From 49cb71f0cd446edc932314c423db57bd2567d0b5 Mon Sep 17 00:00:00 2001
From: William F Godoy <williamfgc@yahoo.com>
Date: Mon, 12 Jun 2017 17:25:41 -0400
Subject: [PATCH] Added gluePyBind11_nompi
Removed IO Open that takes a new communicator (didn't work)
---
bindings/python/ADIOSPy.cpp | 2 +
bindings/python/ADIOSPy.h | 3 +-
bindings/python/EnginePy.cpp | 4 --
bindings/python/IOPy.cpp | 26 -------
bindings/python/IOPy.h | 7 +-
bindings/python/gluePyBind11.cpp | 15 ++--
bindings/python/gluePyBind11_nompi.cpp | 70 +++++++++++++++++++
.../hello/bpTimeWriter/helloBPTimeWriter.py | 11 ++-
examples/hello/bpWriter/helloBPWriter.py | 8 +--
9 files changed, 94 insertions(+), 52 deletions(-)
create mode 100644 bindings/python/gluePyBind11_nompi.cpp
diff --git a/bindings/python/ADIOSPy.cpp b/bindings/python/ADIOSPy.cpp
index f258de2bf..6cdf457b0 100644
--- a/bindings/python/ADIOSPy.cpp
+++ b/bindings/python/ADIOSPy.cpp
@@ -20,6 +20,8 @@ ADIOSPy::ADIOSPy(MPI_Comm mpiComm, const bool debug)
{
}
+ADIOSPy::ADIOSPy(const bool debug) : ADIOSPy(MPI_COMM_SELF, debug) {}
+
IOPy ADIOSPy::DeclareIO(const std::string name)
{
return IOPy(m_ADIOS.DeclareIO(name), m_DebugMode);
diff --git a/bindings/python/ADIOSPy.h b/bindings/python/ADIOSPy.h
index f390697d5..d8c7d2281 100644
--- a/bindings/python/ADIOSPy.h
+++ b/bindings/python/ADIOSPy.h
@@ -24,7 +24,8 @@ class ADIOSPy
{
public:
- ADIOSPy(MPI_Comm mpiComm, const bool debug = false);
+ ADIOSPy(MPI_Comm mpiComm, const bool debug);
+ ADIOSPy(const bool debug);
~ADIOSPy() = default;
IOPy DeclareIO(const std::string name);
diff --git a/bindings/python/EnginePy.cpp b/bindings/python/EnginePy.cpp
index e703f61d1..7994a7f8e 100644
--- a/bindings/python/EnginePy.cpp
+++ b/bindings/python/EnginePy.cpp
@@ -10,12 +10,8 @@
#include "EnginePy.h"
-#include "adios2/ADIOSMacros.h"
-
#include "adiosPyFunctions.h"
-#include <iostream>
-
namespace adios
{
diff --git a/bindings/python/IOPy.cpp b/bindings/python/IOPy.cpp
index e1bfc599d..bc26e1a43 100644
--- a/bindings/python/IOPy.cpp
+++ b/bindings/python/IOPy.cpp
@@ -10,10 +10,6 @@
#include "IOPy.h"
-#include <mpi4py/mpi4py.h>
-
-#include "adiosPyFunctions.h" //PyObjectToMPIComm
-
namespace adios
{
@@ -71,28 +67,6 @@ VariablePy &IOPy::GetVariable(const std::string &name)
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)
{
return EnginePy(m_IO, name, static_cast<adios::OpenMode>(openMode),
diff --git a/bindings/python/IOPy.h b/bindings/python/IOPy.h
index 8838d6a63..a5fff653c 100644
--- a/bindings/python/IOPy.h
+++ b/bindings/python/IOPy.h
@@ -44,12 +44,13 @@ public:
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);
private:
+ /**
+ * Extra map needed as Variables are not created in ADIOS at
+ * DefineVariable, but until Write when type is known from numpy
+ */
std::map<std::string, VariablePy> m_Variables;
};
diff --git a/bindings/python/gluePyBind11.cpp b/bindings/python/gluePyBind11.cpp
index 14ab57d1d..c7fff7f6a 100644
--- a/bindings/python/gluePyBind11.cpp
+++ b/bindings/python/gluePyBind11.cpp
@@ -49,14 +49,13 @@ PYBIND11_PLUGIN(adios2)
}
pybind11::module m("adios2", "ADIOS2 Python bindings using pybind11");
- m.attr("adiosDebugON") = true;
- m.attr("adiosDebugOFF") = false;
- 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.attr("DebugON") = true;
+ m.attr("DebugOFF") = false;
+ m.attr("ConstantDims") = true;
+ m.attr("OpenModeWrite") = static_cast<int>(adios::OpenMode::Write);
+ m.attr("OpenModeRead") = static_cast<int>(adios::OpenMode::Read);
+ m.attr("OpenModeAppend") = static_cast<int>(adios::OpenMode::Append);
+ m.attr("OpenModeReadWrite") = static_cast<int>(adios::OpenMode::ReadWrite);
m.def("ADIOS", &ADIOSPyInit, "Function that creates an ADIOS class object");
pybind11::class_<adios::ADIOSPy>(m, "ADIOSPy")
diff --git a/bindings/python/gluePyBind11_nompi.cpp b/bindings/python/gluePyBind11_nompi.cpp
new file mode 100644
index 000000000..a519a441c
--- /dev/null
+++ b/bindings/python/gluePyBind11_nompi.cpp
@@ -0,0 +1,70 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * gluePyBind11_nompi.cpp
+ *
+ * Created on: Jun 12, 2017
+ * Author: William F Godoy godoywf@ornl.gov
+ */
+
+#include <stdexcept>
+
+#include <adios2.h>
+#include <pybind11/pybind11.h>
+
+#include "ADIOSPy.h"
+#include "EnginePy.h"
+#include "IOPy.h"
+#include "VariablePy.h"
+#include "adiosPyFunctions.h"
+#include "adiosPyTypes.h"
+
+adios::ADIOSPy ADIOSPyInit(const bool debugMode)
+{
+ return adios::ADIOSPy(debugMode);
+}
+
+PYBIND11_PLUGIN(adios2)
+{
+ pybind11::module m("adios2", "ADIOS2 Python bindings using pybind11");
+ m.attr("DebugON") = true;
+ m.attr("DebugOFF") = false;
+ m.attr("ConstantDims") = true;
+ m.attr("OpenModeWrite") = static_cast<int>(adios::OpenMode::Write);
+ m.attr("OpenModeRead") = static_cast<int>(adios::OpenMode::Read);
+ m.attr("OpenModeAppend") = static_cast<int>(adios::OpenMode::Append);
+ m.attr("OpenModeReadWrite") = 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,
+ 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::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,
+ pybind11::arg("timeoutSeconds") = 0.)
+ .def("Close", &adios::EnginePy::Close,
+ pybind11::arg("transportIndex") = -1);
+
+ return m.ptr();
+}
diff --git a/examples/hello/bpTimeWriter/helloBPTimeWriter.py b/examples/hello/bpTimeWriter/helloBPTimeWriter.py
index dc5c81f57..c6cbb6acf 100644
--- a/examples/hello/bpTimeWriter/helloBPTimeWriter.py
+++ b/examples/hello/bpTimeWriter/helloBPTimeWriter.py
@@ -1,14 +1,13 @@
-# 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
+# Author: William F Godoy godoywf@ornl.gov
from mpi4py import MPI
-import adios2
+import adios2
import numpy as np
@@ -22,18 +21,18 @@ myArray = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
nx = myArray.size
# ADIOS
-adios = adios2.ADIOS(comm, adios2.adiosDebugON)
+adios = adios2.ADIOS(comm, adios2.DebugON)
# IO
bpIO = adios.DeclareIO("BPN2N")
# Variables
bpArray = bpIO.DefineVariable("bpArray", [size * nx], [rank * nx], [nx],
- adios2.adiosConstantDims)
+ adios2.ConstantDims)
bpTimeStep = bpIO.DefineVariable("bpTimeStep")
# Engine
-bpFileWriter = bpIO.Open("myArray.bp", adios2.adiosOpenModeWrite)
+bpFileWriter = bpIO.Open("myArray.bp", adios2.OpenModeWrite)
# Doesn't work: bpFileWriter = bpIO.Open("myArray.bp", adiosOpenModeWrite,
# MPI.COMM_WORLD)
diff --git a/examples/hello/bpWriter/helloBPWriter.py b/examples/hello/bpWriter/helloBPWriter.py
index f8c700954..780507684 100644
--- a/examples/hello/bpWriter/helloBPWriter.py
+++ b/examples/hello/bpWriter/helloBPWriter.py
@@ -5,7 +5,7 @@
#
# test_hello.py
# Created on: Feb 2, 2017
-# Author: wfg
+# Author: William F Godoy godoywf@ornl.gov
from mpi4py import MPI
import adios2
@@ -15,17 +15,17 @@ import numpy as np
myArray = np.array([1., 2., 3., 4., 5., 6.])
# ADIOS
-adios = adios2.ADIOS(MPI.COMM_WORLD, adios2.adiosDebugON)
+adios = adios2.ADIOS(MPI.COMM_WORLD, adios2.DebugON)
# IO
bpIO = adios.DeclareIO("BPN2N")
# Variable
ioArray = bpIO.DefineVariable(
- "bpArray", [myArray.size], [0], [myArray.size], adios2.adiosConstantDims)
+ "bpArray", [myArray.size], [0], [myArray.size], adios2.ConstantDims)
# Engine
-bpFileWriter = bpIO.Open("myArray.bp", adios2.adiosOpenModeWrite)
+bpFileWriter = bpIO.Open("myArray.bp", adios2.OpenModeWrite)
# bpFileWriter = bpIO.Open("myArray.bp", adiosOpenModeWrite,
# MPI.COMM_WORLD) //doesn't work
bpFileWriter.Write(ioArray, myArray)
--
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