280 lines
9.1 KiB
C++
280 lines
9.1 KiB
C++
#ifndef XGBOOST_IO_PAGE_FMATRIX_INL_HPP_
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#define XGBOOST_IO_PAGE_FMATRIX_INL_HPP_
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/*!
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* \file page_fmatrix-inl.hpp
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* col iterator based on sparse page
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* \author Tianqi Chen
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*/
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namespace xgboost {
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namespace io {
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/*! \brief thread buffer iterator */
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class ThreadColPageIterator: public utils::IIterator<ColBatch> {
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public:
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ThreadColPageIterator(void) {
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itr.SetParam("buffer_size", "2");
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page_ = NULL;
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}
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virtual ~ThreadColPageIterator(void) {}
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virtual void Init(void) {}
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virtual void BeforeFirst(void) {
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itr.BeforeFirst();
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}
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virtual bool Next(void) {
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if (!itr.Next(page_)) return false;
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out_.col_index = BeginPtr(itr.get_factory().index_set());
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col_data_.resize(page_->offset.size() - 1, SparseBatch::Inst(NULL, 0));
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for (size_t i = 0; i < col_data_.size(); ++i) {
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col_data_[i] = SparseBatch::Inst
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(BeginPtr(page_->data) + page_->offset[i],
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page_->offset[i + 1] - page_->offset[i]);
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}
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out_.col_data = BeginPtr(col_data_);
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out_.size = col_data_.size();
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return true;
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}
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virtual const ColBatch &Value(void) const {
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return out_;
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}
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/*! \brief load and initialize the iterator with fi */
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inline void SetFile(const utils::FileStream &fi) {
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itr.get_factory().SetFile(fi);
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itr.Init();
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}
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// set index set
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inline void SetIndexSet(const std::vector<bst_uint> &fset, bool load_all) {
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itr.get_factory().SetIndexSet(fset, load_all);
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}
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private:
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// output data
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ColBatch out_;
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SparsePage *page_;
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std::vector<SparseBatch::Inst> col_data_;
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utils::ThreadBuffer<SparsePage*, SparsePageFactory> itr;
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};
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/*!
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* \brief sparse matrix that support column access, CSC
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*/
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class FMatrixPage : public IFMatrix {
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public:
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typedef SparseBatch::Entry Entry;
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/*! \brief constructor */
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FMatrixPage(utils::IIterator<RowBatch> *iter,
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const learner::MetaInfo &info) : info(info) {
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this->iter_ = iter;
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}
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// destructor
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virtual ~FMatrixPage(void) {
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if (iter_ != NULL) delete iter_;
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}
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/*! \return whether column access is enabled */
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virtual bool HaveColAccess(void) const {
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return col_size_.size() != 0;
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}
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/*! \brief get number of colmuns */
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virtual size_t NumCol(void) const {
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utils::Check(this->HaveColAccess(), "NumCol:need column access");
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return col_size_.size();
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}
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/*! \brief get number of buffered rows */
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virtual const std::vector<bst_uint> &buffered_rowset(void) const {
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return buffered_rowset_;
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}
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/*! \brief get column size */
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virtual size_t GetColSize(size_t cidx) const {
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return col_size_[cidx];
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}
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/*! \brief get column density */
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virtual float GetColDensity(size_t cidx) const {
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size_t nmiss = num_buffered_row_ - (col_size_[cidx]);
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return 1.0f - (static_cast<float>(nmiss)) / num_buffered_row_;
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}
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virtual void InitColAccess(const std::vector<bool> &enabled,
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float pkeep = 1.0f) {
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if (this->HaveColAccess()) return;
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if (TryLoadColData()) return;
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this->InitColData(enabled, pkeep);
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utils::Check(TryLoadColData(), "failed on creating col.blob");
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}
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/*!
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* \brief get the row iterator associated with FMatrix
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*/
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virtual utils::IIterator<RowBatch>* RowIterator(void) {
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iter_->BeforeFirst();
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return iter_;
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}
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/*!
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* \brief get the column based iterator
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*/
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virtual utils::IIterator<ColBatch>* ColIterator(void) {
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size_t ncol = this->NumCol();
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col_index_.resize(0);
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for (size_t i = 0; i < ncol; ++i) {
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col_index_.push_back(i);
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}
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col_iter_.SetIndexSet(col_index_, false);
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col_iter_.BeforeFirst();
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return &col_iter_;
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}
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/*!
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* \brief colmun based iterator
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*/
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virtual utils::IIterator<ColBatch> *ColIterator(const std::vector<bst_uint> &fset) {
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size_t ncol = this->NumCol();
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col_index_.resize(0);
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for (size_t i = 0; i < fset.size(); ++i) {
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if (fset[i] < ncol) col_index_.push_back(fset[i]);
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}
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col_iter_.SetIndexSet(col_index_, false);
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col_iter_.BeforeFirst();
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return &col_iter_;
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}
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// set the cache file name
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inline void set_cache_file(const std::string &cache_file) {
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col_data_name_ = std::string(cache_file) + ".col.blob";
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col_meta_name_ = std::string(cache_file) + ".col.meta";
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}
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protected:
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inline bool TryLoadColData(void) {
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FILE *fi = fopen64(col_meta_name_.c_str(), "rb");
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if (fi == NULL) return false;
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utils::FileStream fs(fi);
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LoadMeta(&fs);
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fs.Close();
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fi = utils::FopenCheck(col_data_name_.c_str(), "rb");
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if (fi == NULL) return false;
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col_iter_.SetFile(utils::FileStream(fi));
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return true;
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}
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inline void LoadMeta(utils::IStream *fi) {
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utils::Check(fi->Read(&num_buffered_row_, sizeof(num_buffered_row_)) != 0,
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"invalid col.blob file");
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utils::Check(fi->Read(&buffered_rowset_),
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"invalid col.blob file");
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utils::Check(fi->Read(&col_size_),
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"invalid col.blob file");
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}
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inline void SaveMeta(utils::IStream *fo) {
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fo->Write(&num_buffered_row_, sizeof(num_buffered_row_));
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fo->Write(buffered_rowset_);
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fo->Write(col_size_);
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}
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/*!
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* \brief intialize column data
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* \param pkeep probability to keep a row
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*/
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inline void InitColData(const std::vector<bool> &enabled, float pkeep) {
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SparsePage prow, pcol;
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size_t btop = 0;
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// clear rowset
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buffered_rowset_.clear();
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col_size_.resize(info.num_col());
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std::fill(col_size_.begin(), col_size_.end(), 0);
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utils::FileStream fo;
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fo = utils::FileStream(utils::FopenCheck(col_data_name_.c_str(), "wb"));
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// start working
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iter_->BeforeFirst();
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while (iter_->Next()) {
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const RowBatch &batch = iter_->Value();
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for (size_t i = 0; i < batch.size; ++i) {
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bst_uint ridx = static_cast<bst_uint>(batch.base_rowid + i);
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if (pkeep == 1.0f || random::SampleBinary(pkeep)) {
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buffered_rowset_.push_back(ridx);
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prow.Push(batch[i]);
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if (prow.MemCostBytes() >= kPageSize) {
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this->PushColPage(prow, BeginPtr(buffered_rowset_) + btop,
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enabled, &pcol, &fo);
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btop += prow.Size();
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prow.Clear();
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}
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}
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}
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}
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if (prow.Size() != 0) {
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this->PushColPage(prow, BeginPtr(buffered_rowset_) + btop,
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enabled, &pcol, &fo);
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}
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fo.Close();
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num_buffered_row_ = buffered_rowset_.size();
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fo = utils::FileStream(utils::FopenCheck(col_meta_name_.c_str(), "wb"));
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this->SaveMeta(&fo);
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fo.Close();
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}
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inline void PushColPage(const SparsePage &prow,
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const bst_uint *ridx,
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const std::vector<bool> &enabled,
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SparsePage *pcol,
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utils::IStream *fo) {
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pcol->Clear();
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int nthread;
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#pragma omp parallel
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{
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nthread = omp_get_num_threads();
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}
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pcol->Clear();
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utils::ParallelGroupBuilder<SparseBatch::Entry>
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builder(&pcol->offset, &pcol->data);
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builder.InitBudget(info.num_col(), nthread);
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bst_omp_uint ndata = static_cast<bst_uint>(prow.Size());
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#pragma omp parallel for schedule(static)
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for (bst_omp_uint i = 0; i < ndata; ++i) {
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int tid = omp_get_thread_num();
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for (bst_uint j = prow.offset[i]; j < prow.offset[i+1]; ++j) {
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const SparseBatch::Entry &e = prow.data[j];
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if (enabled[e.index]) {
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builder.AddBudget(e.index, tid);
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}
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}
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}
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builder.InitStorage();
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#pragma omp parallel for schedule(static)
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for (bst_omp_uint i = 0; i < ndata; ++i) {
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int tid = omp_get_thread_num();
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for (bst_uint j = prow.offset[i]; j < prow.offset[i+1]; ++j) {
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const SparseBatch::Entry &e = prow.data[j];
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builder.Push(e.index,
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SparseBatch::Entry(ridx[i], e.fvalue),
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tid);
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}
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}
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utils::Assert(pcol->Size() == info.num_col(), "inconsistent col data");
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// sort columns
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bst_omp_uint ncol = static_cast<bst_omp_uint>(pcol->Size());
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#pragma omp parallel for schedule(dynamic, 1)
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for (bst_omp_uint i = 0; i < ncol; ++i) {
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if (pcol->offset[i] < pcol->offset[i + 1]) {
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std::sort(BeginPtr(pcol->data) + pcol->offset[i],
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BeginPtr(pcol->data) + pcol->offset[i + 1], Entry::CmpValue);
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}
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col_size_[i] += pcol->offset[i + 1] - pcol->offset[i];
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}
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pcol->Save(fo);
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}
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private:
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/*! \brief page size 256 M */
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static const size_t kPageSize = 256 << 20UL;
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// shared meta info with DMatrix
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const learner::MetaInfo &info;
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// row iterator
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utils::IIterator<RowBatch> *iter_;
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/*! \brief column based data file name */
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std::string col_data_name_;
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/*! \brief column based data file name */
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std::string col_meta_name_;
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/*! \brief list of row index that are buffered */
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std::vector<bst_uint> buffered_rowset_;
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// number of buffered rows
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size_t num_buffered_row_;
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// count for column data
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std::vector<size_t> col_size_;
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// internal column index for output
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std::vector<bst_uint> col_index_;
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// internal thread backed col iterator
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ThreadColPageIterator col_iter_;
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};
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} // namespace io
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} // namespace xgboost
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#endif // XGBOOST_IO_PAGE_FMATRIX_INL_HPP_
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