();
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} else {
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os << cache_shards[i].substr(0, pos)
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<< ".r" << rabit::GetRank()
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<< "-" << rabit::GetWorldSize()
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<< cache_shards[i].substr(pos, cache_shards[i].length());
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}
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if (i + 1 != cache_shards.size()) {
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os << ':';
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}
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}
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cache_file = os.str();
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}
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} else {
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fname = uri;
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}
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int partid = 0, npart = 1;
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if (load_row_split) {
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partid = rabit::GetRank();
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npart = rabit::GetWorldSize();
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} else {
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// test option to load in part
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npart = dmlc::GetEnv("XGBOOST_TEST_NPART", 1);
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}
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if (npart != 1) {
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LOG(CONSOLE) << "Load part of data " << partid
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<< " of " << npart << " parts";
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}
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// legacy handling of binary data loading
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if (file_format == "auto" && npart == 1) {
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int magic;
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std::unique_ptr<dmlc::Stream> fi(dmlc::Stream::Create(fname.c_str(), "r", true));
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if (fi != nullptr) {
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common::PeekableInStream is(fi.get());
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if (is.PeekRead(&magic, sizeof(magic)) == sizeof(magic) &&
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magic == data::SimpleCSRSource::kMagic) {
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std::unique_ptr<data::SimpleCSRSource> source(new data::SimpleCSRSource());
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source->LoadBinary(&is);
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DMatrix* dmat = DMatrix::Create(std::move(source), cache_file);
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if (!silent) {
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LOG(CONSOLE) << dmat->Info().num_row_ << 'x' << dmat->Info().num_col_ << " matrix with "
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<< dmat->Info().num_nonzero_ << " entries loaded from " << uri;
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}
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return dmat;
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}
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}
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}
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std::unique_ptr<dmlc::Parser<uint32_t> > parser(
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dmlc::Parser<uint32_t>::Create(fname.c_str(), partid, npart, file_format.c_str()));
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DMatrix* dmat = DMatrix::Create(parser.get(), cache_file, page_size);
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if (!silent) {
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LOG(CONSOLE) << dmat->Info().num_row_ << 'x' << dmat->Info().num_col_ << " matrix with "
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<< dmat->Info().num_nonzero_ << " entries loaded from " << uri;
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}
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/* sync up number of features after matrix loaded.
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* partitioned data will fail the train/val validation check
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* since partitioned data not knowing the real number of features. */
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rabit::Allreduce<rabit::op::Max>(&dmat->Info().num_col_, 1);
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// backward compatiblity code.
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if (!load_row_split) {
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MetaInfo& info = dmat->Info();
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if (MetaTryLoadGroup(fname + ".group", &info.group_ptr_) && !silent) {
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LOG(CONSOLE) << info.group_ptr_.size() - 1
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<< " groups are loaded from " << fname << ".group";
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}
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if (MetaTryLoadFloatInfo
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(fname + ".base_margin", &info.base_margin_.HostVector()) && !silent) {
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LOG(CONSOLE) << info.base_margin_.Size()
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<< " base_margin are loaded from " << fname << ".base_margin";
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}
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if (MetaTryLoadFloatInfo
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(fname + ".weight", &info.weights_.HostVector()) && !silent) {
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LOG(CONSOLE) << info.weights_.Size()
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<< " weights are loaded from " << fname << ".weight";
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}
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}
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return dmat;
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}
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DMatrix* DMatrix::Create(dmlc::Parser<uint32_t>* parser,
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const std::string& cache_prefix,
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const size_t page_size) {
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if (cache_prefix.length() == 0) {
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std::unique_ptr<data::SimpleCSRSource> source(new data::SimpleCSRSource());
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source->CopyFrom(parser);
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return DMatrix::Create(std::move(source), cache_prefix);
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} else {
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#if DMLC_ENABLE_STD_THREAD
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if (!data::SparsePageSource<SparsePage>::CacheExist(cache_prefix, ".row.page")) {
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data::SparsePageSource<SparsePage>::CreateRowPage(parser, cache_prefix, page_size);
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}
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std::unique_ptr<data::SparsePageSource<SparsePage>> source(
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new data::SparsePageSource<SparsePage>(cache_prefix, ".row.page"));
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return DMatrix::Create(std::move(source), cache_prefix);
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#else
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LOG(FATAL) << "External memory is not enabled in mingw";
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return nullptr;
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#endif // DMLC_ENABLE_STD_THREAD
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}
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}
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void DMatrix::SaveToLocalFile(const std::string& fname) {
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data::SimpleCSRSource source;
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source.CopyFrom(this);
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std::unique_ptr<dmlc::Stream> fo(dmlc::Stream::Create(fname.c_str(), "w"));
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source.SaveBinary(fo.get());
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}
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DMatrix* DMatrix::Create(std::unique_ptr<DataSource<SparsePage>>&& source,
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const std::string& cache_prefix) {
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if (cache_prefix.length() == 0) {
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return new data::SimpleDMatrix(std::move(source));
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} else {
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#if DMLC_ENABLE_STD_THREAD
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return new data::SparsePageDMatrix(std::move(source), cache_prefix);
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#else
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LOG(FATAL) << "External memory is not enabled in mingw";
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return nullptr;
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#endif // DMLC_ENABLE_STD_THREAD
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}
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}
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} // namespace xgboost
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namespace xgboost {
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data::SparsePageFormat* data::SparsePageFormat::Create(const std::string& name) {
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auto *e = ::dmlc::Registry< ::xgboost::data::SparsePageFormatReg>::Get()->Find(name);
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if (e == nullptr) {
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LOG(FATAL) << "Unknown format type " << name;
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}
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return (e->body)();
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}
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std::pair<std::string, std::string>
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data::SparsePageFormat::DecideFormat(const std::string& cache_prefix) {
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size_t pos = cache_prefix.rfind(".fmt-");
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if (pos != std::string::npos) {
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std::string fmt = cache_prefix.substr(pos + 5, cache_prefix.length());
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size_t cpos = fmt.rfind('-');
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if (cpos != std::string::npos) {
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return std::make_pair(fmt.substr(0, cpos), fmt.substr(cpos + 1, fmt.length()));
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} else {
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return std::make_pair(fmt, fmt);
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}
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} else {
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std::string raw = "raw";
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return std::make_pair(raw, raw);
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}
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}
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void SparsePage::Push(const SparsePage &batch) {
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auto& data_vec = data.HostVector();
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auto& offset_vec = offset.HostVector();
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const auto& batch_offset_vec = batch.offset.HostVector();
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const auto& batch_data_vec = batch.data.HostVector();
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size_t top = offset_vec.back();
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data_vec.resize(top + batch.data.Size());
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std::memcpy(dmlc::BeginPtr(data_vec) + top,
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dmlc::BeginPtr(batch_data_vec),
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sizeof(Entry) * batch.data.Size());
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size_t begin = offset.Size();
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offset_vec.resize(begin + batch.Size());
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for (size_t i = 0; i < batch.Size(); ++i) {
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offset_vec[i + begin] = top + batch_offset_vec[i + 1];
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}
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}
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void SparsePage::Push(const dmlc::RowBlock<uint32_t>& batch) {
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auto& data_vec = data.HostVector();
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auto& offset_vec = offset.HostVector();
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data_vec.reserve(data.Size() + batch.offset[batch.size] - batch.offset[0]);
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offset_vec.reserve(offset.Size() + batch.size);
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CHECK(batch.index != nullptr);
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for (size_t i = 0; i < batch.size; ++i) {
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offset_vec.push_back(offset_vec.back() + batch.offset[i + 1] - batch.offset[i]);
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}
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for (size_t i = batch.offset[0]; i < batch.offset[batch.size]; ++i) {
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uint32_t index = batch.index[i];
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bst_float fvalue = batch.value == nullptr ? 1.0f : batch.value[i];
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data_vec.emplace_back(index, fvalue);
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}
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CHECK_EQ(offset_vec.back(), data.Size());
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}
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void SparsePage::PushCSC(const SparsePage &batch) {
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std::vector<xgboost::Entry>& self_data = data.HostVector();
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std::vector<size_t>& self_offset = offset.HostVector();
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auto const& other_data = batch.data.ConstHostVector();
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auto const& other_offset = batch.offset.ConstHostVector();
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if (other_data.empty()) {
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return;
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}
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if (!self_data.empty()) {
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CHECK_EQ(self_offset.size(), other_offset.size())
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<< "self_data.size(): " << this->data.Size() << ", "
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<< "other_data.size(): " << other_data.size() << std::flush;
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} else {
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self_data = other_data;
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self_offset = other_offset;
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return;
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}
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std::vector<size_t> offset(other_offset.size());
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offset[0] = 0;
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std::vector<xgboost::Entry> data(self_data.size() + other_data.size());
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// n_cols in original csr data matrix, here in csc is n_rows
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size_t const n_features = other_offset.size() - 1;
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size_t beg = 0;
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size_t ptr = 1;
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for (size_t i = 0; i < n_features; ++i) {
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size_t const self_beg = self_offset.at(i);
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size_t const self_length = self_offset.at(i+1) - self_beg;
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// It is possible that the current feature and further features aren't referenced
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// in any rows accumulated thus far. It is also possible for this to happen
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// in the current sparse page row batch as well.
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// Hence, the incremental number of rows may stay constant thus equaling the data size
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CHECK_LE(beg, data.size());
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std::memcpy(dmlc::BeginPtr(data)+beg,
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dmlc::BeginPtr(self_data) + self_beg,
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sizeof(Entry) * self_length);
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beg += self_length;
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size_t const other_beg = other_offset.at(i);
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size_t const other_length = other_offset.at(i+1) - other_beg;
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CHECK_LE(beg, data.size());
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std::memcpy(dmlc::BeginPtr(data)+beg,
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dmlc::BeginPtr(other_data) + other_beg,
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sizeof(Entry) * other_length);
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beg += other_length;
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CHECK_LT(ptr, offset.size());
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offset.at(ptr) = beg;
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ptr++;
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}
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self_data = std::move(data);
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self_offset = std::move(offset);
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}
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void SparsePage::Push(const Inst &inst) {
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auto& data_vec = data.HostVector();
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auto& offset_vec = offset.HostVector();
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offset_vec.push_back(offset_vec.back() + inst.size());
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size_t begin = data_vec.size();
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data_vec.resize(begin + inst.size());
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if (inst.size() != 0) {
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std::memcpy(dmlc::BeginPtr(data_vec) + begin, inst.data(),
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sizeof(Entry) * inst.size());
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}
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}
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namespace data {
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// List of files that will be force linked in static links.
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DMLC_REGISTRY_LINK_TAG(sparse_page_raw_format);
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} // namespace data
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} // namespace xgboost
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