Merge pull request #1059 from williamfgc/bindings (23f6464c) · Commits · Podhorszki, Norbert / ADIOS2

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

+47 −10

Original line number	Diff line number	Diff line
		@@ -17,10 +17,11 @@ namespace adios2
		namespace py11
		{

		ADIOS::ADIOS(const std::string configFile, MPI_Comm mpiComm,
		#ifdef ADIOS2_HAVE_MPI
		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"))
		{
		}

		@@ -28,25 +29,61 @@ ADIOS::ADIOS(MPI_Comm mpiComm, const bool debugMode)
		: ADIOS("", mpiComm, debugMode)
		{
		}

		ADIOS::ADIOS(const std::string configFile, const bool debugMode)
		: ADIOS(configFile, MPI_COMM_SELF, debugMode)
		#else
		ADIOS::ADIOS(const std::string &configFile, const bool debugMode)
		: m_ADIOS(
		std::make_shared<adios2::core::ADIOS>(configFile, debugMode, "Python"))
		{
		}

		ADIOS::ADIOS(const bool debugMode) : ADIOS("", MPI_COMM_SELF, debugMode) {}
		ADIOS::ADIOS(const bool debugMode) : ADIOS("", debugMode) {}
		#endif

		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));
		}

		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() { m_ADIOS->FlushAll(); }
		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

+21 −8

Original line number	Diff line number	Diff line
		@@ -8,10 +8,11 @@
		* Author: William F Godoy godoywf@ornl.gov
		*/

		#ifndef ADIOS2_BINDINGS_PYTHON_SOURCE_ADIOSPY_H_
		#define ADIOS2_BINDINGS_PYTHON_SOURCE_ADIOSPY_H_
		#ifndef ADIOS2_BINDINGS_PYTHON_ADIOS_H_
		#define ADIOS2_BINDINGS_PYTHON_ADIOS_H_

		#include "py11IO.h"
		#include "py11Operator.h"

		#include <memory> //std::shared_ptr
		#include <string>
		@@ -28,24 +29,36 @@ class ADIOS
		{

		public:
		ADIOS(const std::string configFile, MPI_Comm mpiComm, const bool debugMode);
		ADIOS(MPI_Comm mpiComm, const bool debugMode);
		ADIOS(const std::string configFile, const bool debugMode);
		#ifdef ADIOS2_HAVE_MPI
		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 = true);
		ADIOS(const bool debugMode);

		#endif
		~ADIOS() = default;

		/** object inspection true: valid object, false: invalid object */
		explicit operator bool() const noexcept;

		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
		} // end namespace adios2

		#endif /* BINDINGS_PYTHON_SOURCE_ADIOSPY_H_ */
		#endif /* ADIOS2_BINDINGS_PYTHON_ADIOS_H_ */

bindings/Python/py11Attribute.cpp

0 → 100644

+109 −0

Original line number	Diff line number	Diff line
		/*
		* Distributed under the OSI-approved Apache License, Version 2.0. See
		* accompanying file Copyright.txt for details.
		*
		* py11Variable.cpp :
		*
		* Created on: Dec 11, 2018
		* Author: William F Godoy godoywf@ornl.gov
		*/

		#include "py11Attribute.h"
		#include "py11types.h"

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

		#include "adios2/helper/adiosFunctions.h"

		namespace adios2
		{
		namespace py11
		{

		Attribute::Attribute(core::AttributeBase *attribute) : m_Attribute(attribute) {}

		Attribute::operator bool() const noexcept
		{
		return (m_Attribute == nullptr) ? false : true;
		}

		std::string Attribute::Name() const
		{
		helper::CheckForNullptr(m_Attribute, "in call to Attribute::Name");
		return m_Attribute->m_Name;
		}

		std::string Attribute::Type() const
		{
		helper::CheckForNullptr(m_Attribute, "in call to Attribute::Type");
		return m_Attribute->m_Type;
		}

		std::vector<std::string> Attribute::DataString()
		{
		helper::CheckForNullptr(m_Attribute, "in call to Attribute::DataStrings");
		const std::string type = m_Attribute->m_Type;

		std::vector<std::string> data;

		if (type == "string")
		{
		const core::Attribute<std::string> *attribute =
		dynamic_cast<core::Attribute<std::string> *>(m_Attribute);

		data.reserve(attribute->m_Elements);
		if (attribute->m_IsSingleValue)
		{
		data.push_back(attribute->m_DataSingleValue);
		}
		else
		{
		data = attribute->m_DataArray;
		}
		}
		else
		{
		throw std::invalid_argument(
		"ERROR: data type for attribute " + m_Attribute->m_Name +
		" is not string, in call to Attribute::DataStrings\n");
		}
		return data;
		}

		pybind11::array Attribute::Data()
		{
		helper::CheckForNullptr(m_Attribute, "in call to Attribute::Data");
		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
		} // end namespace adios2

bindings/Python/py11Attribute.h

0 → 100644

+52 −0

Original line number	Diff line number	Diff line
		/*
		* Distributed under the OSI-approved Apache License, Version 2.0. See
		* accompanying file Copyright.txt for details.
		*
		* py11Variable.h :
		*
		* Created on: Dec 11, 2018
		* Author: William F Godoy godoywf@ornl.gov
		*/

		#ifndef ADIOS2_BINDINGS_PYTHON_ATTRIBUTE_H_
		#define ADIOS2_BINDINGS_PYTHON_ATTRIBUTE_H_

		#include <pybind11/numpy.h>

		#include "adios2/core/AttributeBase.h"

		namespace adios2
		{
		namespace py11
		{

		class IO;

		class Attribute
		{
		friend class IO;

		public:
		Attribute() = default;

		~Attribute() = default;

		explicit operator bool() const noexcept;

		std::string Name() const;

		std::string Type() const;

		pybind11::array Data();

		std::vector<std::string> DataString();

		private:
		Attribute(core::AttributeBase *attribute);
		core::AttributeBase *m_Attribute = nullptr;
		};

		} // end namespace py11
		} // end namespace adios2

		#endif /* BINDINGS_PYTHON_PYATTRIBUTE_H_ */