Debugging Read

examples/hello/bpReader/helloBPReader.cpp

@@ -37,7 +37,7 @@ int main(int argc, char *argv[])
         /*** IO class object: settings and factory of Settings: Variables,
          * Parameters, Transports, and Execution: Engines */
         adios2::IO &bpIO = adios.DeclareIO("ReadBP");
-        bpIO.SetParameter("Threads", "2");
+        //        /bpIO.SetParameter("Threads", "2");
 
         /** Engine derived class, spawned to start IO operations */
         adios2::Engine &bpReader =

source/adios2/engine/bp/BPFileReader.cpp

@@ -111,7 +111,7 @@ ADIOS2_FOREACH_TYPE_1ARG(declare_type)
 void BPFileReader::ReadVariables(
     IO &io, const std::map<std::string, SubFileInfoMap> &variablesSubFileInfo)
 {
-    const bool &profile = m_BP3Deserializer.m_Profiler.IsActive;
+    const bool profile = m_BP3Deserializer.m_Profiler.IsActive;
 
     // sequentially request bytes from transport manager
     // threaded here?
@@ -138,13 +138,14 @@ void BPFileReader::ReadVariables(
                     const auto &seek = blockInfo.Seeks;
                     const size_t blockStart = seek.first;
                     const size_t blockSize = seek.second - seek.first;
-                    std::vector<char> contiguousData(blockSize);
-                    m_SubFileManager.ReadFile(contiguousData.data(), blockStart,
-                                              blockSize, subFileIndex);
-
-                    // will go to BP3Deserializer along with contiguous data
-                    // m_BP3Deserializer
-
+                    std::vector<char> contiguousMemory(blockSize);
+                    m_SubFileManager.ReadFile(contiguousMemory.data(),
+                                              blockStart, blockSize,
+                                              subFileIndex);
+
+                    m_BP3Deserializer.ClipContiguousMemory(
+                        variableName, m_IO, contiguousMemory,
+                        blockInfo.IntersectionBox);
                 } // end block
             }     // end step
         }         // end subfile

source/adios2/engine/bp/BPFileReader.tcc

@@ -20,6 +20,8 @@ template <class T>
 void BPFileReader::GetSyncCommon(Variable<T> &variable, T *data)
 {
     // subfile info
+    variable.SetData(data);
+
     const std::map<std::string, SubFileInfoMap> variableSubfileInfo =
         m_BP3Deserializer.GetSyncVariableSubFileInfo(variable);
 

source/adios2/toolkit/format/bp3/BP3Deserializer.tcc

@@ -135,7 +135,8 @@ BP3Deserializer::GetSubFileInfo(const Variable<T> &variable) const
     const auto &buffer = m_Metadata.m_Buffer;
 
     const size_t stepStart = variable.m_StepStart;
-    const size_t stepEnd = stepStart + variable.m_StepCount;
+    const size_t stepEnd =
+        stepStart + variable.m_StepCount; // inclusive or exclusive?
 
     // selection, start and count
     const Box<Dims> selection{variable.m_Start, variable.m_Count};
@@ -171,14 +172,16 @@ BP3Deserializer::GetSubFileInfo(const Variable<T> &variable) const
             // if they intersect get info Seeks (first: start, second: end)
             // TODO: map to sizeof(T)?
             info.Seeks.first =
+                blockCharacteristics.Statistics.PayloadOffset +
                 LinearIndex(blockDimensions, info.IntersectionBox.first,
                             m_IsRowMajor, m_IsZeroIndex) *
-                sizeof(T);
+                    sizeof(T);
 
             info.Seeks.second =
+                blockCharacteristics.Statistics.PayloadOffset +
                 LinearIndex(blockDimensions, info.IntersectionBox.second,
                             m_IsRowMajor, m_IsZeroIndex) *
-                sizeof(T);
+                    sizeof(T);
 
             const size_t fileIndex = static_cast<const size_t>(
                 blockCharacteristics.Statistics.FileIndex);