Allow overwriting old datasets in HDF5

openPMD · Aug 4, 2021 · 58e137a · 58e137a
1 parent 4aff022
commit 58e137a
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Showing 2 changed files with 41 additions and 4 deletions.
diff --git a/src/IO/HDF5/HDF5IOHandler.cpp b/src/IO/HDF5/HDF5IOHandler.cpp
@@ -338,6 +338,47 @@ HDF5IOHandlerImpl::createDataset(Writable* writable,
                                 H5P_DEFAULT);
         VERIFY(node_id >= 0, "[HDF5] Internal error: Failed to open HDF5 group during dataset creation");
 
+        if( m_handler->m_backendAccess == Access::APPEND )
+        {
+            // The dataset might already exist in the file from a previous run
+            // We delete it, otherwise we could not create it again with
+            // possibly different parameters.
+            // This is inefficient, as only the link to the dataset will be
+            // removed, but not the actual dataset
+            // But such is life if overwriting an iteration in Append mode
+            H5G_info_t group_info;
+            herr_t status = H5Gget_info( node_id, &group_info );
+            VERIFY(
+                status == 0,
+                "[HDF5] Internal error: Failed to get HDF5 group info for " +
+                    concrete_h5_file_position( writable ) +
+                    " during dataset creation" );
+            for( hsize_t i = 0; i < group_info.nlinks; ++i )
+            {
+                if( H5G_DATASET != H5Gget_objtype_by_idx( node_id, i ) )
+                {
+                    continue;
+                }
+                ssize_t name_length =
+                    H5Gget_objname_by_idx( node_id, i, nullptr, 0 );
+                std::vector< char > charbuffer( name_length + 1 );
+                H5Gget_objname_by_idx(
+                    node_id, i, charbuffer.data(), name_length + 1 );
+                if( std::strncmp(
+                        name.c_str(), charbuffer.data(), name_length + 1 ) !=
+                    0 )
+                {
+                    continue;
+                }
+                status = H5Ldelete( node_id, name.c_str(), H5P_DEFAULT );
+                VERIFY(
+                    status == 0,
+                    "[HDF5] Internal error: Failed to delete old dataset from "
+                    "group for overwriting." );
+                break;
+            }
+        }
+
         Datatype d = parameters.dtype;
         if( d == Datatype::UNDEFINED )
         {

diff --git a/test/SerialIOTest.cpp b/test/SerialIOTest.cpp
@@ -4677,10 +4677,6 @@ TEST_CASE( "append_mode", "[serial]" )
 {
     for( auto const & t : testedFileExtensions() )
     {
-        if( t == "h5" )
-        {
-            continue;
-        }
         if( t == "bp" )
         {
             std::string jsonConfigOld = R"END(