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[REFACTOR] completely remove old src

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This commit is contained in:
tqchen
2016-01-09 22:53:36 -08:00
parent d75e3ed05d
commit 5f28617d7d
6 changed files with 23 additions and 124 deletions
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260
src/data/page_csr_source.h Normal file
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/*!
* Copyright (c) 2014 by Contributors
* \file page_dmatrix-inl.hpp
* row iterator based on sparse page
* \author Tianqi Chen
*/
#ifndef XGBOOST_IO_PAGE_DMATRIX_INL_HPP_
#define XGBOOST_IO_PAGE_DMATRIX_INL_HPP_
#include <vector>
#include <string>
#include <algorithm>
#include "../data.h"
#include "../utils/iterator.h"
#include "../utils/thread_buffer.h"
#include "./simple_fmatrix-inl.hpp"
#include "./sparse_batch_page.h"
#include "./page_fmatrix-inl.hpp"
#include "./libsvm_parser.h"
namespace xgboost {
namespace io {
/*! \brief thread buffer iterator */
class ThreadRowPageIterator: public utils::IIterator<RowBatch> {
public:
ThreadRowPageIterator(void) {
itr.SetParam("buffer_size", "4");
page_ = NULL;
base_rowid_ = 0;
}
virtual ~ThreadRowPageIterator(void) {}
virtual void Init(void) {
}
virtual void BeforeFirst(void) {
itr.BeforeFirst();
base_rowid_ = 0;
}
virtual bool Next(void) {
if (!itr.Next(page_)) return false;
out_ = page_->GetRowBatch(base_rowid_);
base_rowid_ += out_.size;
return true;
}
virtual const RowBatch &Value(void) const {
return out_;
}
/*! \brief load and initialize the iterator with fi */
inline void Load(const utils::FileStream &fi) {
itr.get_factory().SetFile(fi, 0);
itr.Init();
this->BeforeFirst();
}
private:
// base row id
size_t base_rowid_;
// output data
RowBatch out_;
SparsePage *page_;
utils::ThreadBuffer<SparsePage*, SparsePageFactory> itr;
};
/*! \brief data matrix using page */
template<int TKMagic>
class DMatrixPageBase : public DataMatrix {
public:
DMatrixPageBase(void) : DataMatrix(kMagic) {
iter_ = new ThreadRowPageIterator();
}
// virtual destructor
virtual ~DMatrixPageBase(void) {
// do not delete row iterator, since it is owned by fmat
// to be cleaned up in a more clear way
}
/*! \brief save a DataMatrix as DMatrixPage */
inline static void Save(const char *fname_, const DataMatrix &mat, bool silent) {
std::string fname = fname_;
utils::FileStream fs(utils::FopenCheck(fname.c_str(), "wb"));
int magic = kMagic;
fs.Write(&magic, sizeof(magic));
mat.info.SaveBinary(fs);
fs.Close();
fname += ".row.blob";
utils::IIterator<RowBatch> *iter = mat.fmat()->RowIterator();
utils::FileStream fbin(utils::FopenCheck(fname.c_str(), "wb"));
SparsePage page;
iter->BeforeFirst();
while (iter->Next()) {
const RowBatch &batch = iter->Value();
for (size_t i = 0; i < batch.size; ++i) {
page.Push(batch[i]);
if (page.MemCostBytes() >= kPageSize) {
page.Save(&fbin); page.Clear();
}
}
}
if (page.data.size() != 0) page.Save(&fbin);
fbin.Close();
if (!silent) {
utils::Printf("DMatrixPage: %lux%lu is saved to %s\n",
static_cast<unsigned long>(mat.info.num_row()), // NOLINT(*)
static_cast<unsigned long>(mat.info.num_col()), fname_); // NOLINT(*)
}
}
/*! \brief load and initialize the iterator with fi */
inline void LoadBinary(utils::FileStream &fi, // NOLINT(*)
bool silent,
const char *fname_) {
this->set_cache_file(fname_);
std::string fname = fname_;
int tmagic;
utils::Check(fi.Read(&tmagic, sizeof(tmagic)) != 0, "invalid input file format");
this->CheckMagic(tmagic);
this->info.LoadBinary(fi);
// load in the row data file
fname += ".row.blob";
utils::FileStream fs(utils::FopenCheck(fname.c_str(), "rb"));
iter_->Load(fs);
if (!silent) {
utils::Printf("DMatrixPage: %lux%lu matrix is loaded",
static_cast<unsigned long>(info.num_row()), // NOLINT(*)
static_cast<unsigned long>(info.num_col())); // NOLINT(*)
if (fname_ != NULL) {
utils::Printf(" from %s\n", fname_);
} else {
utils::Printf("\n");
}
if (info.group_ptr.size() != 0) {
utils::Printf("data contains %u groups\n", (unsigned)info.group_ptr.size() - 1);
}
}
}
/*! \brief save a LibSVM format file as DMatrixPage */
inline void LoadText(const char *uri,
const char* cache_file,
bool silent,
bool loadsplit) {
if (!silent) {
utils::Printf("start generate text file from %s\n", uri);
}
int rank = 0, npart = 1;
if (loadsplit) {
rank = rabit::GetRank();
npart = rabit::GetWorldSize();
}
this->set_cache_file(cache_file);
std::string fname_row = std::string(cache_file) + ".row.blob";
utils::FileStream fo(utils::FopenCheck(fname_row.c_str(), "wb"));
SparsePage page;
size_t bytes_write = 0;
double tstart = rabit::utils::GetTime();
LibSVMParser parser(
dmlc::InputSplit::Create(uri, rank, npart, "text"), 16);
info.Clear();
while (parser.Next()) {
const LibSVMPage &batch = parser.Value();
size_t nlabel = info.labels.size();
info.labels.resize(nlabel + batch.label.size());
if (batch.label.size() != 0) {
std::memcpy(BeginPtr(info.labels) + nlabel,
BeginPtr(batch.label),
batch.label.size() * sizeof(float));
}
page.Push(batch);
for (size_t i = 0; i < batch.data.size(); ++i) {
info.info.num_col = std::max(info.info.num_col,
static_cast<size_t>(batch.data[i].index+1));
}
if (page.MemCostBytes() >= kPageSize) {
bytes_write += page.MemCostBytes();
page.Save(&fo);
page.Clear();
double tdiff = rabit::utils::GetTime() - tstart;
if (!silent) {
utils::Printf("Writting to %s in %g MB/s, %lu MB written\n",
cache_file, (bytes_write >> 20UL) / tdiff,
(bytes_write >> 20UL));
}
}
info.info.num_row += batch.label.size();
}
if (page.data.size() != 0) {
page.Save(&fo);
}
fo.Close();
iter_->Load(utils::FileStream(utils::FopenCheck(fname_row.c_str(), "rb")));
// save data matrix
utils::FileStream fs(utils::FopenCheck(cache_file, "wb"));
int tmagic = kMagic;
fs.Write(&tmagic, sizeof(tmagic));
this->info.SaveBinary(fs);
fs.Close();
if (!silent) {
utils::Printf("DMatrixPage: %lux%lu is parsed from %s\n",
static_cast<unsigned long>(info.num_row()), // NOLINT(*)
static_cast<unsigned long>(info.num_col()), // NOLINT(*)
uri);
}
}
/*! \brief magic number used to identify DMatrix */
static const int kMagic = TKMagic;
/*! \brief page size 32 MB */
static const size_t kPageSize = 32UL << 20UL;
protected:
virtual void set_cache_file(const std::string &cache_file) = 0;
virtual void CheckMagic(int tmagic) = 0;
/*! \brief row iterator */
ThreadRowPageIterator *iter_;
};
class DMatrixPage : public DMatrixPageBase<0xffffab02> {
public:
DMatrixPage(void) {
fmat_ = new FMatrixPage(iter_, this->info);
}
virtual ~DMatrixPage(void) {
delete fmat_;
}
virtual IFMatrix *fmat(void) const {
return fmat_;
}
virtual void set_cache_file(const std::string &cache_file) {
fmat_->set_cache_file(cache_file);
}
virtual void CheckMagic(int tmagic) {
utils::Check(tmagic == DMatrixPageBase<0xffffab02>::kMagic ||
tmagic == DMatrixPageBase<0xffffab03>::kMagic,
"invalid format,magic number mismatch");
}
/*! \brief the real fmatrix */
FMatrixPage *fmat_;
};
// mix of FMatrix S and DMatrix
// cost half of ram usually as DMatrixSimple
class DMatrixHalfRAM : public DMatrixPageBase<0xffffab03> {
public:
DMatrixHalfRAM(void) {
fmat_ = new FMatrixS(iter_, this->info);
}
virtual ~DMatrixHalfRAM(void) {
delete fmat_;
}
virtual IFMatrix *fmat(void) const {
return fmat_;
}
virtual void set_cache_file(const std::string &cache_file) {
}
virtual void CheckMagic(int tmagic) {
utils::Check(tmagic == DMatrixPageBase<0xffffab02>::kMagic ||
tmagic == DMatrixPageBase<0xffffab03>::kMagic,
"invalid format,magic number mismatch");
}
/*! \brief the real fmatrix */
IFMatrix *fmat_;
};
} // namespace io
} // namespace xgboost
#endif // XGBOOST_IO_PAGE_ROW_ITER_INL_HPP_

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src/data/page_dmatrix.cc Normal file
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/*!
* Copyright (c) 2014 by Contributors
* \file page_fmatrix-inl.hpp
* col iterator based on sparse page
* \author Tianqi Chen
*/
#ifndef XGBOOST_IO_PAGE_FMATRIX_INL_HPP_
#define XGBOOST_IO_PAGE_FMATRIX_INL_HPP_
#include <vector>
#include <string>
#include <algorithm>
namespace xgboost {
namespace io {
/*! \brief thread buffer iterator */
class ThreadColPageIterator: public utils::IIterator<ColBatch> {
public:
ThreadColPageIterator(void) {
itr.SetParam("buffer_size", "2");
page_ = NULL;
}
virtual ~ThreadColPageIterator(void) {}
virtual void Init(void) {}
virtual void BeforeFirst(void) {
itr.BeforeFirst();
}
virtual bool Next(void) {
if (!itr.Next(page_)) return false;
out_.col_index = BeginPtr(itr.get_factory().index_set());
col_data_.resize(page_->offset.size() - 1, SparseBatch::Inst(NULL, 0));
for (size_t i = 0; i < col_data_.size(); ++i) {
col_data_[i] = SparseBatch::Inst
(BeginPtr(page_->data) + page_->offset[i],
static_cast<bst_uint>(page_->offset[i + 1] - page_->offset[i]));
}
out_.col_data = BeginPtr(col_data_);
out_.size = col_data_.size();
return true;
}
virtual const ColBatch &Value(void) const {
return out_;
}
/*! \brief load and initialize the iterator with fi */
inline void SetFile(const utils::FileStream &fi) {
itr.get_factory().SetFile(fi);
itr.Init();
}
// set index set
inline void SetIndexSet(const std::vector<bst_uint> &fset, bool load_all) {
itr.get_factory().SetIndexSet(fset, load_all);
}
private:
// output data
ColBatch out_;
SparsePage *page_;
std::vector<SparseBatch::Inst> col_data_;
utils::ThreadBuffer<SparsePage*, SparsePageFactory> itr;
};
struct ColConvertFactory {
inline bool Init(void) {
return true;
}
inline void Setup(float pkeep,
size_t max_row_perbatch,
size_t num_col,
utils::IIterator<RowBatch> *iter,
std::vector<bst_uint> *buffered_rowset,
const std::vector<bool> *enabled) {
pkeep_ = pkeep;
max_row_perbatch_ = max_row_perbatch;
num_col_ = num_col;
iter_ = iter;
buffered_rowset_ = buffered_rowset;
enabled_ = enabled;
}
inline SparsePage *Create(void) {
return new SparsePage();
}
inline void FreeSpace(SparsePage *a) {
delete a;
}
inline void SetParam(const char *name, const char *val) {}
inline bool LoadNext(SparsePage *val) {
tmp_.Clear();
size_t btop = buffered_rowset_->size();
while (iter_->Next()) {
const RowBatch &batch = iter_->Value();
for (size_t i = 0; i < batch.size; ++i) {
bst_uint ridx = static_cast<bst_uint>(batch.base_rowid + i);
if (pkeep_ == 1.0f || random::SampleBinary(pkeep_)) {
buffered_rowset_->push_back(ridx);
tmp_.Push(batch[i]);
}
}
if (tmp_.MemCostBytes() >= kPageSize ||
tmp_.Size() >= max_row_perbatch_) {
this->MakeColPage(tmp_, BeginPtr(*buffered_rowset_) + btop,
*enabled_, val);
return true;
}
}
if (tmp_.Size() != 0) {
this->MakeColPage(tmp_, BeginPtr(*buffered_rowset_) + btop,
*enabled_, val);
return true;
} else {
return false;
}
}
inline void Destroy(void) {}
inline void BeforeFirst(void) {}
inline void MakeColPage(const SparsePage &prow,
const bst_uint *ridx,
const std::vector<bool> &enabled,
SparsePage *pcol) {
pcol->Clear();
int nthread;
#pragma omp parallel
{
nthread = omp_get_num_threads();
int max_nthread = std::max(omp_get_num_procs() / 2 - 4, 1);
if (nthread > max_nthread) {
nthread = max_nthread;
}
}
pcol->Clear();
utils::ParallelGroupBuilder<SparseBatch::Entry>
builder(&pcol->offset, &pcol->data);
builder.InitBudget(num_col_, nthread);
bst_omp_uint ndata = static_cast<bst_uint>(prow.Size());
#pragma omp parallel for schedule(static) num_threads(nthread)
for (bst_omp_uint i = 0; i < ndata; ++i) {
int tid = omp_get_thread_num();
for (size_t j = prow.offset[i]; j < prow.offset[i+1]; ++j) {
const SparseBatch::Entry &e = prow.data[j];
if (enabled[e.index]) {
builder.AddBudget(e.index, tid);
}
}
}
builder.InitStorage();
#pragma omp parallel for schedule(static) num_threads(nthread)
for (bst_omp_uint i = 0; i < ndata; ++i) {
int tid = omp_get_thread_num();
for (size_t j = prow.offset[i]; j < prow.offset[i+1]; ++j) {
const SparseBatch::Entry &e = prow.data[j];
builder.Push(e.index,
SparseBatch::Entry(ridx[i], e.fvalue),
tid);
}
}
utils::Assert(pcol->Size() == num_col_, "inconsistent col data");
// sort columns
bst_omp_uint ncol = static_cast<bst_omp_uint>(pcol->Size());
#pragma omp parallel for schedule(dynamic, 1) num_threads(nthread)
for (bst_omp_uint i = 0; i < ncol; ++i) {
if (pcol->offset[i] < pcol->offset[i + 1]) {
std::sort(BeginPtr(pcol->data) + pcol->offset[i],
BeginPtr(pcol->data) + pcol->offset[i + 1],
SparseBatch::Entry::CmpValue);
}
}
}
// probability of keep
float pkeep_;
// maximum number of rows per batch
size_t max_row_perbatch_;
// number of columns
size_t num_col_;
// row batch iterator
utils::IIterator<RowBatch> *iter_;
// buffered rowset
std::vector<bst_uint> *buffered_rowset_;
// enabled marks
const std::vector<bool> *enabled_;
// internal temp cache
SparsePage tmp_;
/*! \brief page size 256 M */
static const size_t kPageSize = 256 << 20UL;
};
/*!
* \brief sparse matrix that support column access, CSC
*/
class FMatrixPage : public IFMatrix {
public:
typedef SparseBatch::Entry Entry;
/*! \brief constructor */
FMatrixPage(utils::IIterator<RowBatch> *iter,
const learner::MetaInfo &info) : info(info) {
this->iter_ = iter;
}
// destructor
virtual ~FMatrixPage(void) {
if (iter_ != NULL) delete iter_;
}
/*! \return whether column access is enabled */
virtual bool HaveColAccess(void) const {
return col_size_.size() != 0;
}
/*! \brief get number of columns */
virtual size_t NumCol(void) const {
utils::Check(this->HaveColAccess(), "NumCol:need column access");
return col_size_.size();
}
/*! \brief get number of buffered rows */
virtual const std::vector<bst_uint> &buffered_rowset(void) const {
return buffered_rowset_;
}
/*! \brief get column size */
virtual size_t GetColSize(size_t cidx) const {
return col_size_[cidx];
}
/*! \brief get column density */
virtual float GetColDensity(size_t cidx) const {
size_t nmiss = num_buffered_row_ - (col_size_[cidx]);
return 1.0f - (static_cast<float>(nmiss)) / num_buffered_row_;
}
virtual void InitColAccess(const std::vector<bool> &enabled,
float pkeep, size_t max_row_perbatch) {
if (this->HaveColAccess()) return;
if (TryLoadColData()) return;
this->InitColData(enabled, pkeep, max_row_perbatch);
utils::Check(TryLoadColData(), "failed on creating col.blob");
}
/*!
* \brief get the row iterator associated with FMatrix
*/
virtual utils::IIterator<RowBatch>* RowIterator(void) {
iter_->BeforeFirst();
return iter_;
}
/*!
* \brief get the column based iterator
*/
virtual utils::IIterator<ColBatch>* ColIterator(void) {
size_t ncol = this->NumCol();
col_index_.resize(0);
for (size_t i = 0; i < ncol; ++i) {
col_index_.push_back(static_cast<bst_uint>(i));
}
col_iter_.SetIndexSet(col_index_, false);
col_iter_.BeforeFirst();
return &col_iter_;
}
/*!
* \brief column based iterator
*/
virtual utils::IIterator<ColBatch> *ColIterator(const std::vector<bst_uint> &fset) {
size_t ncol = this->NumCol();
col_index_.resize(0);
for (size_t i = 0; i < fset.size(); ++i) {
if (fset[i] < ncol) col_index_.push_back(fset[i]);
}
col_iter_.SetIndexSet(col_index_, false);
col_iter_.BeforeFirst();
return &col_iter_;
}
// set the cache file name
inline void set_cache_file(const std::string &cache_file) {
col_data_name_ = std::string(cache_file) + ".col.blob";
col_meta_name_ = std::string(cache_file) + ".col.meta";
}
protected:
inline bool TryLoadColData(void) {
std::FILE *fi = fopen64(col_meta_name_.c_str(), "rb");
if (fi == NULL) return false;
utils::FileStream fs(fi);
LoadMeta(&fs);
fs.Close();
fi = utils::FopenCheck(col_data_name_.c_str(), "rb");
if (fi == NULL) return false;
col_iter_.SetFile(utils::FileStream(fi));
return true;
}
inline void LoadMeta(utils::IStream *fi) {
utils::Check(fi->Read(&num_buffered_row_, sizeof(num_buffered_row_)) != 0,
"invalid col.blob file");
utils::Check(fi->Read(&buffered_rowset_),
"invalid col.blob file");
utils::Check(fi->Read(&col_size_),
"invalid col.blob file");
}
inline void SaveMeta(utils::IStream *fo) {
fo->Write(&num_buffered_row_, sizeof(num_buffered_row_));
fo->Write(buffered_rowset_);
fo->Write(col_size_);
}
/*!
* \brief initialize column data
* \param enabled the list of enabled columns
* \param pkeep probability to keep a row
* \param max_row_perbatch maximum row per batch
*/
inline void InitColData(const std::vector<bool> &enabled,
float pkeep, size_t max_row_perbatch) {
// clear rowset
buffered_rowset_.clear();
col_size_.resize(info.num_col());
std::fill(col_size_.begin(), col_size_.end(), 0);
utils::FileStream fo;
fo = utils::FileStream(utils::FopenCheck(col_data_name_.c_str(), "wb"));
iter_->BeforeFirst();
double tstart = rabit::utils::GetTime();
size_t bytes_write = 0;
utils::ThreadBuffer<SparsePage*, ColConvertFactory> citer;
citer.SetParam("buffer_size", "2");
citer.get_factory().Setup(pkeep, max_row_perbatch, info.num_col(),
iter_, &buffered_rowset_, &enabled);
citer.Init();
SparsePage *pcol;
while (citer.Next(pcol)) {
for (size_t i = 0; i < pcol->Size(); ++i) {
col_size_[i] += pcol->offset[i + 1] - pcol->offset[i];
}
pcol->Save(&fo);
size_t spage = pcol->MemCostBytes();
bytes_write += spage;
double tnow = rabit::utils::GetTime();
double tdiff = tnow - tstart;
utils::Printf("Writing to %s in %g MB/s, %lu MB written\n",
col_data_name_.c_str(),
(bytes_write >> 20UL) / tdiff,
(bytes_write >> 20UL));
}
fo.Close();
num_buffered_row_ = buffered_rowset_.size();
fo = utils::FileStream(utils::FopenCheck(col_meta_name_.c_str(), "wb"));
this->SaveMeta(&fo);
fo.Close();
}
private:
/*! \brief page size 256 M */
static const size_t kPageSize = 256 << 20UL;
// shared meta info with DMatrix
const learner::MetaInfo &info;
// row iterator
utils::IIterator<RowBatch> *iter_;
/*! \brief column based data file name */
std::string col_data_name_;
/*! \brief column based data file name */
std::string col_meta_name_;
/*! \brief list of row index that are buffered */
std::vector<bst_uint> buffered_rowset_;
// number of buffered rows
size_t num_buffered_row_;
// count for column data
std::vector<size_t> col_size_;
// internal column index for output
std::vector<bst_uint> col_index_;
// internal thread backed col iterator
ThreadColPageIterator col_iter_;
};
} // namespace io
} // namespace xgboost
#endif // XGBOOST_IO_PAGE_FMATRIX_INL_HPP_