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Use array interface for CSC matrix. (#8672)

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* Use array interface for CSC matrix.

Use array interface for CSC matrix and align the interface with CSR and dense.

- Fix nthread issue in the R package DMatrix.
- Unify the behavior of handling `missing` with other inputs.
- Unify the behavior of handling `missing` around R, Python, Java, and Scala DMatrix.
- Expose `num_non_missing` to the JVM interface.
- Deprecate old CSR and CSC constructors.
This commit is contained in:
Jiaming Yuan
2023-02-05 01:59:46 +08:00
committed by GitHub
parent 213b5602d9
commit c1786849e3
23 changed files with 673 additions and 380 deletions
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83
src/c_api/c_api.cc
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@@ -1,31 +1,32 @@
/**
* Copyright 2014-2023 by XGBoost Contributors
*/
#include "xgboost/c_api.h"
#include <rabit/c_api.h>
#include <cstring>
#include <fstream>
#include <vector>
#include <string>
#include <memory>
#include <string>
#include <vector>
#include "xgboost/base.h"
#include "xgboost/data.h"
#include "xgboost/host_device_vector.h"
#include "xgboost/learner.h"
#include "xgboost/c_api.h"
#include "xgboost/logging.h"
#include "xgboost/version_config.h"
#include "xgboost/json.h"
#include "xgboost/global_config.h"
#include "c_api_error.h"
#include "c_api_utils.h"
#include "../collective/communicator-inl.h"
#include "../common/io.h"
#include "../common/charconv.h"
#include "../common/io.h"
#include "../data/adapter.h"
#include "../data/simple_dmatrix.h"
#include "c_api_error.h"
#include "c_api_utils.h"
#include "xgboost/base.h"
#include "xgboost/data.h"
#include "xgboost/global_config.h"
#include "xgboost/host_device_vector.h"
#include "xgboost/json.h"
#include "xgboost/learner.h"
#include "xgboost/logging.h"
#include "xgboost/string_view.h" // StringView
#include "xgboost/version_config.h"
#if defined(XGBOOST_USE_FEDERATED)
#include "../../plugin/federated/federated_server.h"
@@ -58,6 +59,13 @@ void XGBBuildInfoDevice(Json *p_info) {
} // namespace xgboost
#endif
namespace {
void DeprecatedFunc(StringView old, StringView since, StringView replacement) {
LOG(WARNING) << "`" << old << "` is deprecated since" << since << ", use `" << replacement
<< "` instead.";
}
} // anonymous namespace
XGB_DLL int XGBuildInfo(char const **out) {
API_BEGIN();
xgboost_CHECK_C_ARG_PTR(out);
@@ -298,7 +306,7 @@ XGB_DLL int XGDeviceQuantileDMatrixCreateFromCallback(DataIterHandle iter, DMatr
int nthread, int max_bin,
DMatrixHandle *out) {
API_BEGIN();
LOG(WARNING) << __func__ << " is deprecated. Use `XGQuantileDMatrixCreateFromCallback` instead.";
DeprecatedFunc(__func__, "1.7.0", "XGQuantileDMatrixCreateFromCallback");
*out = new std::shared_ptr<xgboost::DMatrix>{
xgboost::DMatrix::Create(iter, proxy, nullptr, reset, next, missing, nthread, max_bin)};
API_END();
@@ -398,14 +406,11 @@ XGB_DLL int XGProxyDMatrixSetDataCSR(DMatrixHandle handle, char const *indptr,
// End Create from data iterator
XGB_DLL int XGDMatrixCreateFromCSREx(const size_t* indptr,
const unsigned* indices,
const bst_float* data,
size_t nindptr,
size_t nelem,
size_t num_col,
DMatrixHandle* out) {
XGB_DLL int XGDMatrixCreateFromCSREx(const size_t *indptr, const unsigned *indices,
const bst_float *data, size_t nindptr, size_t nelem,
size_t num_col, DMatrixHandle *out) {
API_BEGIN();
DeprecatedFunc(__func__, "2.0.0", "XGDMatrixCreateFromCSR");
data::CSRAdapter adapter(indptr, indices, data, nindptr - 1, nelem, num_col);
*out = new std::shared_ptr<DMatrix>(DMatrix::Create(&adapter, std::nan(""), 1));
API_END();
@@ -443,14 +448,29 @@ XGB_DLL int XGDMatrixCreateFromDense(char const *data,
API_END();
}
XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t* col_ptr,
const unsigned* indices,
const bst_float* data,
size_t nindptr,
size_t,
size_t num_row,
DMatrixHandle* out) {
XGB_DLL int XGDMatrixCreateFromCSC(char const *indptr, char const *indices, char const *data,
xgboost::bst_ulong nrow, char const *c_json_config,
DMatrixHandle *out) {
API_BEGIN();
xgboost_CHECK_C_ARG_PTR(indptr);
xgboost_CHECK_C_ARG_PTR(indices);
xgboost_CHECK_C_ARG_PTR(data);
data::CSCArrayAdapter adapter{StringView{indptr}, StringView{indices}, StringView{data}, nrow};
xgboost_CHECK_C_ARG_PTR(c_json_config);
auto config = Json::Load(StringView{c_json_config});
float missing = GetMissing(config);
auto n_threads = OptionalArg<Integer, int64_t>(config, "nthread", common::OmpGetNumThreads(0));
xgboost_CHECK_C_ARG_PTR(out);
*out = new std::shared_ptr<DMatrix>(DMatrix::Create(&adapter, missing, n_threads));
API_END();
}
XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t *col_ptr, const unsigned *indices,
const bst_float *data, size_t nindptr, size_t, size_t num_row,
DMatrixHandle *out) {
API_BEGIN();
DeprecatedFunc(__func__, "2.0.0", "XGDMatrixCreateFromCSC");
data::CSCAdapter adapter(col_ptr, indices, data, nindptr - 1, num_row);
xgboost_CHECK_C_ARG_PTR(out);
*out = new std::shared_ptr<DMatrix>(DMatrix::Create(&adapter, std::nan(""), 1));
@@ -1203,8 +1223,7 @@ XGB_DLL int XGBoosterGetModelRaw(BoosterHandle handle, xgboost::bst_ulong *out_l
raw_str.resize(0);
common::MemoryBufferStream fo(&raw_str);
LOG(WARNING) << "`" << __func__
<< "` is deprecated, please use `XGBoosterSaveModelToBuffer` instead.";
DeprecatedFunc(__func__, "1.6.0", "XGBoosterSaveModelToBuffer");
learner->Configure();
learner->SaveModel(&fo);