diff --git a/src/common/threading_utils.h b/src/common/threading_utils.h
index 6f2a953a7..896098aac 100644
--- a/src/common/threading_utils.h
+++ b/src/common/threading_utils.h
@@ -160,6 +160,16 @@ inline int32_t OmpSetNumThreads(int32_t* p_threads) {
   omp_set_num_threads(threads);
   return nthread_original;
 }
+inline int32_t OmpSetNumThreadsWithoutHT(int32_t* p_threads) {
+  auto& threads = *p_threads;
+  int32_t nthread_original = omp_get_max_threads();
+  if (threads <= 0) {
+    threads = nthread_original;
+  }
+  omp_set_num_threads(threads);
+  return nthread_original;
+}
+
 }  // namespace common
 }  // namespace xgboost
 
diff --git a/src/data/data.cc b/src/data/data.cc
index 2d56a6f29..f203fd3dc 100644
--- a/src/data/data.cc
+++ b/src/data/data.cc
@@ -844,7 +844,7 @@ void SparsePage::Push(const SparsePage &batch) {
 template <typename AdapterBatchT>
 uint64_t SparsePage::Push(const AdapterBatchT& batch, float missing, int nthread) {
   // Set number of threads but keep old value so we can reset it after
-  int nthread_original = common::OmpSetNumThreads(&nthread);
+  int nthread_original = common::OmpSetNumThreadsWithoutHT(&nthread);
   auto& offset_vec = offset.HostVector();
   auto& data_vec = data.HostVector();
 
diff --git a/src/data/simple_dmatrix.cc b/src/data/simple_dmatrix.cc
index 437da9754..c39909489 100644
--- a/src/data/simple_dmatrix.cc
+++ b/src/data/simple_dmatrix.cc
@@ -93,7 +93,7 @@ BatchSet<EllpackPage> SimpleDMatrix::GetEllpackBatches(const BatchParam& param)
 template <typename AdapterT>
 SimpleDMatrix::SimpleDMatrix(AdapterT* adapter, float missing, int nthread) {
   // Set number of threads but keep old value so we can reset it after
-  int nthread_original = common::OmpSetNumThreads(&nthread);
+  int nthread_original = common::OmpSetNumThreadsWithoutHT(&nthread);
 
   std::vector<uint64_t> qids;
   uint64_t default_max = std::numeric_limits<uint64_t>::max();