Merge branch 'master' of https://github.com/ornladios/ADIOS2.git

Conflicts:
	include/engine/bp/BPFileWriter.h
	source/core/Engine.cpp
	source/engine/bp/BPFileWriter.cpp

include/core/Transport.h

@@ -15,12 +15,11 @@
 #include <string>
 #include <vector>
 
-#include "../utilities/profiling/iochrono/IOChrono.h"
+#include "utilities/profiling/iochrono/IOChrono.h"
 /// \endcond
 
 #include "ADIOS_MPI.h"
 
-
 namespace adios
 {
 
@@ -45,7 +44,7 @@ public:
    * @param mpiComm passed to m_MPIComm
    * @param debugMode passed to m_DebugMode
    */
-  Transport(std::string type, MPI_Comm mpiComm, bool debugMode);
+  Transport(const std::string type, MPI_Comm mpiComm, const bool debugMode);
 
   virtual ~Transport() = default;
 

include/engine/bp/BPFileWriter.h

@@ -31,10 +31,10 @@ public:
    * @param method
    * @param debugMode
    */
+
   BPFileWriter(ADIOS &adios, const std::string name,
                const std::string accessMode, MPI_Comm mpiComm,
                const Method &method);
-
   ~BPFileWriter();
 
   void Write(Variable<char> &variable, const char *values);

include/utilities/profiling/iochrono/Timer.h

@@ -31,10 +31,6 @@ public:
   unsigned long long int m_ProcessTime = 0;
 
   /**
-   *
-   */
-  /**
-   *
    * Timer object constructor using std::chrono class
    * @param process name of process to be measured
    * @param resolution time resolution (mus, ms, s, etc.) from Resolutions in

scripts/developer/setup.sh

@@ -15,4 +15,4 @@ test_cmd scripts/developer/git/setup-aliases \
 
 test_cmd scripts/developer/git/setup-hooks \
   "Failed to setup git hooks" 1
-git config hooks.clang-format true
+git config hooks.clang-format false

source/core/Engine.cpp

@@ -21,10 +21,10 @@ Engine::Engine(ADIOS &adios, const std::string engineType,
                const std::string name, const std::string accessMode,
                MPI_Comm mpiComm, const Method &method,
                const std::string endMessage)
-: m_MPIComm{mpiComm}, m_EngineType{std::move(engineType)},
-  m_Name{std::move(name)}, m_AccessMode{std::move(accessMode)},
-  m_Method{method}, m_ADIOS(adios), m_EndMessage(std::move(endMessage)),
-  m_DebugMode{m_Method.m_DebugMode}, m_nThreads{m_Method.m_nThreads}
+: m_MPIComm(mpiComm), m_EngineType(engineType), m_Name(name),
+  m_AccessMode(accessMode), m_Method(method), m_ADIOS(adios),
+  m_EndMessage(endMessage), m_DebugMode(m_Method.m_DebugMode),
+  m_nThreads(m_Method.m_nThreads)
 {
   if (m_DebugMode == true)
   {
@@ -48,44 +48,93 @@ void Engine::SetCallBack(std::function<void(const void *, std::string,
 
 // should these functions throw an exception?
 
-// clang-format off
-void Engine::Write(Variable<char> &variable,                      const char *values) {}
-void Engine::Write(Variable<unsigned char> &variable,             const unsigned char *values){ }
-void Engine::Write(Variable<short> &variable,                     const short *values) {}
-void Engine::Write(Variable<unsigned short> &variable,            const unsigned short *values) {}
-void Engine::Write(Variable<int> &variable,                       const int *values) {}
-void Engine::Write(Variable<unsigned int> &variable,              const unsigned int *values) {}
-void Engine::Write(Variable<long int> &variable,                  const long int *values) {}
-void Engine::Write(Variable<unsigned long int> &variable,         const unsigned long int *values) {}
-void Engine::Write(Variable<long long int> &variable,             const long long int *values) {}
-void Engine::Write(Variable<unsigned long long int> &variable,    const unsigned long long int *values) {}
-void Engine::Write(Variable<float> &variable,                     const float *values) {}
-void Engine::Write(Variable<double> &variable,                    const double *values) {}
-void Engine::Write(Variable<long double> &variable,               const long double *values) {}
-void Engine::Write(Variable<std::complex<float>> &variable,       const std::complex<float> *values) {}
-void Engine::Write(Variable<std::complex<double>> &variable,      const std::complex<double> *values) {}
-void Engine::Write(Variable<std::complex<long double>> &variable, const std::complex<long double> *values) {}
-void Engine::Write(VariableCompound &variable,                    const void *values) {}
+void Engine::Write(Variable<char> &variable, const char *values) {}
+void Engine::Write(Variable<unsigned char> &variable,
+                   const unsigned char *values)
+{
+}
+void Engine::Write(Variable<short> &variable, const short *values) {}
+void Engine::Write(Variable<unsigned short> &variable,
+                   const unsigned short *values)
+{
+}
+void Engine::Write(Variable<int> &variable, const int *values) {}
+void Engine::Write(Variable<unsigned int> &variable, const unsigned int *values)
+{
+}
+void Engine::Write(Variable<long int> &variable, const long int *values) {}
+void Engine::Write(Variable<unsigned long int> &variable,
+                   const unsigned long int *values)
+{
+}
+void Engine::Write(Variable<long long int> &variable,
+                   const long long int *values)
+{
+}
+void Engine::Write(Variable<unsigned long long int> &variable,
+                   const unsigned long long int *values)
+{
+}
+void Engine::Write(Variable<float> &variable, const float *values) {}
+void Engine::Write(Variable<double> &variable, const double *values) {}
+void Engine::Write(Variable<long double> &variable, const long double *values)
+{
+}
+void Engine::Write(Variable<std::complex<float>> &variable,
+                   const std::complex<float> *values)
+{
+}
+void Engine::Write(Variable<std::complex<double>> &variable,
+                   const std::complex<double> *values)
+{
+}
+void Engine::Write(Variable<std::complex<long double>> &variable,
+                   const std::complex<long double> *values)
+{
+}
+void Engine::Write(VariableCompound &variable, const void *values) {}
 
 // String version
 void Engine::Write(const std::string variableName, const char *values) {}
-void Engine::Write(const std::string variableName, const unsigned char *values) {}
+void Engine::Write(const std::string variableName, const unsigned char *values)
+{
+}
 void Engine::Write(const std::string variableName, const short *values) {}
-void Engine::Write(const std::string variableName, const unsigned short *values) {}
+void Engine::Write(const std::string variableName, const unsigned short *values)
+{
+}
 void Engine::Write(const std::string variableName, const int *values) {}
-void Engine::Write(const std::string variableName, const unsigned int *values) {}
+void Engine::Write(const std::string variableName, const unsigned int *values)
+{
+}
 void Engine::Write(const std::string variableName, const long int *values) {}
-void Engine::Write(const std::string variableName, const unsigned long int *values) {}
-void Engine::Write(const std::string variableName, const long long int *values) {}
-void Engine::Write(const std::string variableName, const unsigned long long int *values) {}
+void Engine::Write(const std::string variableName,
+                   const unsigned long int *values)
+{
+}
+void Engine::Write(const std::string variableName, const long long int *values)
+{
+}
+void Engine::Write(const std::string variableName,
+                   const unsigned long long int *values)
+{
+}
 void Engine::Write(const std::string variableName, const float *values) {}
 void Engine::Write(const std::string variableName, const double *values) {}
 void Engine::Write(const std::string variableName, const long double *values) {}
-void Engine::Write(const std::string variableName, const std::complex<float> *values) {}
-void Engine::Write(const std::string variableName, const std::complex<double> *values) {}
-void Engine::Write(const std::string variableName, const std::complex<long double> *values) {}
+void Engine::Write(const std::string variableName,
+                   const std::complex<float> *values)
+{
+}
+void Engine::Write(const std::string variableName,
+                   const std::complex<double> *values)
+{
+}
+void Engine::Write(const std::string variableName,
+                   const std::complex<long double> *values)
+{
+}
 void Engine::Write(const std::string variableName, const void *values) {}
-// clang-format on
 
 void Engine::Advance(float timeout_sec) {}
 void Engine::Advance(AdvanceMode mode, float timeout_sec) {}

source/core/Transport.cpp

@@ -15,8 +15,9 @@
 namespace adios
 {
 
-Transport::Transport(std::string type, MPI_Comm mpiComm, bool debugMode)
-: m_Type{type}, m_MPIComm{mpiComm}, m_DebugMode{debugMode}
+Transport::Transport(const std::string type, MPI_Comm mpiComm,
+                     const bool debugMode)
+: m_Type(type), m_MPIComm(mpiComm), m_DebugMode(debugMode)
 {
   MPI_Comm_rank(m_MPIComm, &m_RankMPI);
   MPI_Comm_size(m_MPIComm, &m_SizeMPI);

source/engine/bp/BPFileWriter.cpp

@@ -7,9 +7,10 @@
  *  Created on: Dec 19, 2016
  *      Author: wfg
  */
+#include <utility>
 
-#include "engine/bp/BPFileWriter.h"
 #include "ADIOS.h"
+#include "engine/bp/BPFileWriter.h"
 
 // supported transports
 #include "transport/file/FStream.h"
@@ -24,9 +25,9 @@ BPFileWriter::BPFileWriter(ADIOS &adios, const std::string name,
                            const Method &method)
 : Engine(adios, "BPFileWriter", name, accessMode, mpiComm, method,
          " BPFileWriter constructor (or call to ADIOS Open).\n"),
-  m_Buffer{capsule::STLVector(accessMode, m_RankMPI, m_DebugMode)},
-  m_BP1Aggregator{format::BP1Aggregator(m_MPIComm, m_DebugMode)},
-  m_MaxBufferSize{m_Buffer.m_Data.max_size()}
+  m_Buffer(accessMode, m_RankMPI, m_DebugMode),
+  m_BP1Aggregator(m_MPIComm, m_DebugMode),
+  m_MaxBufferSize(m_Buffer.m_Data.max_size())
 {
   m_MetadataSet.TimeStep = 1; // starting at one to be compatible with ADIOS1.x
   Init();

source/transport/file/FStream.cpp

@@ -20,7 +20,7 @@ namespace adios
 namespace transport
 {
 
-FStream::FStream(MPI_Comm mpiComm, bool debugMode)
+FStream::FStream(MPI_Comm mpiComm, const bool debugMode)
 : Transport("fstream", mpiComm, debugMode)
 {
 }