Fix: Late unique_ptr puts without CLOSE_FILE or ADVANCE operations (#1744)

* Add failing test

* Add failing test

* Revert "Add failing test"

This reverts commit 5e04ece.

* Reactivate writing from unique_ptr in finalize()

Author: franzpoeschel

CMakeLists.txt

@@ -803,6 +803,7 @@ if(openPMD_BUILD_TESTING)
             list(APPEND ${out_list}
                 test/Files_SerialIO/close_and_reopen_test.cpp
                 test/Files_SerialIO/filebased_write_test.cpp
+                test/Files_SerialIO/issue_1744_unique_ptrs_at_close_time.cpp
             )
         elseif(${test_name} STREQUAL "ParallelIO" AND openPMD_HAVE_MPI)
             list(APPEND ${out_list}

src/IO/ADIOS/ADIOS2File.cpp

@@ -225,16 +225,18 @@ void ADIOS2File::finalize()
     {
         return;
     }
-    if (!m_uniquePtrPuts.empty())
-    {
-        throw error::Internal(
-            "[ADIOS2 backend] Orphaned unique-ptr put operations found "
-            "when closing file.");
-    }
     // if write accessing, ensure that the engine is opened
-    if (!m_engine && writeOnly(m_mode))
+    // and that all datasets are written
+    // (attributes and unique_ptr datasets are written upon closing a step
+    // or a file which users might never do)
+    bool needToWrite = !m_uniquePtrPuts.empty();
+    if ((needToWrite || !m_engine) && writeOnly(m_mode))
     {
         getEngine();
+        for (auto &entry : m_uniquePtrPuts)
+        {
+            entry.run(*this);
+        }
     }
     if (m_engine)
     {
@@ -250,6 +252,7 @@ void ADIOS2File::finalize()
             m_ADIOS.RemoveIO(m_IOName);
         }
     }
+    m_uniquePtrPuts.clear();
     finalized = true;
 }
 

test/Files_SerialIO/SerialIOTests.hpp

@@ -8,3 +8,7 @@ namespace close_and_reopen_test
 {
 auto close_and_reopen_test() -> void;
 }
+namespace issue_1744_unique_ptrs_at_close_time
+{
+auto issue_1744_unique_ptrs_at_close_time() -> void;
+}

test/Files_SerialIO/issue_1744_unique_ptrs_at_close_time.cpp

@@ -0,0 +1,33 @@
+#include "SerialIOTests.hpp"
+
+#include "openPMD/Dataset.hpp"
+#include "openPMD/openPMD.hpp"
+
+#include <memory>
+#include <numeric>
+
+// clang-format off
+/*
+ * Tests regression introduced with #1743:
+ * terminate called after throwing an instance of 'openPMD::error::Internal'
+ *   what():  Internal error: [ADIOS2 backend] Orphaned unique-ptr put operations found when closing file.
+ * This is a bug. Please report at ' https://github.com/openPMD/openPMD-api/issues'.
+ */
+// clang-format on
+
+namespace issue_1744_unique_ptrs_at_close_time
+{
+auto issue_1744_unique_ptrs_at_close_time() -> void
+{
+    openPMD::Series write(
+        "../samples/issue_1744_unique_ptrs_at_close_time.bp4",
+        openPMD::Access::CREATE,
+        R"({"iteration_encoding": "group_based"})");
+    std::unique_ptr<int[]> data_unique(new int[10]);
+    std::iota(data_unique.get(), data_unique.get() + 10, 0);
+    auto E_x = write.snapshots()[0].meshes["E"]["x"];
+    E_x.resetDataset({openPMD::Datatype::INT, {10}});
+    E_x.storeChunk(std::move(data_unique), {0}, {10});
+    write.close();
+}
+} // namespace issue_1744_unique_ptrs_at_close_time

test/SerialIOTest.cpp

@@ -760,6 +760,14 @@ TEST_CASE("close_and_copy_attributable_test", "[serial]")
     }
 }
 
+TEST_CASE("issue_1744_unique_ptrs_at_close_time", "[serial]")
+{
+#if openPMD_HAVE_ADIOS2
+    issue_1744_unique_ptrs_at_close_time::
+        issue_1744_unique_ptrs_at_close_time();
+#endif
+}
+
 #if openPMD_HAVE_ADIOS2
 TEST_CASE("close_and_reopen_test", "[serial]")
 {