Step-based iteration layout

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>
@@ -224,6 +225,7 @@ class ADIOS2IOHandlerImpl
 
 private:
     adios2::ADIOS m_ADIOS;
+    IterationEncoding m_iterationEncoding = IterationEncoding::groupBased;
     /**
      * The ADIOS2 engine type, to be passed to adios2::IO::SetEngine
      */
@@ -1367,7 +1369,7 @@ class ADIOS2IOHandler : public AbstractIOHandler
 {
 #if openPMD_HAVE_ADIOS2
 
-friend class ADIOS2IOHandlerImpl;
+    friend class ADIOS2IOHandlerImpl;
 
 private:
     ADIOS2IOHandlerImpl m_impl;
@@ -1386,7 +1388,7 @@ friend class ADIOS2IOHandlerImpl;
         }
         catch( ... )
         {
-            std::cerr << "[~ADIOS2IOHandler] An error occurred." << std::endl;
+             std::cerr << "[~ADIOS2IOHandler] An error occurred." << std::endl;
         }
     }
 

include/openPMD/IO/AbstractIOHandlerImpl.hpp

@@ -241,6 +241,7 @@ class AbstractIOHandlerImpl
    *
    * The operation should overwrite existing file positions, even when the Writable was already marked written.
    * The path parameters.path may contain multiple levels (e.g. first/second/third/). This path should be relative (i.e. it should not start with a slash "/").
+   * The number of levels may be zero, i.e. parameters.path may be an empty string.
    * The Writables file position should correspond to the complete opened path (i.e. first/second/third/ should be assigned to the Writables file position).
    * The Writable should be marked written when the operation completes successfully.
    */

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>
@@ -108,7 +109,8 @@ 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
@@ -118,13 +120,15 @@ 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
@@ -134,6 +138,7 @@ struct OPENPMDAPI_EXPORT Parameter< Operation::OPEN_FILE > : public AbstractPara
     }
 
     std::string name = "";
+    IterationEncoding encoding = IterationEncoding::groupBased;
 };
 
 template<>

include/openPMD/Iteration.hpp

@@ -156,13 +156,15 @@ class Iteration : public LegacyAttributable
 
     struct DeferredParseAccess
     {
-        std::string index;
+        std::string path;
+        uint64_t iteration = 0;
         bool fileBased = false;
         std::string filename;
     };
 
     void flushFileBased(std::string const&, uint64_t);
     void flushGroupBased(uint64_t);
+    void flushVariableBased(uint64_t);
     void flush();
     void deferParseAccess( DeferredParseAccess );
     /*

include/openPMD/IterationEncoding.hpp

@@ -31,7 +31,7 @@ namespace openPMD
  */
 enum class IterationEncoding
 {
-    fileBased, groupBased
+    fileBased, groupBased, variableBased
 };
 
 std::ostream&

include/openPMD/Series.hpp

@@ -342,13 +342,20 @@ class SeriesImpl : public AttributableImpl
 
     std::unique_ptr< ParsedInput > parseInput(std::string);
     void init(std::shared_ptr< AbstractIOHandler >, std::unique_ptr< ParsedInput >);
-    void initDefaults();
+    void initDefaults( IterationEncoding );
     std::future< void > flush_impl(
         iterations_iterator begin,
         iterations_iterator end,
         FlushLevel );
     void flushFileBased( iterations_iterator begin, iterations_iterator end );
-    void flushGroupBased( iterations_iterator begin, iterations_iterator end );
+    /*
+     * Group-based and variable-based iteration layouts share a lot of logic
+     * (realistically, the variable-based iteration layout only throws out
+     *  one layer in the hierarchy).
+     * As a convention, methods that deal with both layouts are called
+     * .*GorVBased, short for .*GroupOrVariableBased
+     */
+    void flushGorVBased( iterations_iterator begin, iterations_iterator end );
     void flushMeshesPath();
     void flushParticlesPath();
     void readFileBased( );
@@ -361,7 +368,7 @@ class SeriesImpl : public AttributableImpl
      * as of yet. Such a facility will be required upon implementing things such
      * as resizable datasets.
      */
-    void readGroupBased( bool init = true );
+    void readGorVBased( bool init = true );
     void readBase();
     std::string iterationFilename( uint64_t i );
     void openIteration( uint64_t index, Iteration iteration );

include/openPMD/backend/Attributable.hpp

@@ -215,7 +215,7 @@ class AttributableImpl
     std::vector< std::string > myPath() const;
 
     void flushAttributes();
-    void readAttributes();
+    void readAttributes( bool reread = false );
 
     /** Retrieve the value of a floating point Attribute of user-defined precision with ensured type-safety.
      *

src/IO/ADIOS/ADIOS1IOHandler.cpp

@@ -95,6 +95,9 @@ ADIOS1IOHandlerImpl::flush()
                 case O::CREATE_PATH:
                     createPath(i.writable, deref_dynamic_cast< Parameter< O::CREATE_PATH > >(i.parameter.get()));
                     break;
+                case O::OPEN_PATH:
+                    openPath(i.writable, deref_dynamic_cast< Parameter< O::OPEN_PATH > >(i.parameter.get()));
+                    break;
                 case O::CREATE_DATASET:
                     createDataset(i.writable, deref_dynamic_cast< Parameter< O::CREATE_DATASET > >(i.parameter.get()));
                     break;
@@ -129,9 +132,6 @@ ADIOS1IOHandlerImpl::flush()
                 case O::EXTEND_DATASET:
                     extendDataset(i.writable, deref_dynamic_cast< Parameter< O::EXTEND_DATASET > >(i.parameter.get()));
                     break;
-                case O::OPEN_PATH:
-                    openPath(i.writable, deref_dynamic_cast< Parameter< O::OPEN_PATH > >(i.parameter.get()));
-                    break;
                 case O::CLOSE_PATH:
                     closePath(i.writable, deref_dynamic_cast< Parameter< O::CLOSE_PATH > >(i.parameter.get()));
                     break;
@@ -243,6 +243,7 @@ ADIOS1IOHandler::enqueue(IOTask const& i)
     {
         case Operation::CREATE_FILE:
         case Operation::CREATE_PATH:
+        case Operation::OPEN_PATH:
         case Operation::CREATE_DATASET:
         case Operation::OPEN_FILE:
         case Operation::WRITE_ATT:

src/IO/ADIOS/ADIOS2IOHandler.cpp

@@ -289,6 +289,7 @@ 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
@@ -470,6 +471,7 @@ 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 );
@@ -512,7 +514,9 @@ void ADIOS2IOHandlerImpl::openPath(
     std::string prefix =
         filePositionToString( setAndGetFilePosition( writable->parent ) );
     std::string suffix = auxiliary::removeSlashes( parameters.path );
-    std::string infix = auxiliary::ends_with( prefix, '/' ) ? "" : "/";
+    std::string infix = suffix.empty() || auxiliary::ends_with( prefix, '/' )
+        ? ""
+        : "/";
 
     /* ADIOS has no concept for explicitly creating paths.
      * They are implicitly created with the paths of variables/attributes. */
@@ -1525,9 +1529,27 @@ namespace detail
         adios2::Dims const & count,
         bool const constantDims )
     {
-        adios2::Variable< T > var =
-            IO.DefineVariable< T >( name, shape, start, count, constantDims );
-        if ( !var )
+        /*
+         * Step/Variable-based iteration layout:
+         * The variable may already be defined from a previous step,
+         * so check if it's already here.
+         */
+        adios2::Variable< T > var = IO.InquireVariable< T >( name );
+        if( !var )
+        {
+            var = IO.DefineVariable< T >(
+                name, shape, start, count, constantDims );
+        }
+        else
+        {
+            var.SetShape( shape );
+            if( count.size() > 0 )
+            {
+                var.SetSelection( { start, count } );
+            }
+        }
+
+        if( !var )
         {
             throw std::runtime_error(
                 "[ADIOS2] Internal error: Could not create Variable '" + name + "'." );
@@ -2206,6 +2228,12 @@ namespace detail
             "bp4", "bp3", "hdf5", "file"
         };
 
+        // step/variable-based iteration encoding requires the new schema
+        if( m_impl->m_iterationEncoding == IterationEncoding::variableBased )
+        {
+            m_impl->m_schema = ADIOS2Schema::schema_2021_02_09;
+        }
+
         // set engine type
         bool isStreaming = false;
         {

src/IO/ADIOS/CommonADIOS1IOHandler.cpp

@@ -677,10 +677,13 @@ CommonADIOS1IOHandlerImpl::openPath(
 {
     /* Sanitize path */
     std::string path = parameters.path;
-    if( auxiliary::starts_with(path, '/') )
-        path = auxiliary::replace_first(path, "/", "");
-    if( !auxiliary::ends_with(path, '/') )
-        path += '/';
+    if( !path.empty() )
+    {
+        if( auxiliary::starts_with(path, '/') )
+            path = auxiliary::replace_first(path, "/", "");
+        if( !auxiliary::ends_with(path, '/') )
+            path += '/';
+    }
 
     writable->written = true;
     writable->abstractFilePosition = std::make_shared< ADIOS1FilePosition >(path);

src/IO/ADIOS/ParallelADIOS1IOHandler.cpp

@@ -119,6 +119,9 @@ ParallelADIOS1IOHandlerImpl::flush()
                 case O::CREATE_PATH:
                     createPath(i.writable, deref_dynamic_cast< Parameter< O::CREATE_PATH > >(i.parameter.get()));
                     break;
+                case O::OPEN_PATH:
+                    openPath(i.writable, deref_dynamic_cast< Parameter< O::OPEN_PATH > >(i.parameter.get()));
+                    break;
                 case O::CREATE_DATASET:
                     createDataset(i.writable, deref_dynamic_cast< Parameter< O::CREATE_DATASET > >(i.parameter.get()));
                     break;
@@ -151,9 +154,6 @@ ParallelADIOS1IOHandlerImpl::flush()
                 case O::EXTEND_DATASET:
                     extendDataset(i.writable, deref_dynamic_cast< Parameter< O::EXTEND_DATASET > >(i.parameter.get()));
                     break;
-                case O::OPEN_PATH:
-                    openPath(i.writable, deref_dynamic_cast< Parameter< O::OPEN_PATH > >(i.parameter.get()));
-                    break;
                 case O::CLOSE_PATH:
                     closePath(i.writable, deref_dynamic_cast< Parameter< O::CLOSE_PATH > >(i.parameter.get()));
                     break;
@@ -265,6 +265,7 @@ ParallelADIOS1IOHandler::enqueue(IOTask const& i)
     {
         case Operation::CREATE_FILE:
         case Operation::CREATE_PATH:
+        case Operation::OPEN_PATH:
         case Operation::CREATE_DATASET:
         case Operation::OPEN_FILE:
         case Operation::WRITE_ATT:

src/IO/HDF5/HDF5IOHandler.cpp

@@ -528,19 +528,23 @@ HDF5IOHandlerImpl::openPath(
 
     /* Sanitize path */
     std::string path = parameters.path;
-    if( auxiliary::starts_with(path, '/') )
-        path = auxiliary::replace_first(path, "/", "");
-    if( !auxiliary::ends_with(path, '/') )
-        path += '/';
+    if( !path.empty() )
+    {
+        if( auxiliary::starts_with(path, '/') )
+            path = auxiliary::replace_first(path, "/", "");
+        if( !auxiliary::ends_with(path, '/') )
+            path += '/';
+        path_id = H5Gopen(node_id,
+                        path.c_str(),
+                        H5P_DEFAULT);
+        VERIFY(path_id >= 0, "[HDF5] Internal error: Failed to open HDF5 group during path opening");
 
-    path_id = H5Gopen(node_id,
-                      path.c_str(),
-                      H5P_DEFAULT);
-    VERIFY(path_id >= 0, "[HDF5] Internal error: Failed to open HDF5 group during path opening");
+        herr_t status;
+        status = H5Gclose(path_id);
+        VERIFY(status == 0, "[HDF5] Internal error: Failed to close HDF5 group during path opening");
+    }
 
     herr_t status;
-    status = H5Gclose(path_id);
-    VERIFY(status == 0, "[HDF5] Internal error: Failed to close HDF5 group during path opening");
     status = H5Gclose(node_id);
     VERIFY(status == 0, "[HDF5] Internal error: Failed to close HDF5 group during path opening");