Commit b55301f6 authored by Godoy, William F's avatar Godoy, William F
Browse files

Passes compilation and tests 

Added Operator class 
Implemented Attribute data

To do:

Add more tests
parent 27567e05

bindings/Python/CMakeLists.txt

+3 −0
Original line number Diff line number Diff line 
pybind11_add_module(adios2py MODULE

  py11ADIOS.cpp

  py11IO.cpp

  py11Variable.cpp

  py11Attribute.cpp

  py11Engine.cpp

  py11Operator.cpp

  py11File.cpp

  py11glue.cpp

)

bindings/Python/py11ADIOS.cpp

+41 −8
Original line number Diff line number Diff line
@@ -18,10 +18,10 @@ namespace py11 
{



#ifdef ADIOS2_HAVE_MPI

ADIOS::ADIOS(const std::string configFile, MPI_Comm mpiComm,

ADIOS::ADIOS(const std::string &configFile, MPI_Comm mpiComm,

             const bool debugMode)

: m_DebugMode(debugMode), m_ADIOS(std::make_shared<adios2::core::ADIOS>(

                              configFile, mpiComm, debugMode, "Python"))

: m_ADIOS(std::make_shared<adios2::core::ADIOS>(configFile, mpiComm, debugMode,

                                                "Python"))

{

}
@@ -30,8 +30,9 @@ ADIOS::ADIOS(MPI_Comm mpiComm, const bool debugMode) 
{

}

#else

ADIOS::ADIOS(const std::string configFile, const bool debugMode)

: ADIOS(configFile, debugMode)

ADIOS::ADIOS(const std::string &configFile, const bool debugMode)

: m_ADIOS(

      std::make_shared<adios2::core::ADIOS>(configFile, debugMode, "Python"))

{

}
@@ -42,15 +43,47 @@ ADIOS::operator bool() const noexcept { return m_ADIOS ? true : false; } 


IO ADIOS::DeclareIO(const std::string name)

{

    return IO(m_ADIOS->DeclareIO(name), m_DebugMode);

    CheckPointer("for io name " + name + ", in call to ADIOS::DeclareIO");

    return IO(&m_ADIOS->DeclareIO(name));

}



IO ADIOS::AtIO(const std::string name)

{

    return IO(m_ADIOS->AtIO(name), m_DebugMode);

    CheckPointer("for io name " + name + ", in call to ADIOS::AtIO");

    return IO(&m_ADIOS->AtIO(name));

}



void ADIOS::FlushAll() { m_ADIOS->FlushAll(); }

Operator ADIOS::DefineOperator(const std::string name, const std::string type,

                               const Params &parameters)

{

    CheckPointer("for operator name " + name +

                 ", in call to ADIOS::DefineOperator");

    return Operator(&m_ADIOS->DefineOperator(name, type, parameters));

}



Operator ADIOS::InquireOperator(const std::string name)

{

    CheckPointer("for operator name " + name + ", in call to InquireOperator");

    return Operator(m_ADIOS->InquireOperator(name));

}



void ADIOS::FlushAll()

{

    CheckPointer("in call to ADIOS::FlushAll");

    m_ADIOS->FlushAll();

}



// PRIVATE

void ADIOS::CheckPointer(const std::string hint)

{

    if (!m_ADIOS)

    {

        throw std::invalid_argument("ERROR: invalid ADIOS object, did you call "

                                    "any of the ADIOS explicit "

                                    "constructors?, " +

                                    hint + "\n");

    }

}



} // end namespace py11

} // end namespace adios2

bindings/Python/py11ADIOS.h

+12 −4
Original line number Diff line number Diff line
@@ -12,6 +12,7 @@ 
#define ADIOS2_BINDINGS_PYTHON_ADIOS_H_



#include "py11IO.h"

#include "py11Operator.h"



#include <memory> //std::shared_ptr

#include <string>
@@ -29,10 +30,11 @@ class ADIOS 


public:

#ifdef ADIOS2_HAVE_MPI

    ADIOS(const std::string configFile, MPI_Comm mpiComm, const bool debugMode);

    ADIOS(MPI_Comm mpiComm, const bool debugMode);

    ADIOS(const std::string &configFile, MPI_Comm comm,

          const bool debugMode = true);

    ADIOS(MPI_Comm comm, const bool debugMode = true);

#else

    ADIOS(const std::string configFile, const bool debugMode);

    ADIOS(const std::string &configFile, const bool debugMode = true);

    ADIOS(const bool debugMode);

#endif

    ~ADIOS() = default;
@@ -43,11 +45,17 @@ public: 
    IO DeclareIO(const std::string name);

    IO AtIO(const std::string name);



    Operator DefineOperator(const std::string name, const std::string type,

                            const Params &parameters = Params());



    Operator InquireOperator(const std::string name);



    void FlushAll();



private:

    const bool m_DebugMode = true;

    std::shared_ptr<adios2::core::ADIOS> m_ADIOS;



    void CheckPointer(const std::string hint);

};



} // end namespace py11

bindings/Python/py11Attribute.cpp

+33 −2
Original line number Diff line number Diff line
@@ -9,6 +9,9 @@ 
 */



#include "py11Attribute.h"

#include "py11types.h"



#include <string.h> //std::memcpy



#include "adios2/helper/adiosFunctions.h"
@@ -39,8 +42,36 @@ std::string Attribute::Type() const 
pybind11::array Attribute::Data()

{

    helper::CheckForNullptr(m_Attribute, "in call to Attribute::Data");

    // TODO

    return m_Attribute->m_Name;

    const std::string type = m_Attribute->m_Type;



    if (type == "compound")

    {

        // not supported

    }

#define declare_type(T)                                                        \

    else if (type == helper::GetType<T>())                                     \

    {                                                                          \

        pybind11::array pyArray(pybind11::dtype::of<T>(),                      \

                                m_Attribute->m_Elements);                      \

        if (m_Attribute->m_IsSingleValue)                                      \

        {                                                                      \

            const T value = dynamic_cast<core::Attribute<T> *>(m_Attribute)    \

                                ->m_DataSingleValue;                           \

            std::memcpy(const_cast<void *>(pyArray.data()), &value,            \

                        sizeof(T));                                            \

        }                                                                      \

        else                                                                   \

        {                                                                      \

            const std::vector<T> &values =                                     \

                dynamic_cast<core::Attribute<T> *>(m_Attribute)->m_DataArray;  \

            std::memcpy(const_cast<void *>(pyArray.data()), values.data(),     \

                        sizeof(T) * m_Attribute->m_Elements);                  \

        }                                                                      \

        return pyArray;                                                        \

    }

    ADIOS2_FOREACH_NUMPY_ATTRIBUTE_TYPE_1ARG(declare_type)

#undef declare_type

    return pybind11::array();

}



} // end namespace py11

bindings/Python/py11Engine.cpp

+17 −29
Original line number Diff line number Diff line
@@ -21,10 +21,7 @@ namespace adios2 
namespace py11

{



Engine::Engine(core::Engine *engine, const bool debugMode)

: m_Engine(engine), m_DebugMode(debugMode)

{

}

Engine::Engine(core::Engine *engine) : m_Engine(engine) {}



Engine::operator bool() const noexcept

{
@@ -71,16 +68,12 @@ void Engine::Put(Variable variable, const pybind11::array &array, 
#undef declare_type

    else

    {

        if (m_DebugMode)

        {

            throw std::invalid_argument("ERROR: for variable " +

                                        variable.Name() +

        throw std::invalid_argument("ERROR: for variable " + variable.Name() +

                                    " numpy array type is not supported or "

                                    "is not memory contiguous "

                                    ", in call to Put\n");

    }

}

}



void Engine::Put(Variable variable, const std::string &string)

{
@@ -96,7 +89,8 @@ void Engine::Put(Variable variable, const std::string &string) 
            " is not of string type, in call to Engine::Put");

    }



    m_Engine->Put(*dynamic_cast<core::Variable<std::string> *>(variable),

    m_Engine->Put(

        *dynamic_cast<core::Variable<std::string> *>(variable.m_Variable),

        string);

}
@@ -131,8 +125,6 @@ void Engine::Get(Variable variable, pybind11::array &array, const Mode launch) 
    ADIOS2_FOREACH_NUMPY_TYPE_1ARG(declare_type)

#undef declare_type

    else

    {

        if (m_DebugMode)

    {

        throw std::invalid_argument(

            "ERROR: in variable " + variable.Name() + " of type " +
@@ -142,7 +134,6 @@ void Engine::Get(Variable variable, pybind11::array &array, const Mode launch) 
            ", in call to Get\n");

    }

}

}



void Engine::Get(Variable variable, std::string &string, const Mode launch)

{
@@ -162,12 +153,9 @@ void Engine::Get(Variable variable, std::string &string, const Mode launch) 
    }

    else

    {

        if (m_DebugMode)

        {

            throw std::invalid_argument(

                "ERROR: variable " + variable.Name() + " of type " +

                variable.Type() + " is not string, in call to Engine::Get");

        }

        throw std::invalid_argument("ERROR: variable " + variable.Name() +

                                    " of type " + variable.Type() +

                                    " is not string, in call to Engine::Get");

    }

}