variableBased as default in ADIOS2

examples/5_write_parallel.py

@@ -56,8 +56,7 @@
     # in streaming setups, e.g. an iteration cannot be opened again once
     # it has been closed.
     # `Series.iterations` can be directly accessed in random-access workflows.
-    series.iterations[1].open()
-    mymesh = series.iterations[1]. \
+    mymesh = series.write_iterations()[1]. \
         meshes["mymesh"]
 
     # example 1D domain decomposition in first index
@@ -92,7 +91,7 @@
     # The iteration can be closed in order to help free up resources.
     # The iteration's content will be flushed automatically.
     # An iteration once closed cannot (yet) be reopened.
-    series.iterations[1].close()
+    series.write_iterations()[1].close()
 
     if 0 == comm.rank:
         print("Dataset content has been fully written to disk")

include/openPMD/IO/ADIOS/ADIOS2IOHandler.hpp

@@ -23,6 +23,7 @@
 #include "openPMD/Error.hpp"
 #include "openPMD/IO/ADIOS/ADIOS2Auxiliary.hpp"
 #include "openPMD/IO/ADIOS/ADIOS2FilePosition.hpp"
+#include "openPMD/IO/ADIOS/macros.hpp"
 #include "openPMD/IO/AbstractIOHandler.hpp"
 #include "openPMD/IO/AbstractIOHandlerImpl.hpp"
 #include "openPMD/IO/AbstractIOHandlerImplCommon.hpp"
@@ -860,6 +861,11 @@ class ADIOS2IOHandler : public AbstractIOHandler
         return "ADIOS2";
     }
 
+    bool fullSupportForVariableBasedEncoding() const override
+    {
+        return openPMD_HAS_ADIOS_2_9;
+    }
+
     std::future<void> flush(internal::ParsedFlushParams &) override;
 }; // ADIOS2IOHandler
 } // namespace openPMD

include/openPMD/IO/AbstractIOHandler.hpp

@@ -250,6 +250,7 @@ class AbstractIOHandler
 
     /** The currently used backend */
     virtual std::string backendName() const = 0;
+    virtual bool fullSupportForVariableBasedEncoding() const;
 
     std::string directory;
     /*

include/openPMD/Series.hpp

@@ -68,6 +68,11 @@ class Series;
 
 namespace internal
 {
+    enum class default_or_explicit : bool
+    {
+        default_,
+        explicit_
+    };
     /**
      * @brief Data members for Series. Pinned at one memory location.
      *
@@ -183,6 +188,8 @@ namespace internal
          * The iteration encoding used in this series.
          */
         IterationEncoding m_iterationEncoding{};
+        default_or_explicit m_iterationEncodingSetExplicitly =
+            default_or_explicit::default_;
         /**
          * Detected IO format (backend).
          */
@@ -969,6 +976,9 @@ OPENPMD_private
      */
     void flushStep(bool doFlush);
 
+    Series &setIterationEncoding_internal(
+        IterationEncoding iterationEncoding, internal::default_or_explicit);
+
     /*
      * Returns the current content of the /data/snapshot attribute.
      * (We could also add this to the public API some time)

src/IO/ADIOS/ADIOS2IOHandler.cpp

@@ -1581,6 +1581,7 @@ void ADIOS2IOHandlerImpl::readAttributeAllsteps(
         auto IO = adios.DeclareIO("PreparseSnapshots");
         // @todo check engine type
         IO.SetEngine(realEngineType());
+        IO.SetParameter("StreamReader", "ON"); // this be for BP4
         auto engine = IO.Open(fullPath(*file), adios2::Mode::Read);
         auto status = engine.BeginStep();
         auto type = detail::attributeInfo(IO, name, /* verbose = */ true);

src/IO/AbstractIOHandler.cpp

@@ -116,4 +116,9 @@ std::future<void> AbstractIOHandler::flush(internal::FlushParams const &params)
     json::warnGlobalUnusedOptions(parsedParams.backendConfig);
     return future;
 }
+
+bool AbstractIOHandler::fullSupportForVariableBasedEncoding() const
+{
+    return false;
+}
 } // namespace openPMD

src/Series.cpp

@@ -581,45 +581,7 @@ IterationEncoding Series::iterationEncoding() const
 
 Series &Series::setIterationEncoding(IterationEncoding ie)
 {
-    auto &series = get();
-    if (series.m_deferred_initialization)
-    {
-        runDeferredInitialization();
-    }
-    if (written())
-        throw std::runtime_error(
-            "A files iterationEncoding can not (yet) be changed after it has "
-            "been written.");
-
-    series.m_iterationEncoding = ie;
-    switch (ie)
-    {
-    case IterationEncoding::fileBased:
-        setIterationFormat(series.m_name);
-        setAttribute("iterationEncoding", std::string("fileBased"));
-        // This checks that the name contains the expansion pattern
-        // (e.g. %T) and parses it
-        if (series.m_filenamePadding < 0)
-        {
-            if (!reparseExpansionPattern(series.m_name))
-            {
-                throw error::WrongAPIUsage(
-                    "For fileBased formats the iteration expansion pattern "
-                    "%T must "
-                    "be included in the file name");
-            }
-        }
-        break;
-    case IterationEncoding::groupBased:
-        setIterationFormat(BASEPATH);
-        setAttribute("iterationEncoding", std::string("groupBased"));
-        break;
-    case IterationEncoding::variableBased:
-        setIterationFormat(auxiliary::replace_first(basePath(), "/%T/", ""));
-        setAttribute("iterationEncoding", std::string("variableBased"));
-        break;
-    }
-    IOHandler()->setIterationEncoding(ie);
+    setIterationEncoding_internal(ie, internal::default_or_explicit::default_);
     return *this;
 }
 
@@ -1170,7 +1132,9 @@ Given file pattern: ')END"
                 setWritten(false, Attributable::EnqueueAsynchronously::No);
 
                 initDefaults(input->iterationEncoding);
-                setIterationEncoding(input->iterationEncoding);
+                setIterationEncoding_internal(
+                    input->iterationEncoding,
+                    series.m_iterationEncodingSetExplicitly);
 
                 setWritten(true, Attributable::EnqueueAsynchronously::No);
             }
@@ -1186,12 +1150,14 @@ Given file pattern: ')END"
     }
     case Access::CREATE: {
         initDefaults(input->iterationEncoding);
-        setIterationEncoding(input->iterationEncoding);
+        setIterationEncoding_internal(
+            input->iterationEncoding, series.m_iterationEncodingSetExplicitly);
         break;
     }
     case Access::APPEND: {
         initDefaults(input->iterationEncoding);
-        setIterationEncoding(input->iterationEncoding);
+        setIterationEncoding_internal(
+            input->iterationEncoding, series.m_iterationEncodingSetExplicitly);
         if (input->iterationEncoding != IterationEncoding::fileBased)
         {
             break;
@@ -1857,7 +1823,8 @@ void Series::readOneIterationFileBased(std::string const &filePath)
                 "Unknown iterationEncoding: " + encoding);
         auto old_written = written();
         setWritten(false, Attributable::EnqueueAsynchronously::No);
-        setIterationEncoding(encoding_out);
+        setIterationEncoding_internal(
+            encoding_out, internal::default_or_explicit::explicit_);
         setWritten(old_written, Attributable::EnqueueAsynchronously::Yes);
     }
     else
@@ -2645,6 +2612,59 @@ void Series::flushStep(bool doFlush)
     series.m_wroteAtLeastOneIOStep = true;
 }
 
+Series &Series::setIterationEncoding_internal(
+    IterationEncoding ie, internal::default_or_explicit doe)
+{
+    auto &series = get();
+    switch (doe)
+    {
+    case internal::default_or_explicit::default_:
+    case internal::default_or_explicit::explicit_:
+        // mark this option as set explicitly by the user
+        series.m_iterationEncodingSetExplicitly = doe;
+        break;
+    }
+    if (series.m_deferred_initialization)
+    {
+        runDeferredInitialization();
+    }
+    if (written())
+        throw std::runtime_error(
+            "A files iterationEncoding can not (yet) be changed after it has "
+            "been written.");
+
+    series.m_iterationEncoding = ie;
+    switch (ie)
+    {
+    case IterationEncoding::fileBased:
+        setIterationFormat(series.m_name);
+        setAttribute("iterationEncoding", std::string("fileBased"));
+        // This checks that the name contains the expansion pattern
+        // (e.g. %T) and parses it
+        if (series.m_filenamePadding < 0)
+        {
+            if (!reparseExpansionPattern(series.m_name))
+            {
+                throw error::WrongAPIUsage(
+                    "For fileBased formats the iteration expansion pattern "
+                    "%T must "
+                    "be included in the file name");
+            }
+        }
+        break;
+    case IterationEncoding::groupBased:
+        setIterationFormat(BASEPATH);
+        setAttribute("iterationEncoding", std::string("groupBased"));
+        break;
+    case IterationEncoding::variableBased:
+        setIterationFormat(auxiliary::replace_first(basePath(), "/%T/", ""));
+        setAttribute("iterationEncoding", std::string("variableBased"));
+        break;
+    }
+    IOHandler()->setIterationEncoding(ie);
+    return *this;
+}
+
 auto Series::openIterationIfDirty(IterationIndex_t index, Iteration &iteration)
     -> IterationOpened
 {
@@ -2939,6 +2959,8 @@ void Series::parseJsonOptions(TracingJSON &options, ParsedInput &input)
             options, "iteration_encoding", iterationEncoding);
         if (!iterationEncoding.empty())
         {
+            series.m_iterationEncodingSetExplicitly =
+                internal::default_or_explicit::explicit_;
             auto it = ieDescriptors.find(iterationEncoding);
             if (it != ieDescriptors.end())
             {
@@ -3190,6 +3212,35 @@ Series::snapshots(std::optional<SnapshotWorkflow> const snapshot_workflow)
         }
     }
 
+    /*
+     * ADIOS2 should use variable-based encoding as a default when applicable,
+     * since group-based encoding has severe limitations in ADIOS2.
+     * The below logic checks if variable-based encoding should be used.
+     */
+
+    if (
+        // 1. No encoding has been explicitly selected by the user.
+        //    Flag set by Series::setIterationEncoding().
+        series.m_iterationEncodingSetExplicitly ==
+            internal::default_or_explicit::default_ &&
+        // 2. Iteration encoding was recognized as groupBased by init()
+        //    procedures (and not file-based).
+        series.m_iterationEncoding == IterationEncoding::groupBased &&
+        // 3. The IO workflow will be synchronous, necessary for writing
+        //    variable-based data (but not for reading!).
+        usedSnapshotWorkflow == SnapshotWorkflow::Synchronous &&
+        // 4. The chosen access type is write-only, otherwise the encoding is
+        //    determined by the previous file content.
+        access::writeOnly(access) &&
+        // 5. The backend is ADIOS2 in a recent enough version to support
+        //    modifiable attributes (v2.9).
+        IOHandler()->fullSupportForVariableBasedEncoding())
+    {
+        setIterationEncoding_internal(
+            IterationEncoding::variableBased,
+            internal::default_or_explicit::default_);
+    }
+
     switch (usedSnapshotWorkflow)
     {
     case SnapshotWorkflow::RandomAccess: {

test/Files_SerialIO/close_and_reopen_test.cpp

@@ -181,7 +181,10 @@ auto run_test_groupbased(
 {
     std::string filename =
         "../samples/close_iteration_reopen/groupbased." + ext;
-    Series series(filename, Access::CREATE, write_cfg);
+    Series series(
+        filename,
+        Access::CREATE,
+        json::merge(write_cfg, R"({"iteration_encoding": "group_based"})"));
     {
         auto it = writeIterations(series)[0];
         auto E_x = it.meshes["E"]["x"];

test/ParallelIOTest.cpp

@@ -1213,7 +1213,10 @@ void adios2_streaming(bool variableBasedLayout)
         Series writeSeries(
             "../samples/adios2_stream.sst",
             Access::CREATE,
-            "adios2.engine.type = \"sst\"");
+            variableBasedLayout
+                ? "adios2.engine.type = \"sst\""
+                : "adios2.engine.type = \"sst\"\niteration_encoding = "
+                  "\"group_based\"");
         if (variableBasedLayout)
         {
             writeSeries.setIterationEncoding(IterationEncoding::variableBased);

test/SerialIOTest.cpp

@@ -7027,7 +7027,7 @@ TEST_CASE("unfinished_iteration_test", "[serial]")
     unfinished_iteration_test(
         "bp",
         IterationEncoding::groupBased,
-        R"({"backend": "adios2"})",
+        R"({"backend": "adios2", "iteration_encoding": "group_based"})",
         /* test_linear_access = */ false);
 #if openPMD_HAS_ADIOS_2_9
     unfinished_iteration_test(