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[R] Use new interface for creating DMatrix from CSR. (#8455)

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* [R] Use new interface for creating DMatrix from CSR.

- CSC is still using the old API.

The old API is not aware of `nthread` parameter, which makes DMatrix to use all available
thread during construction and during transformation lie `SparsePage` -> `CSCPage`.
This commit is contained in:
Jiaming Yuan
2022-11-23 21:36:43 +08:00
committed by GitHub
parent 58d211545f
commit 5f1a6fca0d
6 changed files with 68 additions and 33 deletions
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71
R-package/src/xgboost_R.cc
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@@ -164,33 +164,68 @@ XGB_DLL SEXP XGDMatrixCreateFromCSC_R(SEXP indptr, SEXP indices, SEXP data,
return ret;
}
XGB_DLL SEXP XGDMatrixCreateFromCSR_R(SEXP indptr, SEXP indices, SEXP data,
SEXP num_col, SEXP n_threads) {
XGB_DLL SEXP XGDMatrixCreateFromCSR_R(SEXP indptr, SEXP indices, SEXP data, SEXP num_col,
SEXP n_threads) {
SEXP ret;
R_API_BEGIN();
const int *p_indptr = INTEGER(indptr);
const int *p_indices = INTEGER(indices);
const double *p_data = REAL(data);
size_t nindptr = static_cast<size_t>(length(indptr));
size_t ndata = static_cast<size_t>(length(data));
size_t ncol = static_cast<size_t>(INTEGER(num_col)[0]);
std::vector<size_t> row_ptr_(nindptr);
std::vector<unsigned> indices_(ndata);
std::vector<float> data_(ndata);
for (size_t i = 0; i < nindptr; ++i) {
row_ptr_[i] = static_cast<size_t>(p_indptr[i]);
auto nindptr = static_cast<std::size_t>(length(indptr));
auto ndata = static_cast<std::size_t>(length(data));
auto ncol = static_cast<std::size_t>(INTEGER(num_col)[0]);
std::int32_t threads = asInteger(n_threads);
using xgboost::Array;
using xgboost::Integer;
using xgboost::Json;
using xgboost::Object;
using xgboost::String;
// Construct array interfaces
Json jindptr{Object{}};
Json jindices{Object{}};
Json jdata{Object{}};
jindptr["data"] =
Array{std::vector<Json>{Json{reinterpret_cast<Integer::Int>(p_indptr)}, Json{true}}};
jindptr["shape"] = std::vector<Json>{Json{nindptr}};
jindptr["version"] = Integer{3};
jindices["data"] =
Array{std::vector<Json>{Json{reinterpret_cast<Integer::Int>(p_indices)}, Json{true}}};
jindices["shape"] = std::vector<Json>{Json{ndata}};
jindices["version"] = Integer{3};
jdata["data"] =
Array{std::vector<Json>{Json{reinterpret_cast<Integer::Int>(p_data)}, Json{true}}};
jdata["shape"] = std::vector<Json>{Json{ndata}};
jdata["version"] = Integer{3};
if (DMLC_LITTLE_ENDIAN) {
jindptr["typestr"] = String{"<i4"};
jindices["typestr"] = String{"<i4"};
jdata["typestr"] = String{"<i8"};
} else {
jindptr["typestr"] = String{">i4"};
jindices["typestr"] = String{">i4"};
jdata["typestr"] = String{">i8"};
}
int32_t threads = xgboost::common::OmpGetNumThreads(asInteger(n_threads));
xgboost::common::ParallelFor(ndata, threads, [&](xgboost::omp_ulong i) {
indices_[i] = static_cast<unsigned>(p_indices[i]);
data_[i] = static_cast<float>(p_data[i]);
});
std::string indptr, indices, data;
Json::Dump(jindptr, &indptr);
Json::Dump(jindices, &indices);
Json::Dump(jdata, &data);
DMatrixHandle handle;
CHECK_CALL(XGDMatrixCreateFromCSREx(BeginPtr(row_ptr_), BeginPtr(indices_),
BeginPtr(data_), nindptr, ndata,
ncol, &handle));
Json jconfig{Object{}};
// Construct configuration
jconfig["nthread"] = Integer{threads};
jconfig["missing"] = xgboost::Number{std::numeric_limits<float>::quiet_NaN()};
std::string config;
Json::Dump(jconfig, &config);
CHECK_CALL(XGDMatrixCreateFromCSR(indptr.c_str(), indices.c_str(), data.c_str(), ncol,
config.c_str(), &handle));
ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
R_API_END();
UNPROTECT(1);