Added default_init_allocator from http://stackoverflow.com/a/21028912…

source/adios2/engine/bp3/BP3Writer.cpp

@@ -302,7 +302,7 @@ void BP3Writer::WriteProfilingJSONFile()
                                    transportTypes, transportProfilers) +
                                ",\n");
 
-    const std::vector<char> profilingJSON(
+    const helper::adiosvec<char> profilingJSON(
         m_BP3Serializer.AggregateProfilingJSON(lineJSON));
 
     if (m_BP3Serializer.m_RankMPI == 0)

source/adios2/engine/bp4/BP4Reader.cpp

@@ -559,7 +559,7 @@ size_t BP4Reader::UpdateBuffer(const TimePoint &timeoutInstant,
         {
             const size_t maxIdxSize =
                 idxFileSize - m_MDIndexFileAlreadyReadSize;
-            std::vector<char> idxbuf(maxIdxSize);
+            helper::adiosvec<char> idxbuf(maxIdxSize);
             m_MDIndexFileManager.ReadFile(idxbuf.data(), maxIdxSize,
                                           m_MDIndexFileAlreadyReadSize);
             size_t newIdxSize;
@@ -685,7 +685,8 @@ bool BP4Reader::CheckWriterActive()
     size_t flag = 0;
     if (m_BP4Deserializer.m_RankMPI == 0)
     {
-        std::vector<char> header(m_BP4Deserializer.m_IndexHeaderSize, '\0');
+        helper::adiosvec<char> header(m_BP4Deserializer.m_IndexHeaderSize,
+                                      '\0');
         m_MDIndexFileManager.ReadFile(
             header.data(), m_BP4Deserializer.m_IndexHeaderSize, 0, 0);
         bool active = m_BP4Deserializer.ReadActiveFlag(header);

source/adios2/engine/bp4/BP4Writer.cpp

@@ -550,7 +550,7 @@ void BP4Writer::WriteProfilingJSONFile()
                                    transportTypes, transportProfilers) +
                                ",\n");
 
-    const std::vector<char> profilingJSON(
+    const helper::adiosvec<char> profilingJSON(
         m_BP4Serializer.AggregateProfilingJSON(lineJSON));
 
     if (m_BP4Serializer.m_RankMPI == 0)

source/adios2/engine/bp5/BP5Reader.cpp

@@ -302,7 +302,7 @@ void BP5Reader::PerformGets()
         double readTotal = 0.0;
         double subfileTotal = 0.0;
         size_t nReads = 0;
-        std::vector<char> buf(maxReadSize);
+        helper::adiosvec<char> buf(maxReadSize);
 
         while (true)
         {
@@ -393,7 +393,7 @@ void BP5Reader::PerformGets()
     {
         size_t maxOpenFiles = helper::SetWithinLimit(
             (size_t)m_Parameters.MaxOpenFilesAtOnce, (size_t)1, MaxSizeT);
-        std::vector<char> buf(maxReadSize);
+        helper::adiosvec<char> buf(maxReadSize);
         for (auto &Req : ReadRequests)
         {
             if (!Req.DestinationAddr)
@@ -1070,7 +1070,7 @@ size_t BP5Reader::ParseMetadataIndex(format::BufferSTL &bufferSTL,
     return position;
 }
 
-bool BP5Reader::ReadActiveFlag(std::vector<char> &buffer)
+bool BP5Reader::ReadActiveFlag(helper::adiosvec<char> &buffer)
 {
     if (buffer.size() < m_ActiveFlagPosition)
     {
@@ -1094,7 +1094,7 @@ bool BP5Reader::CheckWriterActive()
         auto fsize = m_MDIndexFileManager.GetFileSize(0);
         if (fsize >= m_IndexHeaderSize)
         {
-            std::vector<char> header(m_IndexHeaderSize, '\0');
+            helper::adiosvec<char> header(m_IndexHeaderSize, '\0');
             m_MDIndexFileManager.ReadFile(header.data(), m_IndexHeaderSize, 0,
                                           0);
             bool active = ReadActiveFlag(header);

source/adios2/engine/bp5/BP5Reader.h

@@ -150,7 +150,7 @@ class BP5Reader : public BP5Engine, public Engine
                       const Seconds &pollSeconds,
                       const Seconds &timeoutSeconds);
 
-    bool ReadActiveFlag(std::vector<char> &buffer);
+    bool ReadActiveFlag(helper::adiosvec<char> &buffer);
 
     /* Parse metadata.
      *

source/adios2/engine/bp5/BP5Writer.cpp

@@ -340,7 +340,7 @@ void BP5Writer::WriteMetadataFileIndex(uint64_t MetaDataPos,
         bufsize += 1 + (4 + m_Comm.Size()) * sizeof(uint64_t);
     }
 
-    std::vector<char> buf(bufsize);
+    helper::adiosvec<char> buf(bufsize);
     size_t pos = 0;
     uint64_t d;
     unsigned char record;
@@ -524,14 +524,16 @@ void BP5Writer::EndStep()
     WriteData(databuf);
     m_Profiler.Stop("AWD");
 
-    std::vector<char> MetaBuffer = m_BP5Serializer.CopyMetadataToContiguous(
-        TSInfo.NewMetaMetaBlocks, TSInfo.MetaEncodeBuffer,
-        TSInfo.AttributeEncodeBuffer, m_ThisTimestepDataSize, m_StartDataPos);
+    helper::adiosvec<char> MetaBuffer =
+        m_BP5Serializer.CopyMetadataToContiguous(
+            TSInfo.NewMetaMetaBlocks, TSInfo.MetaEncodeBuffer,
+            TSInfo.AttributeEncodeBuffer, m_ThisTimestepDataSize,
+            m_StartDataPos);
 
     size_t LocalSize = MetaBuffer.size();
     std::vector<size_t> RecvCounts = m_Comm.GatherValues(LocalSize, 0);
 
-    std::vector<char> *RecvBuffer = new std::vector<char>;
+    helper::adiosvec<char> *RecvBuffer = new helper::adiosvec<char>;
     if (m_Comm.Rank() == 0)
     {
         uint64_t TotalSize = 0;
@@ -1087,11 +1089,12 @@ void BP5Writer::InitTransports()
 }
 
 /*generate the header for the metadata index file*/
-void BP5Writer::MakeHeader(std::vector<char> &buffer, size_t &position,
+void BP5Writer::MakeHeader(helper::adiosvec<char> &buffer, size_t &position,
                            const std::string fileType, const bool isActive)
 {
     auto lf_CopyVersionChar = [](const std::string version,
-                                 std::vector<char> &buffer, size_t &position) {
+                                 helper::adiosvec<char> &buffer,
+                                 size_t &position) {
         helper::CopyToBuffer(buffer, position, version.c_str());
     };
 
@@ -1541,7 +1544,7 @@ void BP5Writer::FlushProfiler()
         m_Profiler.GetRankProfilingJSON(transportTypes, transportProfilers) +
         ",\n");
 
-    const std::vector<char> profilingJSON(
+    const helper::adiosvec<char> profilingJSON(
         m_Profiler.AggregateProfilingJSON(lineJSON));
 
     if (m_RankMPI == 0)

source/adios2/engine/bp5/BP5Writer.h

@@ -227,7 +227,7 @@ class BP5Writer : public BP5Engine, public core::Engine
 
     std::vector<std::vector<size_t>> FlushPosSizeInfo;
 
-    void MakeHeader(std::vector<char> &buffer, size_t &position,
+    void MakeHeader(helper::adiosvec<char> &buffer, size_t &position,
                     const std::string fileType, const bool isActive);
 
     std::vector<uint64_t> m_WriterSubfileMap; // rank => subfile index

source/adios2/engine/sst/SstReader.cpp

@@ -682,7 +682,7 @@ void SstReader::PerformGets()
     else if (m_WriterMarshalMethod == SstMarshalBP)
     {
         std::vector<void *> sstReadHandlers;
-        std::vector<std::vector<char>> buffers;
+        std::vector<helper::adiosvec<char>> buffers;
         size_t iter = 0;
 
         if (m_BP3Deserializer->m_DeferredVariables.empty())

source/adios2/engine/sst/SstReader.h

@@ -54,13 +54,14 @@ class SstReader : public Engine
 
 private:
     template <class T>
-    void ReadVariableBlocksRequests(Variable<T> &variable,
-                                    std::vector<void *> &sstReadHandlers,
-                                    std::vector<std::vector<char>> &buffers);
+    void
+    ReadVariableBlocksRequests(Variable<T> &variable,
+                               std::vector<void *> &sstReadHandlers,
+                               std::vector<helper::adiosvec<char>> &buffers);
 
     template <class T>
     void ReadVariableBlocksFill(Variable<T> &variable,
-                                std::vector<std::vector<char>> &buffers,
+                                std::vector<helper::adiosvec<char>> &buffers,
                                 size_t &iter);
 
     template <class T>

source/adios2/engine/sst/SstReader.tcc

@@ -26,7 +26,7 @@ namespace engine
 template <class T>
 void SstReader::ReadVariableBlocksRequests(
     Variable<T> &variable, std::vector<void *> &sstReadHandlers,
-    std::vector<std::vector<char>> &buffers)
+    std::vector<helper::adiosvec<char>> &buffers)
 {
     PERFSTUBS_SCOPED_TIMER_FUNC();
 
@@ -122,9 +122,9 @@ void SstReader::ReadVariableBlocksRequests(
 }
 
 template <class T>
-void SstReader::ReadVariableBlocksFill(Variable<T> &variable,
-                                       std::vector<std::vector<char>> &buffers,
-                                       size_t &iter)
+void SstReader::ReadVariableBlocksFill(
+    Variable<T> &variable, std::vector<helper::adiosvec<char>> &buffers,
+    size_t &iter)
 {
     PERFSTUBS_SCOPED_TIMER_FUNC();
 

source/adios2/helper/adiosComm.h

@@ -8,6 +8,7 @@
 #ifndef ADIOS2_HELPER_ADIOSCOMM_H_
 #define ADIOS2_HELPER_ADIOSCOMM_H_
 
+#include <adios2/helper/adiosType.h>
 #include <memory>
 #include <string>
 #include <vector>
@@ -184,6 +185,10 @@ class Comm
     template <class T>
     void GathervVectors(const std::vector<T> &in, std::vector<T> &out,
                         size_t &position, int rankDestination = 0) const;
+
+    template <class T>
+    void GathervVectors(const helper::adiosvec<T> &in, helper::adiosvec<T> &out,
+                        size_t &position, int rankDestination = 0) const;
     /**
      * Perform AllGather for source value
      * @param source input
@@ -204,6 +209,10 @@ class Comm
     void BroadcastVector(std::vector<T> &vector,
                          const int rankSource = 0) const;
 
+    template <class T>
+    void BroadcastVector(helper::adiosvec<T> &vector,
+                         const int rankSource = 0) const;
+
     std::string BroadcastFile(const std::string &fileName,
                               const std::string hint = "",
                               const int rankSource = 0) const;

source/adios2/helper/adiosComm.inl

@@ -109,6 +109,42 @@ void Comm::GathervVectors(const std::vector<T> &in, std::vector<T> &out,
     position += gatheredSize;
 }
 
+template <class T>
+void Comm::GathervVectors(const helper::adiosvec<T> &in,
+                          helper::adiosvec<T> &out, size_t &position,
+                          int rankDestination) const
+{
+    const size_t inSize = in.size();
+    const std::vector<size_t> counts =
+        this->GatherValues(inSize, rankDestination);
+
+    size_t gatheredSize = 0;
+
+    int rank = this->Rank();
+
+    if (rank == rankDestination) // pre-allocate vector
+    {
+        gatheredSize = std::accumulate(counts.begin(), counts.end(), size_t(0));
+
+        const size_t newSize = position + gatheredSize;
+        try
+        {
+            out.reserve(newSize); // to avoid power of 2 growth
+            out.resize(newSize);
+        }
+        catch (...)
+        {
+            helper::ThrowNested<std::runtime_error>(
+                "Helper", "adiosComm", "GathervVectors",
+                "buffer overflow when resizing to " + std::to_string(newSize));
+        }
+    }
+
+    this->GathervArrays(in.data(), in.size(), counts.data(), counts.size(),
+                        out.data() + position, rankDestination);
+    position += gatheredSize;
+}
+
 template <class T>
 std::vector<T> Comm::AllGatherValues(const T source) const
 {
@@ -170,6 +206,29 @@ void Comm::BroadcastVector(std::vector<T> &vector, const int rankSource) const
     }
 }
 
+template <class T>
+void Comm::BroadcastVector(helper::adiosvec<T> &vector,
+                           const int rankSource) const
+{
+    if (this->Size() == 1)
+    {
+        return;
+    }
+
+    // First Broadcast the size, then the contents
+    size_t inputSize = this->BroadcastValue(vector.size(), rankSource);
+
+    if (rankSource != this->Rank())
+    {
+        vector.resize(inputSize);
+    }
+
+    if (inputSize > 0)
+    {
+        this->Bcast(vector.data(), inputSize, rankSource);
+    }
+}
+
 template <typename TSend, typename TRecv>
 void Comm::Allgather(const TSend *sendbuf, size_t sendcount, TRecv *recvbuf,
                      size_t recvcount, const std::string &hint) const