Don't force initialization for buffers whose contents we will immedia…

…tely destroy (ornladios#4031)

* BufferMalloc

source/adios2/CMakeLists.txt

@@ -80,6 +80,7 @@ add_library(adios2_core
   toolkit/format/buffer/chunk/ChunkV.cpp
   toolkit/format/buffer/ffs/BufferFFS.cpp
   toolkit/format/buffer/heap/BufferSTL.cpp
+  toolkit/format/buffer/heap/BufferMalloc.cpp
   toolkit/format/buffer/malloc/MallocV.cpp
 
   toolkit/format/bp/BPBase.cpp toolkit/format/bp/BPBase.tcc

source/adios2/engine/bp5/BP5Reader.cpp

@@ -70,8 +70,8 @@ void BP5Reader::InstallMetadataForTimestep(size_t Step)
     {
         // variable metadata for timestep
         size_t ThisMDSize =
-            helper::ReadValue<uint64_t>(m_Metadata.m_Buffer, Position, m_Minifooter.IsLittleEndian);
-        char *ThisMD = m_Metadata.m_Buffer.data() + MDPosition;
+            helper::ReadValue<uint64_t>(m_Metadata.Data(), Position, m_Minifooter.IsLittleEndian);
+        char *ThisMD = m_Metadata.Data() + MDPosition;
         if (m_OpenMode == Mode::ReadRandomAccess)
         {
             m_BP5Deserializer->InstallMetaData(ThisMD, ThisMDSize, WriterRank, Step);
@@ -86,8 +86,8 @@ void BP5Reader::InstallMetadataForTimestep(size_t Step)
     {
         // attribute metadata for timestep
         size_t ThisADSize =
-            helper::ReadValue<uint64_t>(m_Metadata.m_Buffer, Position, m_Minifooter.IsLittleEndian);
-        char *ThisAD = m_Metadata.m_Buffer.data() + MDPosition;
+            helper::ReadValue<uint64_t>(m_Metadata.Data(), Position, m_Minifooter.IsLittleEndian);
+        char *ThisAD = m_Metadata.Data() + MDPosition;
         if (ThisADSize > 0)
             m_BP5Deserializer->InstallAttributeData(ThisAD, ThisADSize);
         MDPosition += ThisADSize;
@@ -820,8 +820,7 @@ void BP5Reader::UpdateBuffer(const TimePoint &timeoutInstant, const Seconds &pol
                 for (auto p : m_FilteredMetadataInfo)
                 {
                     m_JSONProfiler.AddBytes("metadataread", p.second);
-                    m_MDFileManager.ReadFile(m_Metadata.m_Buffer.data() + mempos, p.second,
-                                             p.first);
+                    m_MDFileManager.ReadFile(m_Metadata.Data() + mempos, p.second, p.first);
                     mempos += p.second;
                 }
                 m_MDFileAlreadyReadSize = expectedMinFileSize;
@@ -863,14 +862,20 @@ void BP5Reader::UpdateBuffer(const TimePoint &timeoutInstant, const Seconds &pol
             }
         }
 
-        // broadcast buffer to all ranks from zero
-        m_Comm.BroadcastVector(m_Metadata.m_Buffer);
-
         // broadcast metadata index buffer to all ranks from zero
         m_Comm.BroadcastVector(m_MetaMetadata.m_Buffer);
 
         InstallMetaMetaData(m_MetaMetadata);
 
+        size_t inputSize = m_Comm.BroadcastValue(m_Metadata.Size(), 0);
+
+        if (m_Comm.Rank() != 0)
+        {
+            m_Metadata.Resize(inputSize, "metadata broadcast");
+        }
+
+        m_Comm.Bcast(m_Metadata.Data(), inputSize, 0);
+
         if (m_OpenMode == Mode::ReadRandomAccess)
         {
             for (size_t Step = 0; Step < m_MetadataIndexTable.size(); Step++)

source/adios2/engine/bp5/BP5Reader.h

@@ -4,8 +4,6 @@
  *
  * BP5Reader.h
  *
- *  Created on: Aug 1, 2018
- *      Author: Lipeng Wan [email protected]
  */
 
 #ifndef ADIOS2_ENGINE_BP5_BP5READER_H_
@@ -18,6 +16,7 @@
 #include "adios2/helper/adiosComm.h"
 #include "adios2/helper/adiosRangeFilter.h"
 #include "adios2/toolkit/format/bp5/BP5Deserializer.h"
+#include "adios2/toolkit/format/buffer/heap/BufferMalloc.h"
 #include "adios2/toolkit/remote/Remote.h"
 #include "adios2/toolkit/transportman/TransportMan.h"
 
@@ -225,7 +224,7 @@ class BP5Reader : public BP5Engine, public Engine
 
     format::BufferSTL m_MetadataIndex;
     format::BufferSTL m_MetaMetadata;
-    format::BufferSTL m_Metadata;
+    format::BufferMalloc m_Metadata;
 
     void InstallMetaMetaData(format::BufferSTL MetaMetadata);
     void InstallMetadataForTimestep(size_t Step);

source/adios2/helper/adiosMemory.h

@@ -5,8 +5,6 @@
  * adiosMemory.h : Memory copy operations functions using std::copy std::insert
  * and std::memcpy
  *
- *  Created on: May 17, 2017
- *      Author: William F Godoy [email protected]
  */
 
 #ifndef ADIOS2_HELPER_ADIOSMEMORY_H_
@@ -83,7 +81,7 @@ void CopyToBufferThreads(std::vector<char> &buffer, size_t &position, const T *s
                          const size_t elements = 1, const unsigned int threads = 1) noexcept;
 
 template <class T>
-void ReverseCopyFromBuffer(const std::vector<char> &buffer, size_t &position, T *destination,
+void ReverseCopyFromBuffer(const char *buffer, size_t &position, T *destination,
                            const size_t elements = 1) noexcept;
 
 /**
@@ -95,7 +93,7 @@ void ReverseCopyFromBuffer(const std::vector<char> &buffer, size_t &position, T
  * @param elements  number of elements of destination type
  */
 template <class T>
-void CopyFromBuffer(const std::vector<char> &buffer, size_t &position, T *destination,
+void CopyFromBuffer(const char *buffer, size_t &position, T *destination,
                     const size_t elements = 1) noexcept;
 
 /**
@@ -110,6 +108,9 @@ template <class T>
 T ReadValue(const std::vector<char> &buffer, size_t &position,
             const bool isLittleEndian = true) noexcept;
 
+template <class T>
+T ReadValue(const char *buffer, size_t &position, const bool isLittleEndian = true) noexcept;
+
 /** Read in 'nElems' elements from buffer into output array
  * output must be pre-allocated.
  */