diff --git a/bindings/python/Makefile b/bindings/python/Makefile
index 2f9f607d7e79927b4a817b53da7ccf47eeee99de..53d9d5e9b2813973b0eaa077b229a3bdf9bd5904 100644
--- a/bindings/python/Makefile
+++ b/bindings/python/Makefile
@@ -8,11 +8,16 @@ MPICC:=mpic++
CPPFiles:=$(shell find ./source -type f -name "*.cpp")
OBJS:=$(patsubst %.cpp, ./bin/%.o, $(notdir $(CPPFiles)) )
-# Python
+# Python 2.7
PYTHON_VERSION:= 2.7
PYTHON_INC:= /usr/include/python$(PYTHON_VERSION)
PYTHON_LIBLOC:= /usr/lib/python$(PYTHON_VERSION)/config-x86_64-linux-gnu/
-
+
+# Python 3.5 ...doesn't work ImportError: dynamic module does not define init function (initadios2py)
+#PYTHON_VERSION:= 3.5
+#PYTHON_INC:= /usr/include/python$(PYTHON_VERSION)
+#PYTHON_LIBLOC:= /usr/lib/python$(PYTHON_VERSION)/config-3.5m-x86_64-linux-gnu/
+#
# ADIOS2
ADIOS2_INC:= /usr/local/include
diff --git a/bindings/python/README.md b/bindings/python/README.md
index 5f363d7b2b153b4afa72926b734cb5b52a28394d..e2e686715368a393bf43aac3be9882fbc03c0904 100644
--- a/bindings/python/README.md
+++ b/bindings/python/README.md
@@ -2,7 +2,11 @@ Python bindings for ADIOS 2.0 using PyBind11
Dependencies:
- Python 2.7.x and above
+ Python 2.7.x and above (still testing 3.5)
Numpy and MPI4PY
ADIOS2 shared library (libadios2.so)
-
\ No newline at end of file
+
+Examples;
+
+ helloBPWriter.py from adios2/examples/hello/bpWriter
+ helloBPTimeWriter.py from adios2/examples/hello/bpTimeWriter
\ No newline at end of file
diff --git a/bindings/python/helloBPTimeWriter.py b/bindings/python/helloBPTimeWriter.py
new file mode 100644
index 0000000000000000000000000000000000000000..1a02fa7062465f02930540c9a98ecce87d35d7c5
--- /dev/null
+++ b/bindings/python/helloBPTimeWriter.py
@@ -0,0 +1,47 @@
+# clang-format off
+#
+# Distributed under the OSI-approved Apache License, Version 2.0. See
+# accompanying file Copyright.txt for details.
+#
+# test_hello.py
+# Created on: Feb 2, 2017
+# Author: wfg
+
+from mpi4py import MPI
+from adios2py import *
+import numpy as np
+
+
+# MPI
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+size = comm.Get_size()
+
+# User data
+myArray = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
+nx = myArray.size
+
+# ADIOS
+adios = ADIOS(comm, adiosDebugON)
+
+# IO
+bpIO = adios.DeclareIO("BPN2N")
+
+# Variables
+bpArray = bpIO.DefineVariable("bpArray", [size * nx], [rank * nx], [nx],
+ adiosConstantDims)
+bpTimeStep = bpIO.DefineVariable("bpTimeStep")
+
+# Engine
+bpFileWriter = bpIO.Open("myArray.bp", adiosOpenModeWrite)
+# Doesn't work: bpFileWriter = bpIO.Open("myArray.bp", adiosOpenModeWrite,
+# MPI.COMM_WORLD)
+
+for t in range(0, 10):
+ if(rank == 0):
+ bpFileWriter.Write(bpTimeStep, np.array([t]))
+
+ bpFileWriter.Write(bpArray, myArray)
+ bpFileWriter.Advance()
+
+bpFileWriter.Close()
diff --git a/bindings/python/helloBPWriter.py b/bindings/python/helloBPWriter.py
index fb39e326cba510343378045965080a411c1755d8..75eb6ce596e435ee0bb65d8dd5a7363357189a60 100644
--- a/bindings/python/helloBPWriter.py
+++ b/bindings/python/helloBPWriter.py
@@ -1,3 +1,4 @@
+# clang-format off
#
# Distributed under the OSI-approved Apache License, Version 2.0. See
# accompanying file Copyright.txt for details.
@@ -10,17 +11,22 @@ from mpi4py import MPI
from adios2py import *
import numpy as np
-
# User data
-myArray = np.array([1., 2., 3., 4., 5.])
-
-print "Read " + str(adiosRead)
+myArray = np.array([1., 2., 3., 4., 5., 6.])
-adios = ADIOS(MPI.COMM_WORLD, True)
+# ADIOS
+adios = ADIOS(MPI.COMM_WORLD, adiosDebugON)
+# IO
bpIO = adios.DeclareIO("BPN2N")
-ioArray = bpIO.DefineVariable("bpArray", [myArray.size], [0], [myArray.size], True)
-
-bpFileWriter = bpIO.Open("myArray.bp", adiosWrite)
+
+# Variable
+ioArray = bpIO.DefineVariable(
+ "bpArray", [myArray.size], [0], [myArray.size], adiosConstantDims)
+
+# Engine
+bpFileWriter = bpIO.Open("myArray.bp", adiosOpenModeWrite)
+# bpFileWriter = bpIO.Open("myArray.bp", adiosOpenModeWrite,
+# MPI.COMM_WORLD) //doesn't work
bpFileWriter.Write(ioArray, myArray)
bpFileWriter.Close()
diff --git a/bindings/python/source/ADIOSPy.cpp b/bindings/python/source/ADIOSPy.cpp
index c613882bb935ee3ab1397a99dca5dec03f0a2249..f258de2bff7035e1a6005002613ca700be96a0cd 100644
--- a/bindings/python/source/ADIOSPy.cpp
+++ b/bindings/python/source/ADIOSPy.cpp
@@ -12,8 +12,6 @@
#include "adiosPyTypes.h"
-#include <iostream>
-
namespace adios
{
@@ -24,8 +22,6 @@ ADIOSPy::ADIOSPy(MPI_Comm mpiComm, const bool debug)
IOPy ADIOSPy::DeclareIO(const std::string name)
{
- std::cout << "Declaring IO " << name << "\n";
-
return IOPy(m_ADIOS.DeclareIO(name), m_DebugMode);
}
diff --git a/bindings/python/source/EnginePy.cpp b/bindings/python/source/EnginePy.cpp
index b60efe9712288c6bd1e441ab64711fd17511b466..e703f61d15c52a569f5710bab83471f79d2acbe5 100644
--- a/bindings/python/source/EnginePy.cpp
+++ b/bindings/python/source/EnginePy.cpp
@@ -63,6 +63,9 @@ void EnginePy::Advance(const float timeoutSeconds)
m_Engine->Advance(timeoutSeconds);
}
-void EnginePy::Close() { m_Engine->Close(); }
+void EnginePy::Close(const int transportIndex)
+{
+ m_Engine->Close(transportIndex);
+}
} // end namespace adios
diff --git a/bindings/python/source/EnginePy.h b/bindings/python/source/EnginePy.h
index 19f6e1dea69d28ac0041e366dd9ffac40399961c..68130704b2936469d608b8a12cb14f54fa8fee1b 100644
--- a/bindings/python/source/EnginePy.h
+++ b/bindings/python/source/EnginePy.h
@@ -37,7 +37,7 @@ public:
void Advance(const float timeoutSeconds = 0.);
- void Close();
+ void Close(const int transportIndex = -1);
private:
IO &m_IO;
diff --git a/bindings/python/source/IOPy.cpp b/bindings/python/source/IOPy.cpp
index 692b2b018005f261f1500cbb0573565ba76cfc06..e1bfc599d81b2008ef9f42e67924469ae353f5dd 100644
--- a/bindings/python/source/IOPy.cpp
+++ b/bindings/python/source/IOPy.cpp
@@ -12,6 +12,8 @@
#include <mpi4py/mpi4py.h>
+#include "adiosPyFunctions.h" //PyObjectToMPIComm
+
namespace adios
{
@@ -20,44 +22,81 @@ IOPy::IOPy(IO &io, const bool debugMode) : m_IO(io), m_DebugMode(debugMode)
m_IO.m_HostLanguage = "Python";
}
-void IOPy::SetParameters(const pyKwargs &kwargs)
+void IOPy::SetEngine(const std::string engine) { m_IO.SetEngine(engine); }
+
+void IOPy::SetParameters(const pyKwargs &kwargs) noexcept
{
m_IO.SetParameters(KwargsToParams(kwargs));
}
-unsigned int IOPy::AddTransport(const std::string type, const pyKwargs &kwargs)
+unsigned int IOPy::AddTransport(const std::string type,
+ const pyKwargs &kwargs) noexcept
{
return m_IO.AddTransport(type, KwargsToParams(kwargs));
}
-VariablePy IOPy::DefineVariable(const std::string &name, const pyList shape,
- const pyList start, const pyList count,
- const bool isConstantDims)
+VariablePy &IOPy::DefineVariable(const std::string &name, const pyList shape,
+ const pyList start, const pyList count,
+ const bool isConstantDims)
+{
+ if (m_DebugMode)
+ {
+ if (m_Variables.count(name) == 1)
+ {
+ throw std::invalid_argument("ERROR: variable " + name +
+ " already exists, use GetVariable, in "
+ "call to DefineVariable\n");
+ }
+ }
+
+ auto itVariableEmplace =
+ m_Variables.emplace(name, VariablePy(name, shape, start, count,
+ isConstantDims, m_DebugMode));
+ return itVariableEmplace.first->second;
+}
+
+VariablePy &IOPy::GetVariable(const std::string &name)
{
- return VariablePy(name, shape, start, count, isConstantDims, m_DebugMode);
+ auto itVariable = m_Variables.find(name);
+
+ if (m_DebugMode)
+ {
+ if (itVariable == m_Variables.end())
+ {
+ throw std::invalid_argument("ERROR: variable " + name +
+ " doesn't exist, in "
+ "call to GetVariable\n");
+ }
+ }
+ return itVariable->second;
+}
+
+EnginePy IOPy::Open(const std::string &name, const int openMode,
+ adios::pyObject &object)
+{
+ MPI_Comm *mpiCommPtr = PyMPIComm_Get(object.ptr());
+
+ if (import_mpi4py() < 0)
+ {
+ throw std::logic_error("ERROR: could not import mpi4py "
+ "communicator, in call to ADIOS "
+ "constructor\n");
+ }
+
+ if (mpiCommPtr == nullptr)
+ {
+ throw std::runtime_error("ERROR: mpi4py communicator is null, in call "
+ "to ADIOS constructor\n");
+ }
+
+ return EnginePy(m_IO, name, static_cast<adios::OpenMode>(openMode),
+ *mpiCommPtr);
}
EnginePy IOPy::Open(const std::string &name, const int openMode)
{
- // MPI_Comm *mpiCommPtr = PyMPIComm_Get(pyMPIComm.ptr());
- //
- // if (m_DebugMode)
- // {
- // if (mpiCommPtr == NULL)
- // {
- // throw std::runtime_error("ERROR: mpi4py communicator for
- // engine " +
- // name + " is null, in call to IO
- // Open\n");
- // }
- // }
return EnginePy(m_IO, name, static_cast<adios::OpenMode>(openMode),
m_IO.m_MPIComm);
}
-// EnginePy IOPy::Open(const std::string &name, const OpenMode openMode)
-//{
-// return EnginePy(m_IO, name, openMode, m_IO.m_MPIComm);
-//}
-
-} // end namespace
+} // end namespace adios
diff --git a/bindings/python/source/IOPy.h b/bindings/python/source/IOPy.h
index 6bacc3a4183f443d6acfd16f24c6f207a661cf5f..8838d6a63532fac7fa88c5460cb940f0d12f38fd 100644
--- a/bindings/python/source/IOPy.h
+++ b/bindings/python/source/IOPy.h
@@ -32,16 +32,25 @@ public:
~IOPy() = default;
- void SetParameters(const pyKwargs &kwargs);
- unsigned int AddTransport(const std::string type, const pyKwargs &kwargs);
+ void SetEngine(const std::string engineType);
- VariablePy DefineVariable(const std::string &name, const pyList shape,
- const pyList start, const pyList count,
- const bool isConstantDims);
+ void SetParameters(const pyKwargs &kwargs) noexcept;
+ unsigned int AddTransport(const std::string type,
+ const pyKwargs &kwargs) noexcept;
+
+ VariablePy &DefineVariable(const std::string &name, const pyList shape,
+ const pyList start, const pyList count,
+ const bool isConstantDims);
+
+ VariablePy &GetVariable(const std::string &name);
+
+ EnginePy Open(const std::string &name, const int openMode,
+ adios::pyObject &object);
EnginePy Open(const std::string &name, const int openMode);
- // EnginePy Open(const std::string &name, const OpenMode openMode);
+private:
+ std::map<std::string, VariablePy> m_Variables;
};
} // end namespace adios
diff --git a/bindings/python/source/adiosPyFunctions.cpp b/bindings/python/source/adiosPyFunctions.cpp
index 806fd31817e60e2318c2f00ffccca598968ebdf7..92d41807a2b94695d6a0bd04ce4330439a959a92 100644
--- a/bindings/python/source/adiosPyFunctions.cpp
+++ b/bindings/python/source/adiosPyFunctions.cpp
@@ -5,16 +5,15 @@
* adiosPyFunctions.cpp
*
* Created on: Mar 13, 2017
- * Author: wfg
+ * Author: William F Godoy godoywf@ornl.gov
*/
-#include <iostream>
#include "adiosPyFunctions.h"
namespace adios
{
-Dims PyListToDims(const pyList list)
+Dims PyListToDims(const pyList list) noexcept
{
const unsigned int length = pybind11::len(list);
Dims dimensions;
@@ -28,7 +27,7 @@ Dims PyListToDims(const pyList list)
return dimensions;
}
-Params KwargsToParams(const pyKwargs &kwargs)
+Params KwargsToParams(const pyKwargs &kwargs) noexcept
{
Params parameters;
diff --git a/bindings/python/source/adiosPyFunctions.h b/bindings/python/source/adiosPyFunctions.h
index ed97bbaf4f2622249316067e140edeffc38adb84..cf8bc412e2e7cf9d4fc9485e176ccb71c4def357 100644
--- a/bindings/python/source/adiosPyFunctions.h
+++ b/bindings/python/source/adiosPyFunctions.h
@@ -26,7 +26,7 @@ namespace adios
* @param list python list of numbers
* @return adios::Dims
*/
-Dims PyListToDims(const pyList list);
+Dims PyListToDims(const pyList list) noexcept;
/**
* Python dictionary kwargs to adios::Params (std::map<std::string,
@@ -34,7 +34,7 @@ Dims PyListToDims(const pyList list);
* @param kwargs dictionary
* @return adios::Params
*/
-Params KwargsToParams(const pyKwargs &kwargs);
+Params KwargsToParams(const pyKwargs &kwargs) noexcept;
} // end namespace adios
diff --git a/bindings/python/source/gluePyBind11.cpp b/bindings/python/source/gluePyBind11.cpp
index 0c4aa097f026b5b815b4bc4088983dbac1e41782..861557aef0e3b2ac6dd5bcb12529702b14b594f5 100644
--- a/bindings/python/source/gluePyBind11.cpp
+++ b/bindings/python/source/gluePyBind11.cpp
@@ -18,20 +18,24 @@
#include "EnginePy.h"
#include "IOPy.h"
#include "VariablePy.h"
+#include "adiosPyFunctions.h"
#include "adiosPyTypes.h"
-adios::ADIOSPy ADIOSPyInit(adios::pyObject py_comm, const bool debugMode)
+adios::ADIOSPy ADIOSPyInit(adios::pyObject &object, const bool debugMode)
{
- MPI_Comm *mpiCommPtr = PyMPIComm_Get(py_comm.ptr());
+ MPI_Comm *mpiCommPtr = PyMPIComm_Get(object.ptr());
- if (debugMode)
+ if (import_mpi4py() < 0)
{
- if (mpiCommPtr == NULL)
- {
- throw std::runtime_error(
- "ERROR: mpi4py communicator is null, in call "
- "to ADIOS constructor\n");
- }
+ throw std::runtime_error("ERROR: could not import mpi4py "
+ "communicator, in call to ADIOS "
+ "constructor\n");
+ }
+
+ if (mpiCommPtr == nullptr)
+ {
+ throw std::runtime_error("ERROR: mpi4py communicator is null, in call "
+ "to ADIOS constructor\n");
}
return adios::ADIOSPy(*mpiCommPtr, debugMode);
}
@@ -47,39 +51,46 @@ PYBIND11_PLUGIN(adios2py)
pybind11::module m("adios2py", "ADIOS2 Python bindings using pybind11");
m.attr("adiosDebugON") = true;
m.attr("adiosDebugOFF") = false;
- m.attr("adiosWrite") = static_cast<int>(adios::OpenMode::Write);
- m.attr("adiosRead") = static_cast<int>(adios::OpenMode::Read);
- m.attr("adiosAppend") = static_cast<int>(adios::OpenMode::Append);
- m.attr("adiosReadWrite") = static_cast<int>(adios::OpenMode::ReadWrite);
+ m.attr("adiosConstantDims") = true;
+ m.attr("adiosOpenModeWrite") = static_cast<int>(adios::OpenMode::Write);
+ m.attr("adiosOpenModeRead") = static_cast<int>(adios::OpenMode::Read);
+ m.attr("adiosOpenModeAppend") = static_cast<int>(adios::OpenMode::Append);
+ m.attr("adiosOpenModeReadWrite") =
+ static_cast<int>(adios::OpenMode::ReadWrite);
m.def("ADIOS", &ADIOSPyInit, "Function that creates an ADIOS class object");
pybind11::class_<adios::ADIOSPy>(m, "ADIOSPy")
.def("DeclareIO", &adios::ADIOSPy::DeclareIO);
pybind11::class_<adios::IOPy>(m, "IOPy")
+ .def("SetEngine", &adios::IOPy::SetEngine)
.def("SetParameters", &adios::IOPy::SetParameters)
.def("AddTransport", &adios::IOPy::AddTransport)
- .def("DefineVariable", &adios::IOPy::DefineVariable)
- .def("Open", &adios::IOPy::Open);
+ .def("DefineVariable", &adios::IOPy::DefineVariable,
+ pybind11::return_value_policy::reference_internal,
+ pybind11::arg("name"), pybind11::arg("shape") = adios::pyList(),
+ pybind11::arg("start") = adios::pyList(),
+ pybind11::arg("count") = adios::pyList(),
+ pybind11::arg("isConstantDims") = false)
+ .def("GetVariable", &adios::IOPy::GetVariable,
+ pybind11::return_value_policy::reference_internal)
+ // .def("Open", (adios::EnginePy (adios::IOPy::*)(
+ // const std::string &, const int,
+ // adios::pyObject &)) &
+ // adios::IOPy::Open) doesn't work
+ .def("Open", (adios::EnginePy (adios::IOPy::*)(const std::string &,
+ const int)) &
+ adios::IOPy::Open);
pybind11::class_<adios::VariablePy>(m, "VariablePy")
.def("SetDimensions", &adios::VariablePy::SetDimensions);
pybind11::class_<adios::EnginePy>(m, "EnginePy")
.def("Write", &adios::EnginePy::Write)
- .def("Advance", &adios::EnginePy::Advance)
- .def("Close", &adios::EnginePy::Close);
-
- // Trying overloaded function
- // (adios::EnginePy (adios::IOPy::*)(
- // const std::string &, const adios::OpenMode,
- // adios::pyObject)) &
- // &adios::IOPy::Open)
- // .def("Open", (adios::EnginePy (adios::IOPy::*)(const std::string
- // &,
- // const
- // adios::OpenMode)) &
- // &adios::IOPy::Open);
+ .def("Advance", &adios::EnginePy::Advance,
+ pybind11::arg("timeoutSeconds") = 0.)
+ .def("Close", &adios::EnginePy::Close,
+ pybind11::arg("transportIndex") = -1);
return m.ptr();
}