Preview support for Linear read mode without snapshot attribute

Currently only available for BP5 engine, will be generalized into Linear
read mode in #1291.
If the backend does not support the snapshot attribute, then iterate in
ascending order, skipping duplicate and non-linear iteration indices.
Not possible if the Series is parsed ahead of time.

Author: franzpoeschel

src/ReadIterations.cpp

@@ -141,6 +141,10 @@ std::optional<SeriesIterator *> SeriesIterator::nextIterationInStep()
 {
     using ret_t = std::optional<SeriesIterator *>;
 
+    if (m_iterationsInCurrentStep.empty())
+    {
+        return ret_t{};
+    }
     m_iterationsInCurrentStep.pop_front();
     if (m_iterationsInCurrentStep.empty())
     {
@@ -199,16 +203,55 @@ std::optional<SeriesIterator *> SeriesIterator::nextStep()
         auto itEnd = series.iterations.end();
         if (it == itEnd)
         {
-            *this = end();
-            return {this};
+            if (status == AdvanceStatus::RANDOMACCESS ||
+                status == AdvanceStatus::OVER)
+            {
+                *this = end();
+                return {this};
+            }
+            else
+            {
+                /*
+                 * Stream still going but there was no iteration found in the
+                 * current IO step?
+                 * Might be a duplicate iteration resulting from appending,
+                 * will skip such iterations and hope to find something in a
+                 * later IO step. No need to finish right now.
+                 */
+                m_iterationsInCurrentStep = {};
+                m_series->advance(AdvanceMode::ENDSTEP);
+            }
         }
-        ++it;
-        if (it == itEnd)
+        else
         {
-            *this = end();
-            return {this};
+            ++it;
+
+            if (it == itEnd)
+            {
+                if (status == AdvanceStatus::RANDOMACCESS ||
+                    status == AdvanceStatus::OVER)
+                {
+                    *this = end();
+                    return {this};
+                }
+                else
+                {
+                    /*
+                     * Stream still going but there was no iteration found in
+                     * the current IO step? Might be a duplicate iteration
+                     * resulting from appending, will skip such iterations and
+                     * hope to find something in a later IO step. No need to
+                     * finish right now.
+                     */
+                    m_iterationsInCurrentStep = {};
+                    m_series->advance(AdvanceMode::ENDSTEP);
+                }
+            }
+            else
+            {
+                m_iterationsInCurrentStep = {it->first};
+            }
         }
-        m_iterationsInCurrentStep = {it->first};
     }
 
     if (status == AdvanceStatus::OVER)

test/SerialIOTest.cpp

@@ -6069,9 +6069,46 @@ TEST_CASE("varying_zero_pattern", "[serial]")
     }
 }
 
+enum class ParseMode
+{
+    /*
+     * Conventional workflow. Just parse the whole thing and yield iterations
+     * in rising order.
+     */
+    NoSteps,
+    /*
+     * The Series is parsed ahead of time upon opening, but it has steps.
+     * Parsing ahead of time is the conventional workflow to support
+     * random-access.
+     * Reading such a Series with the streaming API is only possible if all
+     * steps are in ascending order, otherwise the openPMD-api has no way of
+     * associating IO steps with interation indices.
+     * Reading such a Series with the Streaming API will become possible with
+     * the Linear read mode to be introduced by #1291.
+     */
+    AheadOfTimeWithoutSnapshot,
+    /*
+     * A Series of the BP5 engine is not parsed ahead of time, but step-by-step,
+     * giving the openPMD-api a way to associate IO steps with iterations.
+     * No snapshot attribute exists, so the fallback mode is chosen:
+     * Iterations are returned in ascending order.
+     * If an IO step returns an iteration whose index is lower than the
+     * last one, it will be skipped.
+     * This mode of parsing will be generalized into the Linear read mode with
+     * PR #1291.
+     */
+    LinearWithoutSnapshot,
+    /*
+     * Snapshot attribute exists and dictates the iteration index returned by
+     * an IO step. Duplicate iterations will be skipped.
+     */
+    WithSnapshot
+};
+
 void append_mode(
     std::string const &extension,
     bool variableBased,
+    ParseMode parseMode,
     std::string jsonConfig = "{}")
 {
 
@@ -6179,26 +6216,60 @@ void append_mode(
     }
     {
         Series read(filename, Access::READ_ONLY);
-        if (variableBased || extension == "bp5")
+        switch (parseMode)
         {
+        case ParseMode::NoSteps: {
+            unsigned counter = 0;
+            uint64_t iterationOrder[] = {0, 1, 2, 3, 4, 7, 10, 11};
+            for (auto const &iteration : read.readIterations())
+            {
+                REQUIRE(iteration.iterationIndex == iterationOrder[counter]);
+                ++counter;
+            }
+            REQUIRE(counter == 8);
+        }
+        break;
+        case ParseMode::LinearWithoutSnapshot: {
+            unsigned counter = 0;
+            uint64_t iterationOrder[] = {0, 1, 2, 3, 4, 10, 11};
+            for (auto const &iteration : read.readIterations())
+            {
+                REQUIRE(iteration.iterationIndex == iterationOrder[counter]);
+                ++counter;
+            }
+            REQUIRE(counter == 7);
+        }
+        break;
+        case ParseMode::WithSnapshot: {
             // in variable-based encodings, iterations are not parsed ahead of
             // time but as they go
             unsigned counter = 0;
             uint64_t iterationOrder[] = {0, 1, 2, 3, 4, 10, 7, 11};
             for (auto const &iteration : read.readIterations())
             {
-                std::cout << "Seeing iteration " << iteration.iterationIndex
-                          << " of series " << filename << std::endl;
                 REQUIRE(iteration.iterationIndex == iterationOrder[counter]);
                 ++counter;
             }
             REQUIRE(counter == 8);
             // Cannot do listSeries here because the Series is already drained
             REQUIRE_THROWS_AS(helper::listSeries(read), error::WrongAPIUsage);
         }
-        else
-        {
+        break;
+        case ParseMode::AheadOfTimeWithoutSnapshot: {
             REQUIRE(read.iterations.size() == 8);
+            unsigned counter = 0;
+            uint64_t iterationOrder[] = {0, 1, 2, 3, 4, 7, 10, 11};
+            /*
+             * Use conventional read API since streaming API is not possible
+             * without Linear read mode.
+             * (See also comments inside ParseMode enum).
+             */
+            for (auto const &iteration : read.iterations)
+            {
+                REQUIRE(iteration.first == iterationOrder[counter]);
+                ++counter;
+            }
+            REQUIRE(counter == 8);
             /*
              * Roadmap: for now, reading this should work by ignoring the last
              * duplicate iteration.
@@ -6208,6 +6279,8 @@ void append_mode(
              */
             helper::listSeries(read);
         }
+        break;
+        }
     }
 #if 100000000 * ADIOS2_VERSION_MAJOR + 1000000 * ADIOS2_VERSION_MINOR +        \
         10000 * ADIOS2_VERSION_PATCH + 100 * ADIOS2_VERSION_TWEAK >=           \
@@ -6244,16 +6317,47 @@ void append_mode(
         }
         {
             Series read(filename, Access::READ_ONLY);
-            // in variable-based encodings, iterations are not parsed ahead of
-            // time but as they go
-            unsigned counter = 0;
-            for (auto const &iteration : read.readIterations())
+            switch (parseMode)
             {
-                REQUIRE(iteration.iterationIndex == counter);
-                ++counter;
+            case ParseMode::LinearWithoutSnapshot: {
+                uint64_t iterationOrder[] = {0, 1, 2, 3, 4, 10};
+                unsigned counter = 0;
+                for (auto const &iteration : read.readIterations())
+                {
+                    REQUIRE(
+                        iteration.iterationIndex == iterationOrder[counter]);
+                    ++counter;
+                }
+                REQUIRE(counter == 6);
+                // Cannot do listSeries here because the Series is already
+                // drained
+                REQUIRE_THROWS_AS(
+                    helper::listSeries(read), error::WrongAPIUsage);
+            }
+            break;
+            case ParseMode::WithSnapshot: {
+                // in variable-based encodings, iterations are not parsed ahead
+                // of time but as they go
+                unsigned counter = 0;
+                uint64_t iterationOrder[] = {0, 1, 2, 3, 4, 10, 7, 5};
+                for (auto const &iteration : read.readIterations())
+                {
+                    REQUIRE(
+                        iteration.iterationIndex == iterationOrder[counter]);
+                    ++counter;
+                }
+                REQUIRE(counter == 8);
+                // Cannot do listSeries here because the Series is already
+                // drained
+                REQUIRE_THROWS_AS(
+                    helper::listSeries(read), error::WrongAPIUsage);
+            }
+            break;
+            case ParseMode::NoSteps:
+            case ParseMode::AheadOfTimeWithoutSnapshot:
+                throw std::runtime_error("Test configured wrong.");
+                break;
             }
-            REQUIRE(counter == 6);
-            helper::listSeries(read);
         }
     }
 #endif
@@ -6263,9 +6367,7 @@ TEST_CASE("append_mode", "[serial]")
 {
     for (auto const &t : testedFileExtensions())
     {
-        if (t == "bp" || t == "bp4" || t == "bp5")
-        {
-            std::string jsonConfigOld = R"END(
+        std::string jsonConfigOld = R"END(
 {
     "adios2":
     {
@@ -6276,7 +6378,7 @@ TEST_CASE("append_mode", "[serial]")
         }
     }
 })END";
-            std::string jsonConfigNew = R"END(
+        std::string jsonConfigNew = R"END(
 {
     "adios2":
     {
@@ -6287,14 +6389,25 @@ TEST_CASE("append_mode", "[serial]")
         }
     }
 })END";
-            append_mode(t, false, jsonConfigOld);
-            append_mode(t, false, jsonConfigNew);
-            append_mode(t, true, jsonConfigOld);
-            append_mode(t, true, jsonConfigNew);
+        if (t == "bp5")
+        {
+            append_mode(
+                t, false, ParseMode::LinearWithoutSnapshot, jsonConfigOld);
+            append_mode(t, false, ParseMode::WithSnapshot, jsonConfigNew);
+            append_mode(t, true, ParseMode::WithSnapshot, jsonConfigOld);
+            append_mode(t, true, ParseMode::WithSnapshot, jsonConfigNew);
+        }
+        else if (t == "bp" || t == "bp4" || t == "bp5")
+        {
+            append_mode(
+                t, false, ParseMode::AheadOfTimeWithoutSnapshot, jsonConfigOld);
+            append_mode(t, false, ParseMode::WithSnapshot, jsonConfigNew);
+            append_mode(t, true, ParseMode::WithSnapshot, jsonConfigOld);
+            append_mode(t, true, ParseMode::WithSnapshot, jsonConfigNew);
         }
         else
         {
-            append_mode(t, false);
+            append_mode(t, false, ParseMode::NoSteps);
         }
     }
 }