Automatically use new attribute layout if using step-based encoding

Also automatically use steps if using new attribute layout

Author: franzpoeschel

include/openPMD/IO/ADIOS/ADIOS2IOHandler.hpp

@@ -32,6 +32,7 @@
 #include "openPMD/auxiliary/Option.hpp"
 #include "openPMD/backend/Writable.hpp"
 #include "openPMD/config.hpp"
+#include "openPMD/IterationEncoding.hpp"
 
 #if openPMD_HAVE_ADIOS2
 #    include <adios2.h>
@@ -198,6 +199,7 @@ class ADIOS2IOHandlerImpl
 
 private:
     adios2::ADIOS m_ADIOS;
+    IterationEncoding m_iterationEncoding = IterationEncoding::groupBased;
     /**
      * The ADIOS2 engine type, to be passed to adios2::IO::SetEngine
      */
@@ -1085,7 +1087,8 @@ namespace detail
         detail::AttributeReader const m_attributeReader;
         PreloadAdiosAttributes preloadAttributes;
         using AttributeLayout = ADIOS2IOHandlerImpl::AttributeLayout;
-        AttributeLayout m_attributeLayout = AttributeLayout::ByAdiosAttributes;
+        AttributeLayout & m_attributeLayout;
+        IterationEncoding & m_iterationEncoding;
 
         /*
          * We call an attribute committed if the step during which it was

include/openPMD/IO/IOTask.hpp

@@ -25,6 +25,7 @@
 #include "openPMD/backend/Attribute.hpp"
 #include "openPMD/ChunkInfo.hpp"
 #include "openPMD/Dataset.hpp"
+#include "openPMD/IterationEncoding.hpp"
 
 #include <memory>
 #include <map>
@@ -107,7 +108,8 @@ template<>
 struct OPENPMDAPI_EXPORT Parameter< Operation::CREATE_FILE > : public AbstractParameter
 {
     Parameter() = default;
-    Parameter(Parameter const & p) : AbstractParameter(), name(p.name) {}
+    Parameter(Parameter const & p) :
+        AbstractParameter(), name(p.name), encoding(p.encoding) {}
 
     std::unique_ptr< AbstractParameter >
     clone() const override
@@ -117,13 +119,15 @@ struct OPENPMDAPI_EXPORT Parameter< Operation::CREATE_FILE > : public AbstractPa
     }
 
     std::string name = "";
+    IterationEncoding encoding = IterationEncoding::groupBased;
 };
 
 template<>
 struct OPENPMDAPI_EXPORT Parameter< Operation::OPEN_FILE > : public AbstractParameter
 {
     Parameter() = default;
-    Parameter(Parameter const & p) : AbstractParameter(), name(p.name) {}
+    Parameter(Parameter const & p) :
+        AbstractParameter(), name(p.name), encoding(p.encoding) {}
 
     std::unique_ptr< AbstractParameter >
     clone() const override
@@ -133,6 +137,7 @@ struct OPENPMDAPI_EXPORT Parameter< Operation::OPEN_FILE > : public AbstractPara
     }
 
     std::string name = "";
+    IterationEncoding encoding = IterationEncoding::groupBased;
 };
 
 template<>

src/IO/ADIOS/ADIOS2IOHandler.cpp

@@ -295,6 +295,7 @@ void ADIOS2IOHandlerImpl::createFile(
             VERIFY( success, "[ADIOS2] Could not create directory." );
         }
 
+        m_iterationEncoding = parameters.encoding;
         associateWithFile( writable, shared_name );
         this->m_dirty.emplace( shared_name );
         getFileData( shared_name ).m_mode = adios2::Mode::Write; // WORKAROUND
@@ -433,6 +434,7 @@ void ADIOS2IOHandlerImpl::openFile(
     writable->written = true;
     writable->abstractFilePosition = std::make_shared< ADIOS2FilePosition >( );
 
+    m_iterationEncoding = parameters.encoding;
     // enforce opening the file
     // lazy opening is deathly in parallel situations
     getFileData( file );
@@ -2056,6 +2058,7 @@ namespace detail
         , m_readDataset( &impl )
         , m_attributeReader()
         , m_attributeLayout( impl.m_attributeLayout )
+        , m_iterationEncoding( impl.m_iterationEncoding )
         , m_engineType( impl.m_engineType )
     {
         if( !m_IO )
@@ -2127,7 +2130,15 @@ namespace detail
             "bp4", "bp3", "hdf5", "file"
         };
 
+        // step/variable-based iteration encoding requires the new attribute
+        // layout
+        if( m_iterationEncoding == IterationEncoding::stepBased )
+        {
+            m_attributeLayout = AttributeLayout::ByAdiosVariables;
+        }
+
         // set engine type
+        bool isStreaming = false;
         {
             // allow overriding through environment variable
             m_engineType = auxiliary::getEnvString(
@@ -2142,6 +2153,7 @@ namespace detail
             auto it = streamingEngines.find( m_engineType );
             if( it != streamingEngines.end() )
             {
+                isStreaming = true;
                 optimizeAttributesStreaming =
                     m_attributeLayout == AttributeLayout::ByAdiosAttributes;
                 streamStatus = StreamStatus::OutsideOfStep;
@@ -2153,16 +2165,34 @@ namespace detail
                 {
                     switch( m_mode )
                     {
-                        case adios2::Mode::Read:
-                            streamStatus = StreamStatus::Undecided;
-                            delayOpeningTheFirstStep = m_attributeLayout ==
-                                AttributeLayout::ByAdiosAttributes;
+                    case adios2::Mode::Read:
+                        /*
+                         * File engines, read mode:
+                         * Use of steps is dictated by what is detected in the
+                         * file being read.
+                         */
+                        streamStatus = StreamStatus::Undecided;
+                        delayOpeningTheFirstStep = m_attributeLayout ==
+                            AttributeLayout::ByAdiosAttributes;
+                        break;
+                    case adios2::Mode::Write:
+                        /*
+                         * File engines, write mode:
+                         * Default for old layout is no steps.
+                         * Default for new layout is to use steps.
+                         */
+                        switch( m_attributeLayout )
+                        {
+                        case AttributeLayout::ByAdiosVariables:
+                            streamStatus = StreamStatus::OutsideOfStep;
                             break;
-                        case adios2::Mode::Write:
+                        case AttributeLayout::ByAdiosAttributes:
                             streamStatus = StreamStatus::NoStream;
                             break;
-                        default:
-                            throw std::runtime_error( "Unreachable!" );
+                        }
+                        break;
+                    default:
+                        throw std::runtime_error( "Unreachable!" );
                     }
                     optimizeAttributesStreaming = false;
                 }
@@ -2200,8 +2230,7 @@ namespace detail
                 m_mode != adios2::Mode::Read )
             {
                 bool tmp = _useAdiosSteps.json();
-                if( streamStatus == StreamStatus::OutsideOfStep &&
-                    !bool( tmp ) )
+                if( isStreaming && !bool( tmp ) )
                 {
                     throw std::runtime_error(
                         "Cannot switch off steps for streaming engines." );

src/Iteration.cpp

@@ -259,6 +259,7 @@ Iteration::flushFileBased(std::string const& filename, uint64_t i)
         {
             Parameter< Operation::OPEN_FILE > fOpen;
             fOpen.name = filename;
+            fOpen.encoding = IterationEncoding::fileBased;
             IOHandler->enqueue(IOTask(s, fOpen));
             flush();
 

src/Series.cpp

@@ -696,6 +696,7 @@ Series::flushGroupBased( iterations_iterator begin, iterations_iterator end )
         {
             Parameter< Operation::CREATE_FILE > fCreate;
             fCreate.name = *m_name;
+            fCreate.encoding = iterationEncoding();
             IOHandler->enqueue(IOTask(this, fCreate));
         }
 
@@ -782,6 +783,7 @@ Series::readFileBased( )
     Parameter< Operation::OPEN_FILE > fOpen;
     Parameter< Operation::CLOSE_FILE > fClose;
     Parameter< Operation::READ_ATT > aRead;
+    fOpen.encoding = iterationEncoding();
 
     if( !auxiliary::directory_exists(IOHandler->directory) )
         throw no_such_file_error("Supplied directory is not valid: " + IOHandler->directory);
@@ -892,6 +894,7 @@ void
 Series::readGroupBased( bool do_init )
 {
     Parameter< Operation::OPEN_FILE > fOpen;
+    fOpen.encoding = iterationEncoding();
     fOpen.name = *m_name;
     IOHandler->enqueue(IOTask(this, fOpen));
     IOHandler->flush();
@@ -1210,6 +1213,7 @@ Series::openIteration( uint64_t index, Iteration iteration )
 {
     // open the iteration's file again
     Parameter< Operation::OPEN_FILE > fOpen;
+    fOpen.encoding = iterationEncoding();
     fOpen.name = iterationFilename( index );
     IOHandler->enqueue( IOTask( this, fOpen ) );
 

test/SerialIOTest.cpp

@@ -3252,20 +3252,9 @@ TEST_CASE( "serial_iterator", "[serial][adios2]" )
 void
 stepBasedSingleIteration( std::string const & file )
 {
-    std::string config = R"END(
-{
-    "adios2":
-    {
-        "new_attribute_layout": true,
-        "engine":
-        {
-            "usesteps": true
-        }
-    }
-})END";
     constexpr Extent::value_type extent = 1000;
     {
-        Series writeSeries( file, Access::CREATE, config );
+        Series writeSeries( file, Access::CREATE );
         writeSeries.setIterationEncoding( IterationEncoding::stepBased );
         auto iterations = writeSeries.writeIterations();
         auto iteration = writeSeries.iterations[ 0 ];
@@ -3279,7 +3268,7 @@ stepBasedSingleIteration( std::string const & file )
     }
 
     {
-        Series readSeries( file, Access::READ_ONLY, config );
+        Series readSeries( file, Access::READ_ONLY );
 
         auto E_x = readSeries.iterations[ 0 ].meshes[ "E" ][ "x" ];
         REQUIRE( E_x.getDimensionality() == 1 );