From e48fd4adfcfeb0ce91831a8616ff804ce2fb8413 Mon Sep 17 00:00:00 2001
From: Chuck Atkins <chuck.atkins@kitware.com>
Date: Tue, 13 Jun 2017 11:45:00 -0400
Subject: [PATCH] Make the adios2 python module compatible for both mpi and
nompi (#14)
---
bindings/CMakeLists.txt | 3 --
bindings/python/ADIOSPy.cpp | 6 ++-
bindings/python/ADIOSPy.h | 2 +
bindings/python/CMakeLists.txt | 15 ++++--
bindings/python/gluePyBind11.cpp | 18 +++++--
bindings/python/gluePyBind11_nompi.cpp | 70 --------------------------
6 files changed, 31 insertions(+), 83 deletions(-)
delete mode 100644 bindings/python/gluePyBind11_nompi.cpp
diff --git a/bindings/CMakeLists.txt b/bindings/CMakeLists.txt
index 2aa4e17f6..1299ac394 100644
--- a/bindings/CMakeLists.txt
+++ b/bindings/CMakeLists.txt
@@ -1,6 +1,3 @@
if(ADIOS_USE_Python)
- if(NOT BUILD_SHARED_LIBS)
- message(ERROR "Python bindings are only supported for shared libraries")
- endif()
add_subdirectory(python)
endif()
diff --git a/bindings/python/ADIOSPy.cpp b/bindings/python/ADIOSPy.cpp
index 6cdf457b0..2e16a24fc 100644
--- a/bindings/python/ADIOSPy.cpp
+++ b/bindings/python/ADIOSPy.cpp
@@ -20,7 +20,11 @@ ADIOSPy::ADIOSPy(MPI_Comm mpiComm, const bool debug)
{
}
-ADIOSPy::ADIOSPy(const bool debug) : ADIOSPy(MPI_COMM_SELF, debug) {}
+ADIOSPy::ADIOSPy(const bool debug)
+: m_DebugMode(debug), m_ADIOS(debug)
+{
+}
+
IOPy ADIOSPy::DeclareIO(const std::string name)
{
diff --git a/bindings/python/ADIOSPy.h b/bindings/python/ADIOSPy.h
index d8c7d2281..d8cc68c9e 100644
--- a/bindings/python/ADIOSPy.h
+++ b/bindings/python/ADIOSPy.h
@@ -15,6 +15,8 @@
#include <string>
/// \endcond
+#include <adios2.h>
+
#include "IOPy.h"
namespace adios
diff --git a/bindings/python/CMakeLists.txt b/bindings/python/CMakeLists.txt
index 1c0627fb0..491ca2714 100644
--- a/bindings/python/CMakeLists.txt
+++ b/bindings/python/CMakeLists.txt
@@ -1,5 +1,6 @@
-find_package(PythonInterp REQUIRED)
-find_package(PythonModule REQUIRED COMPONENTS mpi4py mpi4py/mpi4py.h)
+if(NOT BUILD_SHARED_LIBS)
+ message(ERROR "Python bindings are only supported for shared libraries")
+endif()
pybind11_add_module(adios2py MODULE
ADIOSPy.h
@@ -16,12 +17,18 @@ pybind11_add_module(adios2py MODULE
VariablePy.h
VariablePy.cpp
)
-target_link_libraries(adios2py PUBLIC adios2 PythonModule::mpi4py)
+target_link_libraries(adios2py PRIVATE adios2)
+if(ADIOS_USE_MPI)
+ find_package(PythonModule REQUIRED COMPONENTS mpi4py mpi4py/mpi4py.h)
+ target_link_libraries(adios2py PRIVATE PythonModule::mpi4py)
+endif()
+find_package(PythonInterp REQUIRED)
set(python_package_dir ${CMAKE_INSTALL_LIBDIR}/python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}/site-packages)
set_target_properties(adios2py PROPERTIES
- PREFIX ""
OUTPUT_NAME adios2
+ PREFIX "${PYTHON_MODULE_PREFIX}"
+ SUFFIX "${PYTHON_MODULE_EXTENSION}"
LIBRARY_OUTPUT_DIRECTORY ${ADIOS_BINARY_DIR}/${python_package_dir}
RUNTIME_OUTPUT_DIRECTORY ${ADIOS_BINARY_DIR}/${python_package_dir}
)
diff --git a/bindings/python/gluePyBind11.cpp b/bindings/python/gluePyBind11.cpp
index c7fff7f6a..6a22c6529 100644
--- a/bindings/python/gluePyBind11.cpp
+++ b/bindings/python/gluePyBind11.cpp
@@ -11,9 +11,12 @@
#include <stdexcept>
#include <adios2.h>
-#include <mpi4py/mpi4py.h>
#include <pybind11/pybind11.h>
+#ifdef ADIOS2_HAVE_MPI
+#include <mpi4py/mpi4py.h>
+#endif
+
#include "ADIOSPy.h"
#include "EnginePy.h"
#include "IOPy.h"
@@ -21,6 +24,7 @@
#include "adiosPyFunctions.h"
#include "adiosPyTypes.h"
+#ifdef ADIOS2_HAVE_MPI
adios::ADIOSPy ADIOSPyInit(adios::pyObject &object, const bool debugMode)
{
MPI_Comm *mpiCommPtr = PyMPIComm_Get(object.ptr());
@@ -39,14 +43,22 @@ adios::ADIOSPy ADIOSPyInit(adios::pyObject &object, const bool debugMode)
}
return adios::ADIOSPy(*mpiCommPtr, debugMode);
}
+#else
+adios::ADIOSPy ADIOSPyInit(const bool debugMode)
+{
+ return adios::ADIOSPy(debugMode);
+}
+#endif
PYBIND11_PLUGIN(adios2)
{
+#ifdef ADIOS2_HAVE_MPI
if (import_mpi4py() < 0)
{
throw std::runtime_error(
"ERROR: mpi4py not loaded correctly\n"); /* Python 2.X */
}
+#endif
pybind11::module m("adios2", "ADIOS2 Python bindings using pybind11");
m.attr("DebugON") = true;
@@ -73,10 +85,6 @@ PYBIND11_PLUGIN(adios2)
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);
diff --git a/bindings/python/gluePyBind11_nompi.cpp b/bindings/python/gluePyBind11_nompi.cpp
deleted file mode 100644
index a519a441c..000000000
--- a/bindings/python/gluePyBind11_nompi.cpp
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * 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();
-}
--
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