Writing changes: Write current step(s) to snapshot attribute

Author: franzpoeschel

include/openPMD/Series.hpp

@@ -42,6 +42,7 @@
 #endif
 
 #include <map>
+#include <set>
 #include <string>
 
 // expose private and protected members for invasive testing
@@ -86,6 +87,11 @@ class SeriesData : public AttributableData
      * the same instance.
      */
     auxiliary::Option< WriteIterations > m_writeIterations;
+    /**
+     * For writing: Remember which iterations have been written in the currently
+     * active output step. Use this later when writing the snapshot attribute.
+     */
+    std::set< uint64_t > m_currentlyActiveIterations;
     /**
      * Needed if reading a single iteration of a file-based series.
      * Users may specify the concrete filename of one iteration instead of the
@@ -557,6 +563,8 @@ class Series : public Attributable
         internal::AttributableData & file,
         iterations_iterator it,
         Iteration & iteration );
+
+    void flushStep( bool doFlush );
 }; // Series
 } // namespace openPMD
 

src/Series.cpp

@@ -618,11 +618,16 @@ Series::flushFileBased( iterations_iterator begin, iterations_iterator end )
             switch( openIterationIfDirty( it->first, it->second ) )
             {
                 using IO = IterationOpened;
+            case IO::RemainsClosed:
+                // we might need to proceed further if the close status is
+                // ClosedInFrontend
+                // hence no continue here
+                // otherwise, we might forget to close files physically
+                break;
             case IO::HasBeenOpened:
+                // continue below
                 it->second.flush();
                 break;
-            case IO::RemainsClosed:
-                break;
             }
 
             // Phase 2
@@ -701,11 +706,15 @@ Series::flushGorVBased( iterations_iterator begin, iterations_iterator end )
             switch( openIterationIfDirty( it->first, it->second ) )
             {
                 using IO = IterationOpened;
+            case IO::RemainsClosed:
+                // we might need to proceed further if the close status is
+                // ClosedInFrontend
+                // hence no continue here
+                break;
             case IO::HasBeenOpened:
+                // continue below
                 it->second.flush();
                 break;
-            case IO::RemainsClosed:
-                break;
             }
 
             // Phase 2
@@ -739,6 +748,7 @@ Series::flushGorVBased( iterations_iterator begin, iterations_iterator end )
             {
                 using IO = IterationOpened;
             case IO::HasBeenOpened:
+                series.m_currentlyActiveIterations.emplace( it->first );
                 if( !it->second.written() )
                 {
                     it->second.parent() = getWritable( &series.iterations );
@@ -1250,9 +1260,15 @@ Series::advance(
          * opening an iteration's file by beginning a step on it.
          * So, return now.
          */
+        iteration.get().m_closed = internal::CloseStatus::ClosedInBackend;
         return AdvanceStatus::OK;
     }
 
+    if( mode == AdvanceMode::ENDSTEP )
+    {
+        flushStep( /* doFlush = */ false );
+    }
+
     Parameter< Operation::ADVANCE > param;
     if( itData.m_closed == internal::CloseStatus::ClosedTemporarily &&
         series.m_iterationEncoding == IterationEncoding::fileBased )
@@ -1324,6 +1340,28 @@ Series::advance(
     return *param.status;
 }
 
+void Series::flushStep( bool doFlush )
+{
+    auto & series = get();
+    if( !series.m_currentlyActiveIterations.empty() )
+    {
+        // @todo I don't think this understands changing extents over time
+        // Not strictly necessary yet but it might come biting us later
+        Parameter< Operation::WRITE_ATT > wAttr;
+        wAttr.changesOverSteps = true;
+        wAttr.name = "snapshot";
+        wAttr.resource = std::vector< unsigned long long >{
+            series.m_currentlyActiveIterations.begin(),
+            series.m_currentlyActiveIterations.end() };
+        wAttr.dtype = Datatype::VEC_ULONGLONG;
+        IOHandler()->enqueue( IOTask( &series.iterations, wAttr ) );
+        if( doFlush )
+        {
+            IOHandler()->flush();
+        }
+    }
+}
+
 auto Series::openIterationIfDirty( uint64_t index, Iteration iteration )
     -> IterationOpened
 {
@@ -1586,6 +1624,7 @@ SeriesData::~SeriesData()
         {
             Series impl{ { this, []( auto const * ){} } };
             impl.flush();
+            impl.flushStep( /* doFlush = */ true );
         }
     }
     catch( std::exception const & ex )