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Replaced std::vector with HostDeviceVector in MetaInfo and SparsePage. (#3446)

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* Replaced std::vector with HostDeviceVector in MetaInfo and SparsePage.

- added distributions to HostDeviceVector
- using HostDeviceVector for labels, weights and base margings in MetaInfo
- using HostDeviceVector for offset and data in SparsePage
- other necessary refactoring

* Added const version of HostDeviceVector API calls.

- const versions added to calls that can trigger data transfers, e.g. DevicePointer()
- updated the code that uses HostDeviceVector
- objective functions now accept const HostDeviceVector<bst_float>& for predictions

* Updated src/linear/updater_gpu_coordinate.cu.

* Added read-only state for HostDeviceVector sync.

- this means no copies are performed if both host and devices access
  the HostDeviceVector read-only

* Fixed linter and test errors.

- updated the lz4 plugin
- added ConstDeviceSpan to HostDeviceVector
- using device % dh::NVisibleDevices() for the physical device number,
  e.g. in calls to cudaSetDevice()

* Fixed explicit template instantiation errors for HostDeviceVector.

- replaced HostDeviceVector<unsigned int> with HostDeviceVector<int>

* Fixed HostDeviceVector tests that require multiple GPUs.

- added a mock set device handler; when set, it is called instead of cudaSetDevice()
This commit is contained in:
Andy Adinets
2018-08-30 04:28:47 +02:00
committed by Rory Mitchell
parent 58d783df16
commit 72cd1517d6
45 changed files with 1141 additions and 560 deletions
Download Patch File Download Diff File Expand all files Collapse all files

103
src/c_api/c_api.cc
View File

@@ -250,20 +250,22 @@ XGB_DLL int XGDMatrixCreateFromCSREx(const size_t* indptr,
API_BEGIN();
data::SimpleCSRSource& mat = *source;
mat.page_.offset.reserve(nindptr);
mat.page_.data.reserve(nelem);
mat.page_.offset.resize(1);
mat.page_.offset[0] = 0;
auto& offset_vec = mat.page_.offset.HostVector();
auto& data_vec = mat.page_.data.HostVector();
offset_vec.reserve(nindptr);
data_vec.reserve(nelem);
offset_vec.resize(1);
offset_vec[0] = 0;
size_t num_column = 0;
for (size_t i = 1; i < nindptr; ++i) {
for (size_t j = indptr[i - 1]; j < indptr[i]; ++j) {
if (!common::CheckNAN(data[j])) {
// automatically skip nan.
mat.page_.data.emplace_back(Entry(indices[j], data[j]));
data_vec.emplace_back(Entry(indices[j], data[j]));
num_column = std::max(num_column, static_cast<size_t>(indices[j] + 1));
}
}
mat.page_.offset.push_back(mat.page_.data.size());
offset_vec.push_back(mat.page_.data.Size());
}
mat.info.num_col_ = num_column;
@@ -273,7 +275,7 @@ XGB_DLL int XGDMatrixCreateFromCSREx(const size_t* indptr,
mat.info.num_col_ = num_col;
}
mat.info.num_row_ = nindptr - 1;
mat.info.num_nonzero_ = mat.page_.data.size();
mat.info.num_nonzero_ = mat.page_.data.Size();
*out = new std::shared_ptr<DMatrix>(DMatrix::Create(std::move(source)));
API_END();
}
@@ -305,7 +307,9 @@ XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t* col_ptr,
// FIXME: User should be able to control number of threads
const int nthread = omp_get_max_threads();
data::SimpleCSRSource& mat = *source;
common::ParallelGroupBuilder<Entry> builder(&mat.page_.offset, &mat.page_.data);
auto& offset_vec = mat.page_.offset.HostVector();
auto& data_vec = mat.page_.data.HostVector();
common::ParallelGroupBuilder<Entry> builder(&offset_vec, &data_vec);
builder.InitBudget(0, nthread);
size_t ncol = nindptr - 1; // NOLINT(*)
#pragma omp parallel for schedule(static)
@@ -329,15 +333,16 @@ XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t* col_ptr,
}
}
}
mat.info.num_row_ = mat.page_.offset.size() - 1;
mat.info.num_row_ = mat.page_.offset.Size() - 1;
if (num_row > 0) {
CHECK_LE(mat.info.num_row_, num_row);
// provision for empty rows at the bottom of matrix
auto& offset_vec = mat.page_.offset.HostVector();
for (uint64_t i = mat.info.num_row_; i < static_cast<uint64_t>(num_row); ++i) {
mat.page_.offset.push_back(mat.page_.offset.back());
offset_vec.push_back(offset_vec.back());
}
mat.info.num_row_ = num_row;
CHECK_EQ(mat.info.num_row_, mat.page_.offset.size() - 1); // sanity check
CHECK_EQ(mat.info.num_row_, offset_vec.size() - 1); // sanity check
}
mat.info.num_col_ = ncol;
mat.info.num_nonzero_ = nelem;
@@ -368,7 +373,9 @@ XGB_DLL int XGDMatrixCreateFromMat(const bst_float* data,
API_BEGIN();
data::SimpleCSRSource& mat = *source;
mat.page_.offset.resize(1+nrow);
auto& offset_vec = mat.page_.offset.HostVector();
auto& data_vec = mat.page_.data.HostVector();
offset_vec.resize(1+nrow);
bool nan_missing = common::CheckNAN(missing);
mat.info.num_row_ = nrow;
mat.info.num_col_ = ncol;
@@ -388,9 +395,9 @@ XGB_DLL int XGDMatrixCreateFromMat(const bst_float* data,
}
}
}
mat.page_.offset[i+1] = mat.page_.offset[i] + nelem;
offset_vec[i+1] = offset_vec[i] + nelem;
}
mat.page_.data.resize(mat.page_.data.size() + mat.page_.offset.back());
data_vec.resize(mat.page_.data.Size() + offset_vec.back());
data = data0;
for (xgboost::bst_ulong i = 0; i < nrow; ++i, data += ncol) {
@@ -399,14 +406,14 @@ XGB_DLL int XGDMatrixCreateFromMat(const bst_float* data,
if (common::CheckNAN(data[j])) {
} else {
if (nan_missing || data[j] != missing) {
mat.page_.data[mat.page_.offset[i] + matj] = Entry(j, data[j]);
data_vec[offset_vec[i] + matj] = Entry(j, data[j]);
++matj;
}
}
}
}
mat.info.num_nonzero_ = mat.page_.data.size();
mat.info.num_nonzero_ = mat.page_.data.Size();
*out = new std::shared_ptr<DMatrix>(DMatrix::Create(std::move(source)));
API_END();
}
@@ -461,7 +468,9 @@ XGB_DLL int XGDMatrixCreateFromMat_omp(const bst_float* data, // NOLINT
std::unique_ptr<data::SimpleCSRSource> source(new data::SimpleCSRSource());
data::SimpleCSRSource& mat = *source;
mat.page_.offset.resize(1+nrow);
auto& offset_vec = mat.page_.offset.HostVector();
auto& data_vec = mat.page_.data.HostVector();
offset_vec.resize(1+nrow);
mat.info.num_row_ = nrow;
mat.info.num_col_ = ncol;
@@ -487,7 +496,7 @@ XGB_DLL int XGDMatrixCreateFromMat_omp(const bst_float* data, // NOLINT
++nelem;
}
}
mat.page_.offset[i+1] = nelem;
offset_vec[i+1] = nelem;
}
}
// Inform about any NaNs and resize data matrix
@@ -496,8 +505,8 @@ XGB_DLL int XGDMatrixCreateFromMat_omp(const bst_float* data, // NOLINT
}
// do cumulative sum (to avoid otherwise need to copy)
PrefixSum(&mat.page_.offset[0], mat.page_.offset.size());
mat.page_.data.resize(mat.page_.data.size() + mat.page_.offset.back());
PrefixSum(&offset_vec[0], offset_vec.size());
data_vec.resize(mat.page_.data.Size() + offset_vec.back());
// Fill data matrix (now that know size, no need for slow push_back())
#pragma omp parallel num_threads(nthread)
@@ -508,7 +517,7 @@ XGB_DLL int XGDMatrixCreateFromMat_omp(const bst_float* data, // NOLINT
for (xgboost::bst_ulong j = 0; j < ncol; ++j) {
if (common::CheckNAN(data[ncol * i + j])) {
} else if (nan_missing || data[ncol * i + j] != missing) {
mat.page_.data[mat.page_.offset[i] + matj] =
data_vec[offset_vec[i] + matj] =
Entry(j, data[ncol * i + j]);
++matj;
}
@@ -518,7 +527,7 @@ XGB_DLL int XGDMatrixCreateFromMat_omp(const bst_float* data, // NOLINT
// restore omp state
omp_set_num_threads(nthread_orig);
mat.info.num_nonzero_ = mat.page_.data.size();
mat.info.num_nonzero_ = mat.page_.data.Size();
*out = new std::shared_ptr<DMatrix>(DMatrix::Create(std::move(source)));
API_END();
}
@@ -611,10 +620,11 @@ XGB_DLL int XGDMatrixCreateFromDT(void** data, const char** feature_stypes,
std::unique_ptr<data::SimpleCSRSource> source(new data::SimpleCSRSource());
data::SimpleCSRSource& mat = *source;
mat.page_.offset.resize(1 + nrow);
mat.page_.offset.Resize(1 + nrow);
mat.info.num_row_ = nrow;
mat.info.num_col_ = ncol;
auto& page_offset = mat.page_.offset.HostVector();
#pragma omp parallel num_threads(nthread)
{
// Count elements per row, column by column
@@ -624,15 +634,17 @@ XGB_DLL int XGDMatrixCreateFromDT(void** data, const char** feature_stypes,
for (omp_ulong i = 0; i < nrow; ++i) {
float val = DTGetValue(data[j], dtype, i);
if (!std::isnan(val)) {
mat.page_.offset[i + 1]++;
page_offset[i + 1]++;
}
}
}
}
// do cumulative sum (to avoid otherwise need to copy)
PrefixSum(&mat.page_.offset[0], mat.page_.offset.size());
PrefixSum(&page_offset[0], page_offset.size());
mat.page_.data.resize(mat.page_.data.size() + mat.page_.offset.back());
mat.page_.data.Resize(mat.page_.data.Size() + page_offset.back());
auto& page_data = mat.page_.data.HostVector();
// Fill data matrix (now that know size, no need for slow push_back())
std::vector<size_t> position(nrow);
@@ -644,7 +656,7 @@ XGB_DLL int XGDMatrixCreateFromDT(void** data, const char** feature_stypes,
for (omp_ulong i = 0; i < nrow; ++i) {
float val = DTGetValue(data[j], dtype, i);
if (!std::isnan(val)) {
mat.page_.data[mat.page_.offset[i] + position[i]] = Entry(j, val);
page_data[page_offset[i] + position[i]] = Entry(j, val);
position[i]++;
}
}
@@ -654,7 +666,7 @@ XGB_DLL int XGDMatrixCreateFromDT(void** data, const char** feature_stypes,
// restore omp state
omp_set_num_threads(nthread_orig);
mat.info.num_nonzero_ = mat.page_.data.size();
mat.info.num_nonzero_ = mat.page_.data.Size();
*out = new std::shared_ptr<DMatrix>(DMatrix::Create(std::move(source)));
API_END();
}
@@ -682,24 +694,33 @@ XGB_DLL int XGDMatrixSliceDMatrix(DMatrixHandle handle,
iter->BeforeFirst();
CHECK(iter->Next());
const auto& batch = iter->Value();
const auto& batch = iter->Value();
const auto& src_labels = src.info.labels_.ConstHostVector();
const auto& src_weights = src.info.weights_.ConstHostVector();
const auto& src_base_margin = src.info.base_margin_.ConstHostVector();
auto& ret_labels = ret.info.labels_.HostVector();
auto& ret_weights = ret.info.weights_.HostVector();
auto& ret_base_margin = ret.info.base_margin_.HostVector();
auto& offset_vec = ret.page_.offset.HostVector();
auto& data_vec = ret.page_.data.HostVector();
for (xgboost::bst_ulong i = 0; i < len; ++i) {
const int ridx = idxset[i];
auto inst = batch[ridx];
CHECK_LT(static_cast<xgboost::bst_ulong>(ridx), batch.Size());
ret.page_.data.insert(ret.page_.data.end(), inst.data(),
inst.data() + inst.size());
ret.page_.offset.push_back(ret.page_.offset.back() + inst.size());
data_vec.insert(data_vec.end(), inst.data(),
inst.data() + inst.size());
offset_vec.push_back(offset_vec.back() + inst.size());
ret.info.num_nonzero_ += inst.size();
if (src.info.labels_.size() != 0) {
ret.info.labels_.push_back(src.info.labels_[ridx]);
if (src_labels.size() != 0) {
ret_labels.push_back(src_labels[ridx]);
}
if (src.info.weights_.size() != 0) {
ret.info.weights_.push_back(src.info.weights_[ridx]);
if (src_weights.size() != 0) {
ret_weights.push_back(src_weights[ridx]);
}
if (src.info.base_margin_.size() != 0) {
ret.info.base_margin_.push_back(src.info.base_margin_[ridx]);
if (src_base_margin.size() != 0) {
ret_base_margin.push_back(src_base_margin[ridx]);
}
if (src.info.root_index_.size() != 0) {
ret.info.root_index_.push_back(src.info.root_index_[ridx]);
@@ -771,11 +792,11 @@ XGB_DLL int XGDMatrixGetFloatInfo(const DMatrixHandle handle,
const MetaInfo& info = static_cast<std::shared_ptr<DMatrix>*>(handle)->get()->Info();
const std::vector<bst_float>* vec = nullptr;
if (!std::strcmp(field, "label")) {
vec = &info.labels_;
vec = &info.labels_.HostVector();
} else if (!std::strcmp(field, "weight")) {
vec = &info.weights_;
vec = &info.weights_.HostVector();
} else if (!std::strcmp(field, "base_margin")) {
vec = &info.base_margin_;
vec = &info.base_margin_.HostVector();
} else {
LOG(FATAL) << "Unknown float field name " << field;
}