Merge pull request #5 from williamfgc/bpindataman

Bpindataman

source/adios2/core/ADIOS.cpp

@@ -187,8 +187,8 @@ ADIOS2_FOREACH_TYPE_1ARG(declare_type)
 
 Operator &ADIOS::DefineCallBack(
     const std::string name,
-    const std::function<void(void *, const std::string, const std::string,
-                             const std::string, const Dims &)> &function,
+    const std::function<void(void *, const std::string &, const std::string &,
+                             const std::string &, const Dims &)> &function,
     const Params &parameters)
 {
     std::shared_ptr<Operator> callbackOperator =

source/adios2/core/ADIOS.h

@@ -173,8 +173,9 @@ private:
     /** define CallBack2 */
     Operator &DefineCallBack(
         const std::string name,
-        const std::function<void(void *, const std::string, const std::string,
-                                 const std::string, const Dims &)> &function,
+        const std::function<void(void *, const std::string &,
+                                 const std::string &, const std::string &,
+                                 const Dims &)> &function,
         const Params &parameters);
 };
 

source/adios2/engine/bp/BPFileReader.cpp

@@ -95,7 +95,7 @@ void BPFileReader::InitBuffer()
     BroadcastVector(m_BP3Deserializer.m_Metadata.m_Buffer, m_MPIComm);
 
     // fills IO with Variables and Attributes
-    m_BP3Deserializer.ParseMetadata(m_IO);
+    m_BP3Deserializer.ParseMetadata(m_BP3Deserializer.m_Metadata, m_IO);
 }
 
 #define declare_type(T)                                                        \

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

@@ -32,11 +32,11 @@ BP3Deserializer::BP3Deserializer(MPI_Comm mpiComm, const bool debugMode)
 {
 }
 
-void BP3Deserializer::ParseMetadata(IO &io)
+void BP3Deserializer::ParseMetadata(const BufferSTL &bufferSTL, IO &io)
 {
-    ParseMinifooter();
-    ParsePGIndex();
-    ParseVariablesIndex(io);
+    ParseMinifooter(bufferSTL);
+    ParsePGIndex(bufferSTL);
+    ParseVariablesIndex(bufferSTL, io);
     // ParseAttributesIndex(io);
 }
 
@@ -66,7 +66,7 @@ void BP3Deserializer::ClipContiguousMemory(
 }
 
 // PRIVATE
-void BP3Deserializer::ParseMinifooter()
+void BP3Deserializer::ParseMinifooter(const BufferSTL &bufferSTL)
 {
     auto lf_GetEndianness = [](const uint8_t endianness, bool &isLittleEndian) {
 
@@ -81,7 +81,7 @@ void BP3Deserializer::ParseMinifooter()
         }
     };
 
-    const auto &buffer = m_Metadata.m_Buffer;
+    const auto &buffer = bufferSTL.m_Buffer;
     const size_t bufferSize = buffer.size();
 
     size_t position = bufferSize - 4;
@@ -110,9 +110,9 @@ void BP3Deserializer::ParseMinifooter()
     m_Minifooter.AttributesIndexStart = ReadValue<uint64_t>(buffer, position);
 }
 
-void BP3Deserializer::ParsePGIndex()
+void BP3Deserializer::ParsePGIndex(const BufferSTL &bufferSTL)
 {
-    const auto &buffer = m_Metadata.m_Buffer;
+    const auto &buffer = bufferSTL.m_Buffer;
     auto &position = m_Metadata.m_Position;
     position = m_Minifooter.PGIndexStart;
 
@@ -128,7 +128,7 @@ void BP3Deserializer::ParsePGIndex()
     }
 }
 
-void BP3Deserializer::ParseVariablesIndex(IO &io)
+void BP3Deserializer::ParseVariablesIndex(const BufferSTL &bufferSTL, IO &io)
 {
     auto lf_ReadElementIndex = [&](IO &io, const std::vector<char> &buffer,
                                    size_t position) {
@@ -238,7 +238,7 @@ void BP3Deserializer::ParseVariablesIndex(IO &io)
         } // end switch
     };
 
-    const auto &buffer = m_Metadata.m_Buffer;
+    const auto &buffer = bufferSTL.m_Buffer;
     size_t position = m_Minifooter.VarsIndexStart;
 
     const uint32_t count = ReadValue<uint32_t>(buffer, position);

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

@@ -40,7 +40,7 @@ public:
 
     ~BP3Deserializer() = default;
 
-    void ParseMetadata(IO &io);
+    void ParseMetadata(const BufferSTL &bufferSTL, IO &io);
 
     // Sync functions
     template <class T>
@@ -64,9 +64,9 @@ private:
 
     static std::mutex m_Mutex;
 
-    void ParseMinifooter();
-    void ParsePGIndex();
-    void ParseVariablesIndex(IO &io);
+    void ParseMinifooter(const BufferSTL &bufferSTL);
+    void ParsePGIndex(const BufferSTL &bufferSTL);
+    void ParseVariablesIndex(const BufferSTL &bufferSTL, IO &io);
     void ParseAttributesIndex(IO &io);
 
     /**

source/adios2/toolkit/transportman/dataman/DataMan.cpp

@@ -8,6 +8,8 @@
  *      Author: Jason Wang wangr1@ornl.gov
  */
 
+#include <fstream> //TODO go away
+
 #include "DataMan.h"
 
 #include "adios2/helper/adiosFunctions.h"
@@ -161,8 +163,13 @@ void DataMan::WriteWAN(const void *buffer, size_t size)
     m_Transports[m_CurrentTransport]->Write(
         reinterpret_cast<const char *>(buffer), size);
 
+    std::ofstream bpfile("datamanW.bp", std::ios_base::binary);
+    bpfile.write(reinterpret_cast<const char *>(buffer), size);
+    bpfile.close();
+
     for (int i = 0; i < size / 4; i++)
     {
+
         std::cout << static_cast<const float *>(buffer)[i] << " ";
     }
 }
@@ -225,25 +232,33 @@ void DataMan::ReadThread(std::shared_ptr<Transport> trans,
     {
         while (m_Listening)
         {
-            char *buffer = new char[m_BufferSize];
+            // char *buffer = new char[m_BufferSize];
+            std::vector<char> buffer(m_BufferSize);
+
             Transport::Status status;
-            trans->IRead(buffer, m_BufferSize, status);
+            trans->IRead(buffer.data(), m_BufferSize, status);
 
             if (status.Bytes > 0)
             {
                 m_BP3Deserializer->m_Data.Resize(
                     status.Bytes, "in DataMan Streaming Listener");
 
-                std::memcpy(m_BP3Deserializer->m_Data.m_Buffer.data(), buffer,
-                            status.Bytes);
+                std::memcpy(m_BP3Deserializer->m_Data.m_Buffer.data(),
+                            buffer.data(), status.Bytes);
 
                 /* TODO: remove this part  */
 
-                m_Callback->RunCallback2(buffer, "ss", "rr", "char", {128});
+                m_Callback->RunCallback2(buffer.data(), "ss", "rr", "char",
+                                         adios2::Dims{128});
+
+                std::ofstream bpfile("datamanR.bp", std::ios_base::binary);
+                bpfile.write(m_BP3Deserializer->m_Data.m_Buffer.data(),
+                             m_BP3Deserializer->m_Data.m_Buffer.size());
+                bpfile.close();
 
-                m_BP3Deserializer->ParseMetadata(*m_IO);
+                m_BP3Deserializer->ParseMetadata(m_BP3Deserializer->m_Data,
+                                                 *m_IO);
 
-                /*
                 const auto variablesInfo = m_IO->GetAvailableVariables();
                 for (const auto &variableInfoPair : variablesInfo)
                 {
@@ -256,9 +271,7 @@ void DataMan::ReadThread(std::shared_ptr<Transport> trans,
                                   << "\t Value: " << parameter.second << "\n";
                     }
                 }
-                */
             }
-            delete[] buffer;
         }
     }
 }