Functional Python bindings MPI and nonMPI modes

Removed stl containers that pybind11 takes care of

bindings/python/EnginePy.cpp

@@ -30,7 +30,7 @@ void EnginePy::PutSync(VariableBase *variable, const pybind11::array &array)
     {
         auto &io = m_Engine.GetIO();
 
-        if (array == pybind11::array())
+        if (array.is(pybind11::array()))
         {
             if (m_DebugMode)
             {
@@ -60,7 +60,7 @@ void EnginePy::PutSync(VariableBase *variable, const pybind11::array &array)
 #define declare_type(T)                                                        \
     else if (variable->m_Type == GetType<T>())                                 \
     {                                                                          \
-        m_Engine.PutSync(dynamic_cast<adios2::Variable<T> &>(variable),        \
+        m_Engine.PutSync(*dynamic_cast<adios2::Variable<T> *>(variable),       \
                          reinterpret_cast<const T *>(array.data()));           \
     }
     ADIOS2_FOREACH_TYPE_1ARG(declare_type)
@@ -69,7 +69,7 @@ void EnginePy::PutSync(VariableBase *variable, const pybind11::array &array)
     {
         if (m_DebugMode)
         {
-            throw std::invalid_argument("ERROR: variable " + variable.m_Name +
+            throw std::invalid_argument("ERROR: variable " + variable->m_Name +
                                         " numpy array type is not supported or "
                                         "is not memory contiguous "
                                         ", in call to PutSync\n");

bindings/python/IOPy.cpp

@@ -42,7 +42,7 @@ VariableBase &IOPy::DefineVariable(const std::string &name, const Dims &shape,
 
     VariableBase *variable = nullptr;
 
-    if (array == pybind11::array())
+    if (array.is(pybind11::array()))
     {
         // put in placeholder
         auto itVariableEmplace = m_VariablesPlaceholder.emplace(

bindings/python/gluePyBind11.cpp

@@ -12,6 +12,7 @@
 
 #include <adios2.h>
 #include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
 
 #ifdef ADIOS2_HAVE_MPI
 #include <mpi4py/mpi4py.h>
@@ -74,7 +75,7 @@ adios2::ADIOSPy ADIOSPyInit(const bool debugMode)
 }
 #endif
 
-PYBIND11_PLUGIN(adios2)
+PYBIND11_MODULE(adios2, m)
 {
 #ifdef ADIOS2_HAVE_MPI
     if (import_mpi4py() < 0)
@@ -84,7 +85,9 @@ PYBIND11_PLUGIN(adios2)
     }
 #endif
 
-    pybind11::module m("adios2", "ADIOS2 Python bindings using pybind11");
+    // pybind11::module m("adios2", "ADIOS2 Python bindings using pybind11");
+    m.doc() = "ADIOS2 Python bindings powered by pybind11";
+
     m.attr("DebugON") = true;
     m.attr("DebugOFF") = false;
     m.attr("ConstantDims") = true;
@@ -108,10 +111,24 @@ PYBIND11_PLUGIN(adios2)
         .value("EndOfStream", adios2::StepStatus::EndOfStream)
         .value("OtherError", adios2::StepStatus::OtherError)
         .export_values();
+#ifdef ADIOS2_HAVE_MPI
+    m.def("ADIOS", &ADIOSPyInit, "Function that creates an ADIOS class object",
+          pybind11::arg("object") = nullptr, pybind11::arg("debugMode") = true);
+
+    m.def("ADIOS", &ADIOSPyInitConfig, "Function that creates an ADIOS class "
+                                       "object using a config file",
+          pybind11::arg("configFile") = "", pybind11::arg("object") = nullptr,
+          pybind11::arg("debugMode") = true);
+#else
+    m.def("ADIOS", &ADIOSPyInit,
+          "Function that creates an ADIOS class object in non MPI mode",
+          pybind11::arg("debugMode") = true);
 
-    m.def("ADIOS", &ADIOSPyInit, "Function that creates an ADIOS class object");
     m.def("ADIOS", &ADIOSPyInitConfig,
-          "Function that creates an ADIOS class object using a config file");
+          "Function that creates an ADIOS class "
+          "object using a config file in non MPI mode",
+          pybind11::arg("configFile") = "", pybind11::arg("debugMode") = true);
+#endif
 
     pybind11::class_<adios2::ADIOSPy>(m, "ADIOSPy")
         .def("DeclareIO", &adios2::ADIOSPy::DeclareIO);
@@ -141,6 +158,4 @@ PYBIND11_PLUGIN(adios2)
         .def("EndStep", &adios2::EnginePy::EndStep)
         .def("Close", &adios2::EnginePy::Close,
              pybind11::arg("transportIndex") = -1);
-
-    return m.ptr();
 }

examples/hello/bpWriter/helloBPWriter.py

@@ -2,10 +2,9 @@
 # Distributed under the OSI-approved Apache License, Version 2.0.  See
 # accompanying file Copyright.txt for details.
 #
-# helloBPWriter.py
+# helloBPWriter_nompi.py : only works with non MPI version
 #  Created on: Feb 2, 2017
 #      Author: William F Godoy godoywf@ornl.gov
-
 from mpi4py import MPI
 import numpy
 import adios2
@@ -30,7 +29,6 @@ ioArray = bpIO.DefineVariable(
     "bpArray", [size * Nx], [rank * Nx], [Nx], adios2.ConstantDims)
 
 # ADIOS Engine
-bpFileWriter = bpIO.Open("npArray.bp", adios2.OpenModeWrite)
-# doesn't work: bpFileWriter = bpIO.Open("npArray.bp", adios2.OpenModeWrite, newcomm)
+bpFileWriter = bpIO.Open("npArray.bp", adios2.Mode.Write)
 bpFileWriter.PutSync(ioArray, myArray)
 bpFileWriter.Close()

examples/hello/bpWriter/helloBPWriter_nompi.py

+#
+# Distributed under the OSI-approved Apache License, Version 2.0.  See
+# accompanying file Copyright.txt for details.
+#
+# helloBPWriter.py : only works with MPI version
+#  Created on: Feb 2, 2017
+#      Author: William F Godoy godoywf@ornl.gov
+
+import numpy
+import adios2
+
+# User data
+myArray = numpy.array([0, 1., 2., 3., 4., 5., 6., 7., 8., 9.])
+Nx = myArray.size
+
+#  debug mode
+adios = adios2.ADIOS(adios2.DebugON)
+
+# ADIOS IO
+bpIO = adios.DeclareIO("BPFile_N2N")
+
+# ADIOS Variable name, shape, start, offset, constant dims
+ioArray = bpIO.DefineVariable(
+    "bpArray", [], [], [Nx], adios2.ConstantDims)
+
+# ADIOS Engine
+bpFileWriter = bpIO.Open("npArray.bp", adios2.Mode.Write)
+bpFileWriter.PutSync(ioArray, myArray)
+bpFileWriter.Close()

testing/adios2/bindings/python/TestBPWriteTypes.py

@@ -18,7 +18,7 @@ import adios2
 data = SmallTestData()
 
 comm = MPI.COMM_WORLD
-adios = adios2.ADIOS(comm, adios2.DebugON)
+adios = adios2.ADIOS(comm)
 
 bpIO = adios.DeclareIO("NPTypes")
 
@@ -50,19 +50,19 @@ varR64 = bpIO.DefineVariable(
 
 
 # ADIOS Engine
-bpFileWriter = bpIO.Open("npTypes.bp", adios2.ModeWrite)
+bpFileWriter = bpIO.Open("npTypes.bp", adios2.Mode.Write)
 
-bpFileWriter.Write(varI8, data.I8)
-bpFileWriter.Write(varI16, data.I16)
-bpFileWriter.Write(varI32, data.I32)
-bpFileWriter.Write(varI64, data.I64)
+bpFileWriter.PutSync(varI8, data.I8)
+bpFileWriter.PutSync(varI16, data.I16)
+bpFileWriter.PutSync(varI32, data.I32)
+bpFileWriter.PutSync(varI64, data.I64)
 
-bpFileWriter.Write(varU8, data.U8)
-bpFileWriter.Write(varU16, data.U16)
-bpFileWriter.Write(varU32, data.U32)
-bpFileWriter.Write(varU64, data.U64)
+bpFileWriter.PutSync(varU8, data.U8)
+bpFileWriter.PutSync(varU16, data.U16)
+bpFileWriter.PutSync(varU32, data.U32)
+bpFileWriter.PutSync(varU64, data.U64)
 
-bpFileWriter.Write(varR32, data.R32)
-bpFileWriter.Write(varR64, data.R64)
+bpFileWriter.PutSync(varR32, data.R32)
+bpFileWriter.PutSync(varR64, data.R64)
 
 bpFileWriter.Close()

testing/adios2/bindings/python/TestBPWriteTypes_nompi.py

@@ -48,19 +48,19 @@ varR64 = bpIO.DefineVariable(
 
 
 # ADIOS Engine
-bpFileWriter = bpIO.Open("npTypes.bp", adios2.ModeWrite)
+bpFileWriter = bpIO.Open("npTypes.bp", adios2.Mode.Write)
 
-bpFileWriter.Write(varI8, data.I8)
-bpFileWriter.Write(varI16, data.I16)
-bpFileWriter.Write(varI32, data.I32)
-bpFileWriter.Write(varI64, data.I64)
+bpFileWriter.PutSync(varI8, data.I8)
+bpFileWriter.PutSync(varI16, data.I16)
+bpFileWriter.PutSync(varI32, data.I32)
+bpFileWriter.PutSync(varI64, data.I64)
 
-bpFileWriter.Write(varU8, data.U8)
-bpFileWriter.Write(varU16, data.U16)
-bpFileWriter.Write(varU32, data.U32)
-bpFileWriter.Write(varU64, data.U64)
+bpFileWriter.PutSync(varU8, data.U8)
+bpFileWriter.PutSync(varU16, data.U16)
+bpFileWriter.PutSync(varU32, data.U32)
+bpFileWriter.PutSync(varU64, data.U64)
 
-bpFileWriter.Write(varR32, data.R32)
-bpFileWriter.Write(varR64, data.R64)
+bpFileWriter.PutSync(varR32, data.R32)
+bpFileWriter.PutSync(varR64, data.R64)
 
 bpFileWriter.Close()