From b0cc773ad9838608ed99c30932c18044550174fb Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Wed, 10 Jun 2026 22:30:26 -0400
Subject: [PATCH] Fix GH issue 203: disconnected SMARTS crash with
 multithreaded preprocessing

buildQueryBatchParallel ran addQueryToBatch inside an OpenMP parallel region.
The validation error for fragment (disconnected) queries escaped the region and
called std::terminate whenever more than one preprocessing thread was used, so
the error only surfaced as a RuntimeError on the single-threaded path. Capture
the first exception with OpenMPExceptionRegistry and rethrow once the region
joins.
---
 nvmolkit/tests/test_substructure.py | 17 +++++++++++++++++
 src/substruct/CMakeLists.txt        |  2 +-
 src/substruct/molecules.cpp         | 17 +++++++++++++++--
 3 files changed, 33 insertions(+), 3 deletions(-)

diff --git a/nvmolkit/tests/test_substructure.py b/nvmolkit/tests/test_substructure.py
index 5d3fda33..2fd6161c 100644
--- a/nvmolkit/tests/test_substructure.py
+++ b/nvmolkit/tests/test_substructure.py
@@ -202,6 +202,23 @@ def test_buffer_overflow_rdkit_fallback(self):
         assert len(results[0][0]) == 10, f"Should get all 10 matches via RDKit fallback, got {len(results[0][0])}"
         assert matches_equal(results[0][0], rdkit_matches), "Matches should be identical to RDKit results"
 
+    @pytest.mark.parametrize("preprocessing_threads", [1, 2, -1])
+    def test_disconnected_smarts_raises(self, preprocessing_threads: int):
+        """Disconnected (fragment) SMARTS must raise rather than crash the process.
+
+        Regression test for GH issue 203: with more than one preprocessing
+        thread the validation error escaped the OpenMP region and terminated the
+        process. The unsupported-query error must surface as a RuntimeError for
+        every preprocessing-thread count.
+        """
+        targets = [Chem.MolFromSmiles(smi) for smi in ("CC", "CCC", "CCCC")]
+        queries = [Chem.MolFromSmarts("C.C")]
+
+        config = SubstructSearchConfig(preprocessingThreads=preprocessing_threads)
+
+        with pytest.raises(RuntimeError, match="disconnected"):
+            hasSubstructMatch(targets, queries, config)
+
     def test_no_match_possible(self):
         """Test when no match is possible."""
         targets = [Chem.MolFromSmiles("CCCC")]
diff --git a/src/substruct/CMakeLists.txt b/src/substruct/CMakeLists.txt
index d52bb24d..b620bc08 100644
--- a/src/substruct/CMakeLists.txt
+++ b/src/substruct/CMakeLists.txt
@@ -22,7 +22,7 @@ target_include_directories(molecules PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 target_link_libraries(
   molecules
   PUBLIC device_vector flatBitVect OpenMP::OpenMP_CXX packed_bonds device
-  PRIVATE ${RDKit_LIBS} nvtx)
+  PRIVATE ${RDKit_LIBS} nvtx openmp_helpers)
 
 add_library(substruct_kernels substruct_kernels.cu)
 target_include_directories(substruct_kernels PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
diff --git a/src/substruct/molecules.cpp b/src/substruct/molecules.cpp
index 3613b9b0..fc14e853 100644
--- a/src/substruct/molecules.cpp
+++ b/src/substruct/molecules.cpp
@@ -25,11 +25,13 @@
 
 #include <algorithm>
 #include <cstring>
+#include <exception>
 #include <functional>
 #include <stdexcept>
 #include <string>
 
 #include "nvtx.h"
+#include "openmp_helpers.h"
 #include "packed_bonds.h"
 #include "rdkit_compat.h"
 #include "substruct_debug.h"
@@ -2128,6 +2130,12 @@ MoleculesHost buildQueryBatchParallel(const std::vector<const RDKit::ROMol*>& mo
     threadBatches[t].reserve(molsPerThread, atomsPerThread);
   }
 
+  // addQueryToBatch validates each query and throws on unsupported inputs (e.g.
+  // disconnected SMARTS). An exception escaping the OpenMP region would call
+  // std::terminate, so capture the first failure and rethrow after the region
+  // joins.
+  detail::OpenMPExceptionRegistry exceptionRegistry;
+
 #pragma omp parallel num_threads(numThreads)
   {
     const int       tid = omp_get_thread_num();
@@ -2136,10 +2144,15 @@ MoleculesHost buildQueryBatchParallel(const std::vector<const RDKit::ROMol*>& mo
 
 #pragma omp for schedule(static)
     for (int i = 0; i < numMols; ++i) {
-      const int molIdx = useSortOrder ? sortOrder[i] : i;
-      addQueryToBatch(molecules[molIdx], localBatch);
+      try {
+        const int molIdx = useSortOrder ? sortOrder[i] : i;
+        addQueryToBatch(molecules[molIdx], localBatch);
+      } catch (...) {
+        exceptionRegistry.store(std::current_exception());
+      }
     }
   }
+  exceptionRegistry.rethrow();
 
   MoleculesHost result;
   {