Reset Iterations after closing

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franzpoeschel · Nov 21, 2023 · 47da1e9 · 47da1e9
1 parent 7d38a13
commit 47da1e9
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Showing 6 changed files with 39 additions and 7 deletions.
diff --git a/include/openPMD/IO/IOTask.hpp b/include/openPMD/IO/IOTask.hpp
@@ -30,6 +30,7 @@
 #include "openPMD/backend/Attribute.hpp"
 #include "openPMD/backend/ParsePreference.hpp"
 
+#include <any>
 #include <map>
 #include <memory>
 #include <string>
@@ -209,6 +210,8 @@ struct OPENPMDAPI_EXPORT Parameter<Operation::CLOSE_FILE>
     Parameter &operator=(Parameter &&) = default;
     Parameter &operator=(Parameter const &) = default;
 
+    std::any keep_this_data_alive;
+
     std::unique_ptr<AbstractParameter> to_heap() && override
     {
         return std::unique_ptr<AbstractParameter>(

diff --git a/include/openPMD/Iteration.hpp b/include/openPMD/Iteration.hpp
@@ -397,6 +397,8 @@ class Iteration : public Attributable
      *
      */
     void runDeferredParseAccess();
+
+    Iteration resetIteration();
 }; // Iteration
 
 extern template float Iteration::time<float>() const;

diff --git a/src/Iteration.cpp b/src/Iteration.cpp
@@ -866,6 +866,22 @@ void Iteration::linkHierarchy(Writable &w)
     Attributable::linkHierarchy(w);
     meshes.linkHierarchy(this->writable());
     particles.linkHierarchy(this->writable());
+    meshes.writable().ownKeyWithinParent = {"meshes"};
+    particles.writable().ownKeyWithinParent = {"particles"};
+}
+
+Iteration Iteration::resetIteration()
+{
+    Iteration copied = *this;
+    auto parent = writable().parent;
+
+    setData(std::make_shared<internal::IterationData>());
+    meshes = {};
+    particles = {};
+    writable().written = true;
+
+    this->linkHierarchy(*parent);
+    return copied;
 }
 
 void Iteration::runDeferredParseAccess()

diff --git a/src/ReadIterations.cpp b/src/ReadIterations.cpp
@@ -529,8 +529,10 @@ void SeriesIterator::deactivateDeadIteration(iteration_index_t index)
     {
     case IterationEncoding::fileBased: {
         Parameter<Operation::CLOSE_FILE> param;
-        data.series->IOHandler()->enqueue(
-            IOTask(&data.series->iterations[index], std::move(param)));
+        Iteration resetted = data.series->iterations[index].resetIteration();
+        auto writable = &resetted.writable();
+        param.keep_this_data_alive = std::move(resetted);
+        data.series->IOHandler()->enqueue(IOTask(writable, std::move(param)));
         data.series->IOHandler()->flush({FlushLevel::UserFlush});
     }
     break;

diff --git a/src/Series.cpp b/src/Series.cpp
@@ -780,7 +780,10 @@ void Series::flushFileBased(
                 internal::CloseStatus::ClosedInFrontend)
             {
                 Parameter<Operation::CLOSE_FILE> fClose;
-                IOHandler()->enqueue(IOTask(&it->second, std::move(fClose)));
+                Iteration resetted = it->second.resetIteration();
+                auto writable = &resetted.writable();
+                fClose.keep_this_data_alive = std::move(resetted);
+                IOHandler()->enqueue(IOTask(writable, std::move(fClose)));
                 it->second.get().m_closed =
                     internal::CloseStatus::ClosedInBackend;
             }
@@ -838,7 +841,10 @@ void Series::flushFileBased(
                 internal::CloseStatus::ClosedInFrontend)
             {
                 Parameter<Operation::CLOSE_FILE> fClose;
-                IOHandler()->enqueue(IOTask(&it->second, std::move(fClose)));
+                Iteration resetted = it->second.resetIteration();
+                auto writable = &resetted.writable();
+                fClose.keep_this_data_alive = std::move(resetted);
+                IOHandler()->enqueue(IOTask(writable, std::move(fClose)));
                 it->second.get().m_closed =
                     internal::CloseStatus::ClosedInBackend;
             }
@@ -1876,7 +1882,10 @@ AdvanceStatus Series::advance(
             if (itData.m_closed != internal::CloseStatus::ClosedTemporarily)
             {
                 Parameter<Operation::CLOSE_FILE> fClose;
-                IOHandler()->enqueue(IOTask(&iteration, std::move(fClose)));
+                Iteration resetted = iteration.resetIteration();
+                auto writable = &resetted.writable();
+                fClose.keep_this_data_alive = std::move(resetted);
+                IOHandler()->enqueue(IOTask(writable, std::move(fClose)));
             }
             itData.m_closed = internal::CloseStatus::ClosedInBackend;
             break;

diff --git a/test/SerialIOTest.cpp b/test/SerialIOTest.cpp
@@ -6833,13 +6833,13 @@ void varying_pattern(std::string const &file_ending)
             REQUIRE(it.getAttribute("my_step").get<int>() == int(step));
         }
 
-        helper::listSeries(series, true, std::cout);
-
         for (auto i : {0, 8000, 10000, 100000, 2000000})
         {
             auto it = series.iterations[i];
             REQUIRE(it.getAttribute("my_step").get<int>() == i);
         }
+
+        helper::listSeries(series, true, std::cout);
     }
 }