ADIOS.h

/*
 * ADIOS.h
 *
 *  Created on: Oct 3, 2016
 *      Author: wfg
 */

#ifndef ADIOS_H_
#define ADIOS_H_

/// \cond EXCLUDE_FROM_DOXYGEN
#include <complex>
#include <map>
#include <memory> //std::shared_ptr
#include <ostream>
#include <set>
#include <string>
#include <vector>
/// \endcond

#ifdef ADIOS_NOMPI
#include "mpidummy.h"
#else
#include <mpi.h>
#endif

#include "ADIOSTypes.h"
#include "core/Method.h"
#include "core/Support.h"
#include "core/Transform.h"
#include "core/Variable.h"
#include "core/VariableCompound.h"
#include "functions/adiosTemplates.h"

namespace adios
{

class Engine;

/**
 * @brief Unique class interface between user application and ADIOS library
 */
class ADIOS
{

public
    : // PUBLIC Constructors and Functions define the User Interface with ADIOS
  MPI_Comm m_MPIComm = MPI_COMM_SELF; ///< only used as reference to MPI
                                      ///communicator passed from parallel
                                      ///constructor, MPI_Comm is a pointer
                                      ///itself. Public as called from C

  int m_RankMPI = 0; ///< current MPI rank process
  int m_SizeMPI = 1; ///< current MPI processes size

  std::string m_HostLanguage = "C++";

  /**
   * @brief ADIOS empty constructor. Used for non XML config file API calls.
   */
  ADIOS(const Verbose verbose = Verbose::WARN, const bool debugMode = false);

  /**
   * @brief Serial constructor for config file, only allowed and compiled in
   * libadios_nompi.a
   * @param configFileName passed to m_ConfigFile
   * @param debugMode true: on throws exceptions and do additional checks,
   * false: off (faster, but unsafe)
   */
  ADIOS(const std::string configFileName, const Verbose verbose = Verbose::WARN,
        const bool debugMode = false);

  /**
   * @brief Parallel constructor for XML config file and MPI
   * @param configFileName passed to m_XMLConfigFile
   * @param mpiComm MPI communicator ...const to be discussed
   * @param debugMode true: on, false: off (faster, but unsafe)
   */

  ADIOS(const std::string configFileName, MPI_Comm mpiComm,
        const Verbose verbose = Verbose::WARN, const bool debugMode = false);

  /**
   * @brief Parallel MPI communicator without XML config file
   * @param mpiComm MPI communicator passed to m_MPIComm*
   * @param debugMode true: on, false: off (faster)
   */
  ADIOS(MPI_Comm mpiComm, const Verbose verbose = Verbose::WARN,
        const bool debugMode = false);

  ~ADIOS(); ///< empty, using STL containers for memory management

  void InitMPI(); ///< sets rank and size in m_rank and m_Size, respectively.

  /**
   * Look for template specialization
   * @param name
   * @param dimensions
   * @param globalDimensions
   * @param globalOffsets
   * @return
   */
  template <class T>
  inline Variable<T> &DefineVariable(const std::string name,
                                     const Dims dimensions = Dims{1},
                                     const Dims globalDimensions = Dims(),
                                     const Dims globalOffsets = Dims())
  {
    throw std::invalid_argument("ERROR: type not supported for variable " +
                                name + " in call to DefineVariable\n");
  }

  template <class T> inline Variable<T> &GetVariable(const std::string name)
  {
    throw std::invalid_argument("ERROR: type not supported for variable " +
                                name + " in call to GetVariable\n");
  }

  template <class T>
  VariableCompound &DefineVariableCompound(const std::string name,
                                           const Dims dimensions = Dims{1},
                                           const Dims globalDimensions = Dims(),
                                           const Dims globalOffsets = Dims())
  {
    CheckVariableInput(name, dimensions);
    const unsigned int size = m_Compound.size();
    m_Compound.emplace(size, VariableCompound(name, sizeof(T), dimensions,
                                              globalDimensions, globalOffsets,
                                              m_DebugMode));
    m_Variables.emplace(name, std::make_pair(GetType<T>(), size));
    return m_Compound.at(size);
  }

  VariableCompound &GetVariableCompound(const std::string name);

  /**
   * Declares a new method. If the method is defined in the user config file,
   * it will be already created during processing the config file,
   * the method is set up with the user settings and this function just returns
   * that method.
   * Otherwise it will create and return a new Method with default settings.
   * Use method.isUserDefined() to distinguish between the two cases.
   * @param methodName must be unique
   */
  Method &DeclareMethod(const std::string methodName);

  /**
   * @brief Open to Write, Read. Creates a new engine from previously defined
   * method
   * @param streamName unique stream or file name
   * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or
   * "update"
   * @param mpiComm option to modify communicator from ADIOS class constructor
   * @param method looks for corresponding Method object in ADIOS to initialize
   * the engine
   * @param iomode Independent or collective open/advance by writers/readers?
   * Write() operations are always independent.
   * @param timeout_sec Wait some time before reporting on missing stream (i.e.
   * wait for it for a while)
    * @return Derived class of base Engine depending on Method parameters,
   * shared_ptr for potential flexibility
   */
  std::shared_ptr<Engine> Open(const std::string streamName,
                               const std::string accessMode, MPI_Comm mpiComm,
                               const Method &method,
                               const IOMode iomode = IOMode::INDEPENDENT,
                               const float timeout_sec = 0.0);

  /**
   * @brief Open to Write, Read. Creates a new engine from previously defined
   * method.
   * Reuses MPI communicator from ADIOS constructor.
   * @param streamName unique stream or file name
   * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or
   * "update"
   * @param method contains engine parameters
   * @param iomode Independent or collective open/advance by writers/readers?
   * Write() operations are always independent.
   * @param timeout_sec Wait some time before reporting on missing stream (i.e.
   * wait for it for a while)
    * @return Derived class of base Engine depending on Method parameters,
   * shared_ptr for potential flexibility
   */
  std::shared_ptr<Engine> Open(const std::string streamName,
                               const std::string accessMode,
                               const Method &method,
                               const IOMode iomode = IOMode::INDEPENDENT,
                               const float timeout_sec = 0.0);

  /**
   * Version required by the XML config file implementation, searches method
   * inside ADIOS through a unique name
   * @param streamName unique stream or file name
   * @param accessMode "w" or "write", "r" or "read", "a" or "append"
   * @param mpiComm mpi Communicator
   * @param methodName used to search method object inside ADIOS object
   * @param iomode Independent or collective open/advance by writers/readers?
   * Write() operations are always independent.
   * @param timeout_sec Wait some time before reporting on missing stream (i.e.
   * wait for it for a while)
   * @return Derived class of base Engine depending on Method parameters,
   * shared_ptr for potential flexibility
   */
  std::shared_ptr<Engine> Open(const std::string streamName,
                               const std::string accessMode, MPI_Comm mpiComm,
                               const std::string methodName,
                               const IOMode iomode = IOMode::INDEPENDENT,
                               const float timeout_sec = 0.0);

  /**
   * Version required by the XML config file implementation, searches method
   * inside ADIOS through a unique name.
   * Reuses ADIOS MPI Communicator from constructor.
   * @param streamName unique stream or file name
   * @param accessMode "w" or "write", "r" or "read", "a" or "append"
   * @param methodName used to search method object inside ADIOS object
   * @param iomode Independent or collective open/advance by writers/readers?
   * Write() operations are always independent.
   * @param timeout_sec Wait some time before reporting on missing stream (i.e.
   * wait for it for a while)
   * @return Derived class of base Engine depending on Method parameters,
   * shared_ptr for potential flexibility
   */
  std::shared_ptr<Engine> Open(const std::string streamName,
                               const std::string accessMode,
                               const std::string methodName,
                               const IOMode iomode = IOMode::INDEPENDENT,
                               const float timeout_sec = 0.0);

  /**
   * @brief Open to Read all steps from a file. No streaming, advancing is
   * possible here. All steps in the file
   * are immediately available for reading. Creates a new engine from previously
   * defined method.
   * @param fileName file name
   * @param mpiComm option to modify communicator from ADIOS class constructor
   * @param method looks for corresponding Method object in ADIOS to initialize
   * the engine
   * @param iomode Independent or collective open/advance by writers/readers?
   * Write() operations are always independent.
   * @return Derived class of base Engine depending on Method parameters,
   * shared_ptr for potential flexibility
   */
  std::shared_ptr<Engine>
  OpenFileReader(const std::string fileName, MPI_Comm mpiComm,
                 const Method &method,
                 const IOMode iomode = IOMode::INDEPENDENT);

  /**
   * @brief Open to Read all steps from a file. No streaming, advancing is
   * possible here. All steps in the file
   * are immediately available for reading. Creates a new engine from previously
   * defined method.
   * Version required by the XML config file implementation, searches method
   * inside ADIOS through a unique name.
   * @param fileName file name
   * @param mpiComm option to modify communicator from ADIOS class constructor
   * @param methodName used to search method object inside ADIOS object
    * @param iomode Independent or collective open/advance by writers/readers?
   * Write() operations are always independent.
   * @return Derived class of base Engine depending on Method parameters,
   * shared_ptr for potential flexibility
   */
  std::shared_ptr<Engine>
  OpenFileReader(const std::string fileName, MPI_Comm mpiComm,
                 const std::string methodName,
                 const IOMode iomode = IOMode::INDEPENDENT);

  /**
   * @brief Dumps groups information to a file stream or standard output.
   * Note that either the user closes this fileStream or it's closed at the end.
   * @param logStream either std::cout standard output, or a std::ofstream file
   */
  void MonitorVariables(std::ostream &logStream);

protected: // no const to allow default empty and copy constructors
  std::map<unsigned int, Variable<char>> m_Char;
  std::map<unsigned int, Variable<unsigned char>> m_UChar;
  std::map<unsigned int, Variable<short>> m_Short;
  std::map<unsigned int, Variable<unsigned short>> m_UShort;
  std::map<unsigned int, Variable<int>> m_Int;
  std::map<unsigned int, Variable<unsigned int>> m_UInt;
  std::map<unsigned int, Variable<long int>> m_LInt;
  std::map<unsigned int, Variable<unsigned long int>> m_ULInt;
  std::map<unsigned int, Variable<long long int>> m_LLInt;
  std::map<unsigned int, Variable<unsigned long long int>> m_ULLInt;
  std::map<unsigned int, Variable<float>> m_Float;
  std::map<unsigned int, Variable<double>> m_Double;
  std::map<unsigned int, Variable<long double>> m_LDouble;
  std::map<unsigned int, Variable<std::complex<float>>> m_CFloat;
  std::map<unsigned int, Variable<std::complex<double>>> m_CDouble;
  std::map<unsigned int, Variable<std::complex<long double>>> m_CLDouble;
  std::map<unsigned int, VariableCompound> m_Compound;

  std::string m_ConfigFile; ///< XML File to be read containing configuration
                            ///information
  bool m_DebugMode = false; ///< if true will do more checks, exceptions,
                            ///warnings, expect slower code

  // Variables
  std::map<std::string, std::pair<std::string, unsigned int>>
      m_Variables; ///< Makes variable name unique, key: variable name, value:
                   ///pair.first = type, pair.second = index in corresponding
                   ///vector of Variable

  std::vector<std::shared_ptr<Transform>>
      m_Transforms; ///< transforms associated with ADIOS run

  /**
   * @brief List of Methods (engine metadata) defined from either ADIOS XML
   * configuration file or the DeclareMethod function.
   * <pre>
   *     Key: std::string unique method name
   *     Value: Method class
   * </pre>
   */
  std::map<std::string, Method> m_Methods;
  std::set<std::string>
      m_EngineNames; ///< set used to check Engine name uniqueness in debug mode

  /**
   * @brief Checks for group existence in m_Groups, if failed throws
   * std::invalid_argument exception
   * @param itGroup m_Groups iterator, usually from find function
   * @param groupName unique name, passed for thrown exception only
   * @param hint adds information to thrown exception
   */
  void CheckVariableInput(const std::string name, const Dims &dimensions) const;

  /**
   * Checks for variable name, if not found throws an invalid exception
   * @param itVariable iterator pointing to the variable name in m_Variables
   * @param name variable name
   * @param hint message to be thrown for debugging purporses
   */
  void CheckVariableName(
      std::map<std::string,
               std::pair<std::string, unsigned int>>::const_iterator itVariable,
      const std::string name, const std::string hint) const;

  /**
   * @brief Checks for method existence in m_Methods, if failed throws
   * std::invalid_argument exception
   * @param itMethod m_Methods iterator, usually from find function
   * @param methodName unique name, passed for thrown exception only
   * @param hint adds information to thrown exception
   */
  void CheckMethod(std::map<std::string, Method>::const_iterator itMethod,
                   const std::string methodName, const std::string hint) const;

  template <class T> unsigned int GetVariableIndex(const std::string name)
  {
    auto itVariable = m_Variables.find(name);
    CheckVariableName(
        itVariable, name,
        "in call to GetVariable<" + GetType<T>() +
            ">, or call to GetVariableCompound if <T> = <compound>\n");
    return itVariable->second.second;
  }
};

// template specializations of DefineVariable:
template <>
inline Variable<char> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_Char.size();
  m_Char.emplace(size, Variable<char>(name, dimensions, globalDimensions,
                                      globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<char>(), size));
  return m_Char.at(size);
}

template <>
inline Variable<unsigned char> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_UChar.size();
  m_UChar.emplace(size,
                  Variable<unsigned char>(name, dimensions, globalDimensions,
                                          globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<unsigned char>(), size));
  return m_UChar.at(size);
}

template <>
inline Variable<short> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_Short.size();
  m_Short.emplace(size, Variable<short>(name, dimensions, globalDimensions,
                                        globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<unsigned char>(), size));
  return m_Short.at(size);
}

template <>
inline Variable<unsigned short> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_UShort.size();
  m_UShort.emplace(size,
                   Variable<unsigned short>(name, dimensions, globalDimensions,
                                            globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<unsigned short>(), size));
  return m_UShort.at(size);
}

template <>
inline Variable<int> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_Int.size();
  m_Int.emplace(size, Variable<int>(name, dimensions, globalDimensions,
                                    globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<int>(), size));
  return m_Int.at(size);
}

template <>
inline Variable<unsigned int> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_UInt.size();
  m_UInt.emplace(size,
                 Variable<unsigned int>(name, dimensions, globalDimensions,
                                        globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<unsigned int>(), size));
  return m_UInt.at(size);
}

template <>
inline Variable<long int> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_LInt.size();
  m_LInt.emplace(size, Variable<long int>(name, dimensions, globalDimensions,
                                          globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<long int>(), size));
  return m_LInt.at(size);
}

template <>
inline Variable<unsigned long int> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_LInt.size();
  m_ULInt.emplace(
      size, Variable<unsigned long int>(name, dimensions, globalDimensions,
                                        globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<unsigned long int>(), size));
  return m_ULInt.at(size);
}

template <>
inline Variable<long long int> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_LLInt.size();
  m_LLInt.emplace(size,
                  Variable<long long int>(name, dimensions, globalDimensions,
                                          globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<long long int>(), size));
  return m_LLInt.at(size);
}

template <>
inline Variable<unsigned long long int> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_ULLInt.size();
  m_ULLInt.emplace(
      size, Variable<unsigned long long int>(name, dimensions, globalDimensions,
                                             globalOffsets, m_DebugMode));
  m_Variables.emplace(name,
                      std::make_pair(GetType<unsigned long long int>(), size));
  return m_ULLInt.at(size);
}

template <>
inline Variable<float> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_Float.size();
  m_Float.emplace(size, Variable<float>(name, dimensions, globalDimensions,
                                        globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<float>(), size));
  return m_Float.at(size);
}

template <>
inline Variable<double> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_Double.size();
  m_Double.emplace(size, Variable<double>(name, dimensions, globalDimensions,
                                          globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<double>(), size));
  return m_Double.at(size);
}

template <>
inline Variable<long double> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_LDouble.size();
  m_LDouble.emplace(size,
                    Variable<long double>(name, dimensions, globalDimensions,
                                          globalOffsets, m_DebugMode));
  m_Variables.emplace(name, std::make_pair(GetType<long double>(), size));
  return m_LDouble.at(size);
}

template <>
inline Variable<std::complex<float>> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_CFloat.size();
  m_CFloat.emplace(
      size, Variable<std::complex<float>>(name, dimensions, globalDimensions,
                                          globalOffsets, m_DebugMode));
  m_Variables.emplace(name,
                      std::make_pair(GetType<std::complex<float>>(), size));
  return m_CFloat.at(size);
}

template <>
inline Variable<std::complex<double>> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_CDouble.size();
  m_CDouble.emplace(
      size, Variable<std::complex<double>>(name, dimensions, globalDimensions,
                                           globalOffsets, m_DebugMode));
  m_Variables.emplace(name,
                      std::make_pair(GetType<std::complex<double>>(), size));
  return m_CDouble.at(size);
}

template <>
inline Variable<std::complex<long double>> &
ADIOS::DefineVariable(const std::string name, const Dims dimensions,
                      const Dims globalDimensions, const Dims globalOffsets)
{
  CheckVariableInput(name, dimensions);
  const unsigned int size = m_CLDouble.size();
  m_CLDouble.emplace(size, Variable<std::complex<long double>>(
                               name, dimensions, globalDimensions,
                               globalOffsets, m_DebugMode));
  m_Variables.emplace(
      name, std::make_pair(GetType<std::complex<long double>>(), size));
  return m_CLDouble.at(size);
}

// Get template specialization
template <> inline Variable<char> &ADIOS::GetVariable(const std::string name)
{
  return m_Char.at(GetVariableIndex<char>(name));
}

template <>
inline Variable<unsigned char> &ADIOS::GetVariable(const std::string name)
{
  return m_UChar.at(GetVariableIndex<unsigned char>(name));
}

template <> inline Variable<short> &ADIOS::GetVariable(const std::string name)
{
  return m_Short.at(GetVariableIndex<short>(name));
}

template <>
inline Variable<unsigned short> &ADIOS::GetVariable(const std::string name)
{
  return m_UShort.at(GetVariableIndex<unsigned short>(name));
}

template <> inline Variable<int> &ADIOS::GetVariable(const std::string name)
{
  return m_Int.at(GetVariableIndex<int>(name));
}

template <>
inline Variable<unsigned int> &ADIOS::GetVariable(const std::string name)
{
  return m_UInt.at(GetVariableIndex<unsigned int>(name));
}

template <>
inline Variable<long int> &ADIOS::GetVariable(const std::string name)
{
  return m_LInt.at(GetVariableIndex<unsigned int>(name));
}

template <>
inline Variable<unsigned long int> &ADIOS::GetVariable(const std::string name)
{
  return m_ULInt.at(GetVariableIndex<unsigned long int>(name));
}

template <>
inline Variable<long long int> &ADIOS::GetVariable(const std::string name)
{
  return m_LLInt.at(GetVariableIndex<long long int>(name));
}

template <>
inline Variable<unsigned long long int> &
ADIOS::GetVariable(const std::string name)
{
  return m_ULLInt.at(GetVariableIndex<unsigned long long int>(name));
}

template <> inline Variable<float> &ADIOS::GetVariable(const std::string name)
{
  return m_Float.at(GetVariableIndex<float>(name));
}

template <> inline Variable<double> &ADIOS::GetVariable(const std::string name)
{
  return m_Double.at(GetVariableIndex<double>(name));
}

template <>
inline Variable<long double> &ADIOS::GetVariable(const std::string name)
{
  return m_LDouble.at(GetVariableIndex<long double>(name));
}

template <>
inline Variable<std::complex<float>> &ADIOS::GetVariable(const std::string name)
{
  return m_CFloat.at(GetVariableIndex<std::complex<float>>(name));
}

template <>
inline Variable<std::complex<double>> &
ADIOS::GetVariable(const std::string name)
{
  return m_CDouble.at(GetVariableIndex<std::complex<double>>(name));
}

template <>
inline Variable<std::complex<long double>> &
ADIOS::GetVariable(const std::string name)
{
  return m_CLDouble.at(GetVariableIndex<std::complex<long double>>(name));
}

} // end namespace

#endif /* ADIOS_H_ */