Commit c75a2734 authored by William F Godoy's avatar William F Godoy
Browse files

Python low-level API

parent b8119c1f

bindings/Python/py11Attribute.cpp

+2 −2
Original line number Diff line number Diff line
@@ -39,7 +39,7 @@ std::string Attribute::Type() const 
    return m_Attribute->m_Type;

}



std::vector<std::string> Attribute::DataStrings()

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

{

    helper::CheckForNullptr(m_Attribute, "in call to Attribute::DataStrings");

    const std::string type = m_Attribute->m_Type;
@@ -58,7 +58,7 @@ std::vector<std::string> Attribute::DataStrings() 
        }

        else

        {

            data = attribute->m_Elements;

            data = attribute->m_DataArray;

        }

    }

    else

bindings/Python/py11Attribute.h

+1 −1
Original line number Diff line number Diff line
@@ -39,7 +39,7 @@ public: 


    pybind11::array Data();



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

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



private:

    Attribute(core::AttributeBase *attribute);

bindings/Python/py11glue.cpp

+2 −1
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ 
 * Distributed under the OSI-approved Apache License, Version 2.0.  See

 * accompanying file Copyright.txt for details.

 *

 * gluePyBind11.cpp

 * py11glue.cpp

 *

 *  Created on: Mar 16, 2017

 *      Author: William F Godoy godoywf@ornl.gov
@@ -408,6 +408,7 @@ PYBIND11_MODULE(adios2, m) 
             })

        .def("Name", &adios2::py11::Attribute::Name)

        .def("Type", &adios2::py11::Attribute::Type)

        .def("DataString", &adios2::py11::Attribute::DataString)

        .def("Data", &adios2::py11::Attribute::Data);



    pybind11::class_<adios2::py11::Engine>(m, "Engine")

testing/adios2/bindings/python/TestBPWriteReadTypes.py

+84 −20
Original line number Diff line number Diff line
@@ -24,12 +24,26 @@ def check_name(name, name_list): 
        raise ValueError(str(name) + ' not found in list')





def check_array(np1, np2, hint):

    if((np1 == np2).all() is False):

        print("InData: " + str(np1))

        print("Data: " + str(np2))

        raise ValueError('Array read failed ' + str(hint))





# MPI

comm = MPI.COMM_WORLD

rank = comm.Get_rank()

size = comm.Get_size()

Nx = 8



# list of tested attributes and variables

attr_names = ["attrString", "attrI8", "attrI16", "attrI32", "attrI64",

              "attrU8", "attrU16", "attrU32", "attrU64", "attrR32", "attrR64"]

var_names = ["varStr", "varI8", "varI16", "varI32", "varI64",

             "varU8", "varU16", "varU32", "varU64",

                      "varR32", "varR64"]



# Start ADIOS

adios = adios2.ADIOS(comm)

ioWriter = adios.DeclareIO("writer")
@@ -68,8 +82,17 @@ varR32 = ioWriter.DefineVariable( 
varR64 = ioWriter.DefineVariable(

    "varR64", data.R64, shape, start, count, adios2.ConstantDims)



attString = ioWriter.DefineAttribute("attrString", ["hello attribute"])

attString = ioWriter.DefineAttribute("attrString", ["one", "two", "three"])

attI8 = ioWriter.DefineAttribute("attrI8", data.I8)

attI16 = ioWriter.DefineAttribute("attrI16", data.I16)

attI32 = ioWriter.DefineAttribute("attrI32", data.I32)

attI64 = ioWriter.DefineAttribute("attrI64", data.I64)

attU8 = ioWriter.DefineAttribute("attrU8", data.U8)

attU16 = ioWriter.DefineAttribute("attrU16", data.U16)

attU32 = ioWriter.DefineAttribute("attrU32", data.U32)

attU64 = ioWriter.DefineAttribute("attrU64", data.U64)

attR32 = ioWriter.DefineAttribute("attrR32", data.R32)

attR64 = ioWriter.DefineAttribute("attrR64", data.R64)



ioWriter.SetEngine("BPFile")

ioParams = {}
@@ -85,7 +108,6 @@ if(engineType != "BPFile"): 
ioWriter.SetParameter("profileunits", "microseconds")

ioWriter.AddTransport("file")





ioParams = ioWriter.Parameters()

print("Final IO parameters")

for key, value in ioParams.items():
@@ -125,6 +147,66 @@ reader = ioReader.Open("npTypes.bp", adios2.Mode.Read) 


attrString = ioReader.InquireAttribute("attrString")

attrI8 = ioReader.InquireAttribute("attrI8")

attrI16 = ioReader.InquireAttribute("attrI16")

attrI32 = ioReader.InquireAttribute("attrI32")

attrI64 = ioReader.InquireAttribute("attrI64")

attrU8 = ioReader.InquireAttribute("attrU8")

attrU16 = ioReader.InquireAttribute("attrU16")

attrU32 = ioReader.InquireAttribute("attrU32")

attrU64 = ioReader.InquireAttribute("attrU64")

attrR32 = ioReader.InquireAttribute("attrR32")

attrR64 = ioReader.InquireAttribute("attrR64")



check_object(attrString, "attrString")

check_object(attrI8, "attrI8")

check_object(attrI16, "attrI16")

check_object(attrI32, "attrI32")

check_object(attrI64, "attrI64")

check_object(attrU8, "attrU8")

check_object(attrU16, "attrU16")

check_object(attrU32, "attrU32")

check_object(attrU64, "attrU64")

check_object(attrR32, "attrR32")

check_object(attrR64, "attrR64")



attrStringData = attrString.DataString()

if(attrStringData[0] != "one"):

    raise ValueError('attrStringData[0] failed')

if(attrStringData[1] != "two"):

    raise ValueError('attrStringData[1] failed')

if(attrStringData[2] != "three"):

    raise ValueError('attrStringData[2] failed')



attrI8Data = attrI8.Data()

attrI16Data = attrI16.Data()

attrI32Data = attrI32.Data()

attrI64Data = attrI64.Data()

attrU8Data = attrU8.Data()

attrU16Data = attrU16.Data()

attrU32Data = attrU32.Data()

attrU64Data = attrU64.Data()

attrR32Data = attrR32.Data()

attrR64Data = attrR64.Data()



check_array(attrI8Data, data.I8, 'I8')

check_array(attrI16Data, data.I16, 'I16')

check_array(attrI32Data, data.I32, 'I32')

check_array(attrI64Data, data.I64, 'I64')

check_array(attrU8Data, data.U8, 'U8')

check_array(attrU16Data, data.U16, 'U16')

check_array(attrU32Data, data.U32, 'U32')

check_array(attrU64Data, data.U64, 'U64')

check_array(attrR32Data, data.R32, 'R32')

check_array(attrR64Data, data.R64, 'R64')



attributesInfo = ioReader.AvailableAttributes()

for name, info in attributesInfo.items():

    check_name(name, attr_names)

    if rank == 0:

        print("attribute_name: " + name)

        for key, value in info.items():

            print("\t" + key + ": " + value)

        print("\n")



varStr = ioReader.InquireVariable("varStr")

varI8 = ioReader.InquireVariable("varI8")
@@ -138,9 +220,6 @@ varU64 = ioReader.InquireVariable("varU64") 
varR32 = ioReader.InquireVariable("varR32")

varR64 = ioReader.InquireVariable("varR64")



check_object(attrString, "attrString")

check_object(attrString, "attrI8")



check_object(varStr, "varStr")

check_object(varI8, "varI8")

check_object(varI16, "varI16")
@@ -153,21 +232,6 @@ check_object(varU64, "varU64") 
check_object(varR32, "varR32")

check_object(varR64, "varR64")





attr_names = ["attrString", "attrI8"]

var_names = ["varStr", "varI8", "varI16", "varI32", "varI64",

             "varU8", "varU16", "varU32", "varU64",

                      "varR32", "varR64"]



attributesInfo = ioReader.AvailableAttributes()

for name, info in attributesInfo.items():

    check_name(name, attr_names)

    if rank == 0:

        print("attribute_name: " + name)

        for key, value in info.items():

            print("\t" + key + ": " + value)

        print("\n")



variablesInfo = ioReader.AvailableVariables()

for name, info in variablesInfo.items():

    check_name(name, var_names)

testing/adios2/bindings/python/TestBPWriteReadTypes_nompi.py

+10 −10
Original line number Diff line number Diff line
@@ -23,28 +23,28 @@ bpIO = adios.DeclareIO("NPTypes") 
# ADIOS Variable name, shape, start, offset, constant dims

# All local variables

varI8 = bpIO.DefineVariable(

    "varI8", [], [], [data.I8.size], adios2.ConstantDims, data.I8)

    "varI8",  data.I8, [], [], [data.I8.size], adios2.ConstantDims)

varI16 = bpIO.DefineVariable(

    "varI16", [], [], [data.I16.size], adios2.ConstantDims, data.I16)

    "varI16", data.I16, [], [], [data.I16.size], adios2.ConstantDims)

varI32 = bpIO.DefineVariable(

    "varI32", [], [], [data.I32.size], adios2.ConstantDims, data.I32)

    "varI32", data.I32, [], [], [data.I32.size], adios2.ConstantDims)

varI64 = bpIO.DefineVariable(

    "varI64", [], [], [data.I64.size], adios2.ConstantDims, data.I64)

    "varI64", data.I64, [], [], [data.I64.size], adios2.ConstantDims)



varU8 = bpIO.DefineVariable(

    "varUI8", [], [], [data.U8.size], adios2.ConstantDims, data.U8)

    "varUI8", data.U8, [], [], [data.U8.size], adios2.ConstantDims)

varU16 = bpIO.DefineVariable(

    "varUI16", [], [], [data.U16.size], adios2.ConstantDims, data.U16)

    "varUI16", data.U16, [], [], [data.U16.size], adios2.ConstantDims)

varU32 = bpIO.DefineVariable(

    "varUI32", [], [], [data.U32.size], adios2.ConstantDims, data.U32)

    "varUI32", data.U32, [], [], [data.U32.size], adios2.ConstantDims)

varU64 = bpIO.DefineVariable(

    "varUI64", [], [], [data.U64.size], adios2.ConstantDims, data.U64)

    "varUI64",  data.U64, [], [], [data.U64.size], adios2.ConstantDims)



varR32 = bpIO.DefineVariable(

    "varR32", [], [], [data.R32.size], adios2.ConstantDims, data.R32)

    "varR32", data.R32, [], [], [data.R32.size], adios2.ConstantDims)



varR64 = bpIO.DefineVariable(

    "varR64", [], [], [data.R64.size], adios2.ConstantDims, data.R64)

    "varR64",  data.R64, [], [], [data.R64.size], adios2.ConstantDims)





# ADIOS Engine