Fixes

franzpoeschel · Dec 16, 2024 · 058dc4c · 058dc4c
1 parent d255eaa
commit 058dc4c
Show file tree

Hide file tree

Showing 7 changed files with 49 additions and 19 deletions.
diff --git a/include/openPMD/IO/ADIOS/ADIOS2IOHandler.hpp b/include/openPMD/IO/ADIOS/ADIOS2IOHandler.hpp
@@ -434,7 +434,8 @@ class ADIOS2IOHandlerImpl
         Offset const &offset,
         Extent const &extent,
         adios2::IO &IO,
-        std::string const &varName)
+        std::string const &varName,
+        std::optional<size_t> stepSelection)
     {
         {
             auto requiredType = adios2::GetType<T>();
@@ -461,6 +462,10 @@ class ADIOS2IOHandlerImpl
             throw std::runtime_error(
                 "[ADIOS2] Internal error: Failed opening ADIOS2 variable.");
         }
+        if (stepSelection.has_value())
+        {
+            var.SetStepSelection({*stepSelection, 1});
+        }
         // TODO leave this check to ADIOS?
         adios2::Dims shape = var.Shape();
         auto actualDim = shape.size();

diff --git a/src/IO/ADIOS/ADIOS2File.cpp b/src/IO/ADIOS/ADIOS2File.cpp
@@ -62,12 +62,8 @@ void DatasetReader::call(
     std::string const &fileName,
     std::optional<size_t> stepSelection)
 {
-    adios2::Variable<T> var =
-        impl->verifyDataset<T>(bp.param.offset, bp.param.extent, IO, bp.name);
-    if (stepSelection.has_value())
-    {
-        var.SetStepSelection({*stepSelection, 1});
-    }
+    adios2::Variable<T> var = impl->verifyDataset<T>(
+        bp.param.offset, bp.param.extent, IO, bp.name, stepSelection);
     if (!var)
     {
         throw std::runtime_error(
@@ -96,7 +92,11 @@ void WriteDataset::call(ADIOS2File &ba, detail::BufferedPut &bp)
                 auto ptr = static_cast<T const *>(arg.get());
 
                 adios2::Variable<T> var = ba.m_impl->verifyDataset<T>(
-                    bp.param.offset, bp.param.extent, ba.m_IO, bp.name);
+                    bp.param.offset,
+                    bp.param.extent,
+                    ba.m_IO,
+                    bp.name,
+                    std::nullopt);
 
                 ba.getEngine().Put(var, ptr);
             }
@@ -160,7 +160,11 @@ struct RunUniquePtrPut
     {
         auto ptr = static_cast<T const *>(bufferedPut.data.get());
         adios2::Variable<T> var = ba.m_impl->verifyDataset<T>(
-            bufferedPut.offset, bufferedPut.extent, ba.m_IO, bufferedPut.name);
+            bufferedPut.offset,
+            bufferedPut.extent,
+            ba.m_IO,
+            bufferedPut.name,
+            std::nullopt);
         ba.getEngine().Put(var, ptr);
     }
 

diff --git a/src/IO/ADIOS/ADIOS2IOHandler.cpp b/src/IO/ADIOS/ADIOS2IOHandler.cpp
@@ -1123,7 +1123,7 @@ namespace detail
             auto &IO = ba.m_IO;
             auto &engine = ba.getEngine();
             adios2::Variable<T> variable = impl->verifyDataset<T>(
-                params.offset, params.extent, IO, varName);
+                params.offset, params.extent, IO, varName, std::nullopt);
             adios2::Dims offset(params.offset.begin(), params.offset.end());
             adios2::Dims extent(params.extent.begin(), params.extent.end());
             variable.SetSelection({std::move(offset), std::move(extent)});
@@ -1439,7 +1439,7 @@ void ADIOS2IOHandlerImpl::readAttributeAllsteps(
     auto engine = IO.Open(fullPath(*file), adios2::Mode::Read);
     auto status = engine.BeginStep();
     auto type = detail::attributeInfo(IO, name, /* verbose = */ true);
-    switchAdios2AttributeType<ReadAttributeAllsteps>(
+    switchType<ReadAttributeAllsteps>(
         type, IO, engine, name, status, *param.resource);
     engine.Close();
 }

diff --git a/src/IO/AbstractIOHandlerImpl.cpp b/src/IO/AbstractIOHandlerImpl.cpp
@@ -319,7 +319,10 @@ std::future<void> AbstractIOHandlerImpl::flush()
                     i.writable->parent,
                     "->",
                     i.writable,
-                    "] READ_DATASET");
+                    "] READ_DATASET, offset=",
+                    [&parameter]() { return vec_as_string(parameter.offset); },
+                    ", extent=",
+                    [&parameter]() { return vec_as_string(parameter.extent); });
                 readDataset(i.writable, parameter);
                 break;
             }

diff --git a/src/IO/IOTask.cpp b/src/IO/IOTask.cpp
@@ -149,10 +149,23 @@ namespace internal
         case Operation::AVAILABLE_CHUNKS:
             return "AVAILABLE_CHUNKS";
             break;
-        default:
-            return "unknown";
+        case Operation::CHECK_FILE:
+            return "CHECK_FILE";
+            break;
+        case Operation::READ_ATT_ALLSTEPS:
+            return "READ_ATT_ALLSTEPS";
+            break;
+        case Operation::DEREGISTER:
+            return "DEREGISTER";
+            break;
+        case Operation::TOUCH:
+            return "TOUCH";
+            break;
+        case Operation::SET_WRITTEN:
+            return "SET_WRITTEN";
             break;
         }
+        return "unknown";
     }
 } // namespace internal
 

diff --git a/src/Iteration.cpp b/src/Iteration.cpp
@@ -459,7 +459,8 @@ void Iteration::readGorVBased(
                 Parameter<Operation::ADVANCE> param;
                 param.mode = Parameter<Operation::ADVANCE>::StepSelection{
                     randomAccess.step};
-                IOHandler()->enqueue(IOTask(this, std::move(param)));
+                IOHandler()->enqueue(
+                    IOTask(&retrieveSeries().writable(), std::move(param)));
             },
         },
         doBeginStep);

diff --git a/src/Series.cpp b/src/Series.cpp
@@ -1453,7 +1453,7 @@ void Series::flushGorVBased(
                     Parameter<Operation::ADVANCE> param;
                     param.mode = Parameter<Operation::ADVANCE>::StepSelection{
                         series.m_snapshotToStep.at(it->first)};
-                    IOHandler()->enqueue(IOTask(&it->second, std::move(param)));
+                    IOHandler()->enqueue(IOTask(this, std::move(param)));
                 }
                 it->second.flush(flushParams);
                 break;
@@ -2196,9 +2196,13 @@ creating new iterations.
              * must happen after opening the first step.
              */
             internal::BeginStep beginStep = randomAccessSteps()
-                ? internal::
-                      BeginStep{internal::BeginStepTypes::BeginStepRandomAccess{
-                          series.m_snapshotToStep.at(it)}}
+                ? (series.m_snapshotToStep.empty()
+                       ? internal::BeginStep{internal::BeginStepTypes::
+                                                 DontBeginStep{}}
+                       : internal::BeginStep{internal::BeginStepTypes::
+                                                 BeginStepRandomAccess{
+                                                     series.m_snapshotToStep.at(
+                                                         it)}})
                 : internal::BeginStep{
                       internal::BeginStepTypes::BeginStepSynchronously{}};
             if (auto err = internal::withRWAccess(