Parallel HDF5: Try fixing strict collective requirements of HDF5 >= 2.0

CMakeLists.txt

@@ -426,6 +426,11 @@ set(CORE_SOURCE
         src/backend/PatchRecord.cpp
         src/backend/PatchRecordComponent.cpp
         src/backend/Writable.cpp
+        src/backend/scientific_defaults/ScientificDefaults.cpp
+        src/backend/scientific_defaults/ScientificDefaults_auxiliary.cpp
+        src/backend/scientific_defaults/ProcessParsedAttribute.cpp
+        src/backend/scientific_defaults/AttributeReader.cpp
+        src/backend/scientific_defaults/ConfigAttribute.cpp
         src/auxiliary/OneDimensionalBlockSlicer.cpp
         src/helper/list_series.cpp
         src/snapshots/ContainerImpls.cpp

include/openPMD/IO/AbstractIOHandler.hpp

@@ -26,6 +26,7 @@
 #include "openPMD/IterationEncoding.hpp"
 #include "openPMD/config.hpp"
 #include "openPMD/version.hpp"
+#include <ostream>
 
 #if openPMD_HAVE_MPI
 #include <mpi.h>
@@ -81,6 +82,66 @@ enum class FlushLevel
     CreateOrOpenFiles
 };
 
+std::ostream &operator<<(std::ostream &, FlushLevel);
+
+namespace flush_level
+{
+    inline constexpr auto global_flushpoint(FlushLevel fl)
+    {
+        switch (fl)
+        {
+        case FlushLevel::UserFlush:
+            return true;
+        case FlushLevel::InternalFlush:
+        case FlushLevel::SkeletonOnly:
+        case FlushLevel::CreateOrOpenFiles:
+            return false;
+        }
+        return false; // unreachable
+    }
+    // same as global_flushpoint for now, but we will soon introduce
+    // immediate_flush
+    inline constexpr auto write_datasets(FlushLevel fl)
+    {
+        switch (fl)
+        {
+        case FlushLevel::UserFlush:
+            return true;
+        case FlushLevel::InternalFlush:
+        case FlushLevel::SkeletonOnly:
+        case FlushLevel::CreateOrOpenFiles:
+            return false;
+        }
+        return false; // unreachable
+    }
+    inline constexpr auto write_attributes(FlushLevel fl)
+    {
+        switch (fl)
+        {
+        case FlushLevel::UserFlush:
+        case FlushLevel::InternalFlush:
+            return true;
+        case FlushLevel::SkeletonOnly:
+        case FlushLevel::CreateOrOpenFiles:
+            return false;
+        }
+        return false; // unreachable
+    }
+    inline constexpr auto flush_hierarchy(FlushLevel fl)
+    {
+        switch (fl)
+        {
+        case FlushLevel::UserFlush:
+        case FlushLevel::InternalFlush:
+        case FlushLevel::SkeletonOnly:
+            return true;
+        case FlushLevel::CreateOrOpenFiles:
+            return false;
+        }
+        return false; // unreachable
+    }
+} // namespace flush_level
+
 enum class OpenpmdStandard
 {
     v_1_0_0,
@@ -121,6 +182,7 @@ namespace internal
      * To be used for reading
      */
     FlushParams const defaultFlushParams{};
+    FlushParams const publicFlush{FlushLevel::UserFlush};
 
     struct ParsedFlushParams;
 

include/openPMD/IO/AbstractIOHandlerImpl.hpp

@@ -39,7 +39,7 @@ class AbstractIOHandlerImpl
 
     virtual ~AbstractIOHandlerImpl() = default;
 
-    std::future<void> flush();
+    std::future<void> flush(FlushLevel);
 
     /**
      * Close the file corresponding with the writable and release file handles.

include/openPMD/IO/IOTask.hpp

@@ -35,6 +35,7 @@
 #include <cstddef>
 #include <memory>
 #include <optional>
+#include <ostream>
 #include <string>
 #include <utility>
 #include <variant>
@@ -89,6 +90,8 @@ OPENPMDAPI_EXPORT_ENUM_CLASS(Operation){
 }; // note: if you change the enum members here, please update
    // docs/source/dev/design.rst
 
+std::ostream &operator<<(std::ostream &os, Operation op);
+
 namespace internal
 {
     /*

include/openPMD/IO/JSON/JSONIOHandlerImpl.hpp

@@ -241,7 +241,7 @@ class JSONIOHandlerImpl : public AbstractIOHandlerImpl
 
     void touch(Writable *, Parameter<Operation::TOUCH> const &) override;
 
-    std::future<void> flush();
+    std::future<void> flush(internal::ParsedFlushParams &params);
 
 private:
 #if openPMD_HAVE_MPI

include/openPMD/Iteration.hpp

@@ -27,6 +27,8 @@
 #include "openPMD/auxiliary/Variant.hpp"
 #include "openPMD/backend/Attributable.hpp"
 #include "openPMD/backend/Container.hpp"
+#include "openPMD/backend/HierarchyVisitor.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults.hpp"
 
 #include <cstdint>
 #include <deque>
@@ -145,13 +147,28 @@ namespace internal
         std::optional<DeferredParseAccess> m_deferredParseAccess{};
     };
 } // namespace internal
+
+class Meshes : public Container<Mesh>
+{
+public:
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+};
+
+class Particles : public Container<ParticleSpecies>
+{
+public:
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+};
+
 /** @brief  Logical compilation of data from one snapshot (e.g. a single
  * simulation cycle).
  *
  * @see
  * https://github.com/openPMD/openPMD-standard/blob/latest/STANDARD.md#required-attributes-for-the-basepath
  */
-class Iteration : public Attributable
+class Iteration
+    : public Attributable
+    , internal::ScientificDefaults
 {
     template <typename T, typename T_key, typename T_container>
     friend class Container;
@@ -164,6 +181,8 @@ class Iteration : public Attributable
     friend class StatefulSnapshotsContainer;
     template <typename>
     friend struct traits::GenerationPolicy;
+    friend class internal::ScientificDefaults;
+    friend class Attributable;
 
 public:
     Iteration(Iteration const &) = default;
@@ -279,8 +298,10 @@ class Iteration : public Attributable
     [[deprecated("This attribute is no longer set by the openPMD-api.")]] bool
     closedByWriter() const;
 
-    Container<Mesh> meshes{};
-    Container<ParticleSpecies> particles{}; // particleSpecies?
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
+    Meshes meshes{};
+    Particles particles{};
 
     virtual ~Iteration() = default;
 
@@ -442,14 +463,18 @@ class Iteration : public Attributable
      *
      * @param w The Writable representing the parent.
      */
-    virtual void linkHierarchy(Writable &w);
+    void linkHierarchy(Writable &w) override;
 
     /**
      * @brief Access an iteration in read mode that has potentially not been
      *      parsed yet.
      *
      */
     void runDeferredParseAccess();
+
+protected:
+    void scientificDefaults_impl(
+        internal::WriteOrRead, OpenpmdStandard) override;
 }; // Iteration
 
 namespace traits
@@ -513,4 +538,10 @@ class IndexedIteration : public Iteration
         : Iteration(std::forward<Iteration_t>(it)), iterationIndex(index)
     {}
 };
+
+class Iterations : public Container<Iteration, Iteration::IterationIndex_t>
+{
+public:
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+};
 } // namespace openPMD

include/openPMD/Mesh.hpp

@@ -23,7 +23,10 @@
 #include "openPMD/UnitDimension.hpp"
 #include "openPMD/backend/Attributable.hpp"
 #include "openPMD/backend/BaseRecord.hpp"
+#include "openPMD/backend/Container.hpp"
 #include "openPMD/backend/MeshRecordComponent.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults_auxiliary.hpp"
 
 #include <ostream>
 #include <string>
@@ -41,6 +44,8 @@ class Mesh : public BaseRecord<MeshRecordComponent>
 {
     friend class Container<Mesh>;
     friend class Iteration;
+    friend class internal::ScientificDefaults;
+    friend class Attributable;
 
 public:
     Mesh(Mesh const &) = default;
@@ -322,12 +327,19 @@ class Mesh : public BaseRecord<MeshRecordComponent>
         typename = std::enable_if_t<std::is_floating_point<T>::value>>
     Mesh &setTimeOffset(T timeOffset);
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
 private:
     Mesh();
 
     void
     flush_impl(std::string const &, internal::FlushParams const &) override;
     void read();
+    auto retrieveDimensionality() const -> uint64_t;
+
+protected:
+    void scientificDefaults_impl(
+        internal::WriteOrRead, OpenpmdStandard) override;
 }; // Mesh
 
 template <typename T>

include/openPMD/ParticlePatches.hpp

@@ -38,6 +38,8 @@ class ParticlePatches : public Container<PatchRecord>
     size_t numPatches() const;
     ~ParticlePatches() override = default;
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
 private:
     ParticlePatches() = default;
     void read();

include/openPMD/ParticleSpecies.hpp

@@ -24,23 +24,32 @@
 #include "openPMD/Record.hpp"
 #include "openPMD/backend/Attributable.hpp"
 #include "openPMD/backend/Container.hpp"
+#include "openPMD/backend/HierarchyVisitor.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults_auxiliary.hpp"
 
 #include <string>
 
 namespace openPMD
 {
 
-class ParticleSpecies : public Container<Record>
+class ParticleSpecies
+    : public Container<Record>
+    , internal::ScientificDefaults
 {
     friend class Container<ParticleSpecies>;
     friend class Container<Record>;
     friend class Iteration;
     template <typename T>
     friend T &internal::makeOwning(T &self, Series);
+    friend class internal::ScientificDefaults;
+    friend class Attributable;
 
 public:
     ParticlePatches particlePatches;
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
 private:
     ParticleSpecies();
 
@@ -53,6 +62,10 @@ class ParticleSpecies : public Container<Record>
     {
         return m_containerData;
     }
+
+protected:
+    void scientificDefaults_impl(
+        internal::WriteOrRead, OpenpmdStandard) override;
 };
 
 namespace traits

include/openPMD/Record.hpp

@@ -23,6 +23,7 @@
 #include "openPMD/RecordComponent.hpp"
 #include "openPMD/UnitDimension.hpp"
 #include "openPMD/backend/BaseRecord.hpp"
+#include "openPMD/backend/scientific_defaults/ScientificDefaults.hpp"
 
 #include <string>
 #include <type_traits>
@@ -34,6 +35,7 @@ class Record : public BaseRecord<RecordComponent>
     friend class Container<Record>;
     friend class Iteration;
     friend class ParticleSpecies;
+    friend class internal::ScientificDefaults;
 
 public:
     Record(Record const &) = default;
@@ -48,13 +50,19 @@ class Record : public BaseRecord<RecordComponent>
     template <typename T>
     Record &setTimeOffset(T);
 
+    void visitHierarchy(HierarchyVisitor &v, bool recursive) override;
+
 private:
     Record();
 
     void
     flush_impl(std::string const &, internal::FlushParams const &) override;
 
     [[nodiscard]] internal::HomogenizeExtents read();
+
+protected:
+    void scientificDefaults_impl(
+        internal::WriteOrRead, OpenpmdStandard) override;
 }; // Record
 
 template <typename T>