diff --git a/doc/API_design/API_example_use.cpp b/doc/API_design/API_example_use.cpp
index a35146935cf564dea610accee6ad67efdfbe6ce6..701bb8994bf973330fb61381b2d2d5fa84741563 100644
--- a/doc/API_design/API_example_use.cpp
+++ b/doc/API_design/API_example_use.cpp
@@ -31,7 +31,7 @@ int main(int argc, char *argv[])
// Global class/object that serves for init, finalize and provides ADIOS
// functions
- adios::ADIOS adios("config.xml", comm, /*verbose=*/adios::INFO,
+ adios::ADIOS adios("config.xml", comm, /*verbose=*/adios::Verbose::INFO,
/*debugflag=*/false);
/*************
@@ -83,8 +83,8 @@ int main(int argc, char *argv[])
"Ragged", adios::Dims{nproc, adios::VARYING_DIMENSION}); // ragged array
// add transform to variable
- adios::Transform zfp = adios::transform::ZFP();
- var2D.AddTransform(zfp, "accuracy=0.001");
+ adios::Transform compress = adios::transform::BZip2();
+ var2D.AddTransform(compress, "level=5");
// open...write.write.write...advance...write.write.write...advance...
// ...close cycle
@@ -120,7 +120,7 @@ int main(int argc, char *argv[])
// write and
// its offsets in the global spaces. This could have been done in
// adios.DefineVariable()
- adios::Selection sel = adios.SelectionBoundingBox(
+ adios::SelectionBoundingBox sel = adios::SelectionBoundingBox(
{1, NX}, {rank, NX}); // local dims and offsets; both as list
var2D.SetSelection(
sel); // Shall we call it SetSpaceSelection, SetOutputSelection?
@@ -135,7 +135,7 @@ int main(int argc, char *argv[])
// Size of the bounding box should match the
// "space" selection which was given above. Default memspace is the full
// selection.
- adios::Selection memspace = adios.SelectionBoundingBox(
+ adios::SelectionBoundingBox memspace = adios::SelectionBoundingBox(
{1, NX}, {0, 1}); // local dims and offsets; both as list
var2D.SetMemorySelection(memspace);
@@ -226,10 +226,10 @@ int main(int argc, char *argv[])
// we
// READ and
// its offsets in the global spaces
- adios::Selection bbsel = adios.SelectionBoundingBox(
+ adios::SelectionBoundingBox bbsel = adios::SelectionBoundingBox(
{1, NX}, {0, 0}); // local dims and offsets; both as list
var2D.SetSelection(bbsel);
- adios::Selection memspace = adios.SelectionBoundingBox(
+ adios::SelectionBoundingBox memspace = adios::SelectionBoundingBox(
{1, NX}, {0, 1}); // local dims and offsets; both as list
var2D.SetMemorySelection(memspace);
reader->Read<double>(var2D, *Temperature);
@@ -292,9 +292,9 @@ int main(int argc, char *argv[])
// we
// READ and
// its offsets in the global spaces if we know this somehow
- adios::Selection bbsel = adios.SelectionBoundingBox(
+ adios::SelectionBoundingBox bbsel = adios::SelectionBoundingBox(
{1, NX}, {0, 0}); // local dims and offsets; both as list
- var2D->SetSelection(bbsel);
+ var2D.SetSelection(bbsel);
reader->Read<double>(var2D, *Temperature);
// Let ADIOS allocate space for the incoming (per-writer) item
@@ -399,7 +399,7 @@ int main(int argc, char *argv[])
// Open a file with all steps immediately available
std::shared_ptr<adios::Engine> reader = adios.OpenFileReader(
- "filename.bp", comm, rmethod, adios::COLLECTIVE_IO);
+ "filename.bp", comm, rmethod, adios::IOMode::COLLECTIVE);
/* NX */
/* There is a single value for each step. We can read all into a 1D
diff --git a/examples/heatTransfer/IO_adios2.cpp b/examples/heatTransfer/IO_adios2.cpp
deleted file mode 100644
index aea0493ca7dfbbea62f9568f63c4a289bbaa1bba..0000000000000000000000000000000000000000
--- a/examples/heatTransfer/IO_adios2.cpp
+++ /dev/null
@@ -1,115 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * IO_ADIOS2.cpp
- *
- * Created on: Feb 2017
- * Author: Norbert Podhorszki
- */
-
-#include "IO.h"
-#include "ADIOS_CPP.h"
-
-#include <string>
-
-static int rank_saved;
-adios::ADIOS *ad = nullptr;
-std::shared_ptr<adios::Engine> bpWriter;
-adios::Variable<double> *varT = nullptr;
-
-IO::IO(const Settings &s, MPI_Comm comm)
-{
- rank_saved = s.rank;
- m_outputfilename = s.outputfile + ".bp";
- ad = new adios::ADIOS("adios2.xml", comm, adios::Verbose::INFO);
-
- // Define method for engine creation
- // 1. Get method def from config file or define new one
-
- adios::Method &bpWriterSettings = ad->DeclareMethod("output");
- if (!bpWriterSettings.IsUserDefined())
- {
- // if not defined by user, we can change the default settings
- bpWriterSettings.SetEngine("BP"); // BP is the default engine
- bpWriterSettings.AllowThreads(
- 1); // allow 1 extra thread for data processing
- bpWriterSettings.AddTransport(
- "File", "lucky=yes"); // ISO-POSIX file is the default transport
- // Passing parameters to the transport
- bpWriterSettings.SetParameters(
- "have_metadata_file",
- "yes"); // Passing parameters to the engine
- bpWriterSettings.SetParameters(
- "Aggregation",
- std::to_string((s.nproc + 1) / 2)); // number of aggregators
- }
-
- // define T as 2D global array
- varT = &ad->DefineVariable<double>(
- "T", {s.gndx, s.gndy}, // Global dimensions
- {s.ndx,
- s.ndy}, // local size, could be defined later using SetSelection()
- {s.offsx, s.offsy} // offset of the local array in the global space
- );
-
- // add transform to variable
- // adios::Transform tr = adios::transform::BZIP2( );
- // varT.AddTransform( tr, "" );
- // varT.AddTransform( tr,"accuracy=0.001" ); // for ZFP
-
- bpWriter = ad->Open(m_outputfilename, "w", comm, bpWriterSettings);
-
- // ad->Open(m_outputfilename, "w", comm, bpWriterSettings);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: failed to open ADIOS bpWriter\n");
-}
-
-IO::~IO()
-{
- bpWriter->Close();
- delete ad;
-}
-
-void /*IO::*/ old_style_write(int step, const HeatTransfer &ht,
- const Settings &s, MPI_Comm comm)
-{
- bpWriter->Write<double>(*varT, ht.data_noghost().data());
- bpWriter->Advance();
-}
-
-void IO::write(int step, const HeatTransfer &ht, const Settings &s,
- MPI_Comm comm)
-{
- /* This selection is redundant and not required, since we defined
- * the selection already in DefineVariable(). It is here just as an example.
- */
- // Make a selection to describe the local dimensions of the variable we
- // write
- // and
- // its offsets in the global spaces. This could have been done in
- // adios.DefineVariable()
- adios::Selection sel = adios.SelectionBoundingBox(
- {s.ndx, s.ndy},
- {s.offsx, s.offsy}); // local dims and offsets; both as list
- var2D.SetSelection(sel);
-
- /* Select the area that we want to write from the data pointer we pass to
- the
- writer.
- Think HDF5 memspace, just not hyperslabs, only a bounding box selection.
- Engine will copy this bounding box from the data pointer into the output
- buffer.
- Size of the bounding box should match the "space" selection which was
- given
- above.
- Default memspace is always the full selection.
- */
- adios::Selection memspace =
- adios.SelectionBoundingBox({s.ndx, s.ndy}, {1, 1});
- var2D.SetMemorySelection(memspace);
-
- bpWriter->Write<double>(*varT, ht.data());
- bpWriter->Advance();
-}
diff --git a/examples/heatTransfer/write/IO_adios2.cpp b/examples/heatTransfer/write/IO_adios2.cpp
index 72d118ea15748e2d9852879ccc7f519f184ba72f..0f0c06bb795e0972564d8f5884b52955a08207c9 100644
--- a/examples/heatTransfer/write/IO_adios2.cpp
+++ b/examples/heatTransfer/write/IO_adios2.cpp
@@ -31,12 +31,13 @@ IO::IO(const Settings &s, MPI_Comm comm)
if (!bpWriterSettings.IsUserDefined())
{
// if not defined by user, we can change the default settings
- bpWriterSettings.SetEngine("BPFileWriter"); // BP is the default engine
- bpWriterSettings.AllowThreads(1); // for data processing
-
- bpWriterSettings.AddTransport(
- "File", "lucky=yes"); // ISO-POSIX file is the default transport
- // Passing parameters to the transport
+ // BPFileWriter is the default engine
+ bpWriterSettings.SetEngine("BPFileWriter");
+ // Allow an extra thread for data processing
+ bpWriterSettings.AllowThreads(1);
+ // ISO-POSIX file is the default transport
+ // Passing parameters to the transport
+ bpWriterSettings.AddTransport("File", "lucky=yes");
const std::string aggregatorsParam("Aggregators=" +
std::to_string((s.nproc + 1) / 2));
diff --git a/examples/hello/adios1Writer/helloADIOS1Writer.cpp b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
index 87101533b4795379e3b2c94966c44d01fea83403..fc6064b27b8fa5ee50be1a86f9c1b001a3227684 100644
--- a/examples/hello/adios1Writer/helloADIOS1Writer.cpp
+++ b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
@@ -64,10 +64,10 @@ int main(int argc, char *argv[])
// Define method for engine creation, it is basically straight-forward
// parameters
- adios::Method &bpWriterSettings = adios.DeclareMethod(
- "SingleFile"); // default method type is BPWriter
+ adios::Method &bpWriterSettings = adios.DeclareMethod("hello");
bpWriterSettings.SetEngine("ADIOS1Writer");
bpWriterSettings.SetParameters("profile_units=mus");
+ bpWriterSettings.SetIOMode(adios::IOMode::COLLECTIVE);
bpWriterSettings.AddTransport(
"File", "profile_units=mus",
"have_metadata_file=no"); // uses default POSIX library
@@ -75,8 +75,7 @@ int main(int argc, char *argv[])
// Create engine smart pointer due to polymorphism,
// Open returns a smart pointer to Engine containing the Derived class
// Writer
- auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings,
- adios::IOMode::COLLECTIVE);
+ auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings);
if (bpWriter == nullptr)
throw std::ios_base::failure(
diff --git a/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp b/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
index 5955b33436df32cd835391a75c85bf2bc8f7f53b..2b850253a997c94106cd472043f05d4e7050372e 100644
--- a/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
+++ b/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
@@ -42,8 +42,8 @@ int main(int argc, char *argv[])
// Define method for engine creation, it is basically straight-forward
// parameters
- adios::Method &bpWriterSettings = adios.DeclareMethod(
- "SinglePOSIXFile"); // default method type is Writer
+ adios::Method &bpWriterSettings = adios.DeclareMethod("hello");
+ bpWriterSettings.SetIOMode(adios::IOMode::COLLECTIVE);
bpWriterSettings.SetParameters("profile_units=mus");
bpWriterSettings.AddTransport("File", "have_metadata_file=yes",
"profile_units=mus");
@@ -52,8 +52,7 @@ int main(int argc, char *argv[])
// Open returns a smart pointer to Engine containing the Derived class
// Writer
auto bpFileWriter =
- adios.Open("myDoubles_nompi.bp", "w", bpWriterSettings,
- adios::IOMode::COLLECTIVE);
+ adios.Open("myDoubles_nompi.bp", "w", bpWriterSettings);
if (bpFileWriter == nullptr)
throw std::ios_base::failure(
diff --git a/include/core/Method.h b/include/core/Method.h
index dc40806126f6da99aac4cc03be2479c62f00eecc..e2f06a6f4857348cdbfcff10e7b3c9fad74f48a5 100644
--- a/include/core/Method.h
+++ b/include/core/Method.h
@@ -48,7 +48,6 @@ public:
/// unsafe
std::string m_Type; ///< Method's engine type
unsigned int m_nThreads = 1;
- adios::IOMode m_IOMode = adios::IOMode::INDEPENDENT;
std::map<std::string, std::string> m_Parameters; ///< method parameters
std::vector<std::map<std::string, std::string>>
@@ -78,6 +77,12 @@ public:
*/
void SetEngine(const std::string type);
+ /**
+ * Set the IO mode (collective or independent)
+ * @param IO mode
+ */
+ void SetIOMode(const IOMode mode);
+
/**
* Set how many threads the engine can use for its operations (e.g. file io,
* compression, staging).
@@ -135,6 +140,7 @@ public:
private:
Verbose m_Verbose = Verbose::WARN;
+ adios::IOMode m_IOMode = adios::IOMode::INDEPENDENT;
void AddTransportParameters(const std::string type,
const std::vector<std::string> ¶meters);
diff --git a/include/engine/adios1/ADIOS1Reader.h b/include/engine/adios1/ADIOS1Reader.h
index 53fb32bec3f8cf8c09ef7584c4f06213ed47bfba..baf55f4166b70ef934b077de1d79e569cc43ed3b 100644
--- a/include/engine/adios1/ADIOS1Reader.h
+++ b/include/engine/adios1/ADIOS1Reader.h
@@ -101,6 +101,8 @@ public:
private:
void Init(); ///< called from constructor, gets the selected ADIOS1
/// transport method from settings
+ void InitParameters();
+ void InitTransports();
template <class T>
Variable<T> *InquireVariableCommon(const std::string &name,
diff --git a/source/core/Method.cpp b/source/core/Method.cpp
index 720382cc26074a531918f3c6d21c210ad56dae1f..0c91ed23a3d35da0b5b776954d07eccf84a2233a 100644
--- a/source/core/Method.cpp
+++ b/source/core/Method.cpp
@@ -29,6 +29,7 @@ bool Method::IsUserDefined()
}
void Method::SetEngine(const std::string type) { m_Type = type; }
+void Method::SetIOMode(const IOMode mode) { m_IOMode = mode; };
void Method::AllowThreads(const unsigned int nThreads)
{
diff --git a/source/engine/adios1/ADIOS1Reader.cpp b/source/engine/adios1/ADIOS1Reader.cpp
index 55a745a0e7370a437665321105cc3ecafd5e9f26..f938277af392b605f7fffa082d61e2f2a7cd7ee7 100644
--- a/source/engine/adios1/ADIOS1Reader.cpp
+++ b/source/engine/adios1/ADIOS1Reader.cpp
@@ -2,14 +2,14 @@
* Distributed under the OSI-approved Apache License, Version 2.0. See
* accompanying file Copyright.txt for details.
*
- * BPFileReader.cpp
+ * ADIOS1Reader.cpp
*
* Created on: Feb 27, 2017
* Author: wfg
*/
+#include "engine/adios1/ADIOS1Reader.h"
#include "core/Support.h"
-#include "engine/bp/BPFileReader.h"
#include "functions/adiosFunctions.h" // CSVToVector
#include "transport/file/FStream.h" // uses C++ fstream
#include "transport/file/FileDescriptor.h" // uses POSIX
@@ -21,127 +21,128 @@ namespace adios
ADIOS1Reader::ADIOS1Reader(ADIOS &adios, const std::string &name,
const std::string accessMode, MPI_Comm mpiComm,
const Method &method)
-: Engine(adios, "BPFileReader", name, accessMode, mpiComm, method,
- " BPFileReader constructor (or call to ADIOS Open).\n")
+: Engine(adios, "ADIOS1Reader", name, accessMode, mpiComm, method,
+ " ADIOS1Reader constructor (or call to ADIOS Open).\n")
{
Init();
+ adios_read_init_method(read_method, mpiComm, "");
}
-BPFileReader::~BPFileReader() {}
+ADIOS1Reader::~ADIOS1Reader() {}
Variable<void> *
-BPFileReader::InquireVariable(const std::string &variableName,
+ADIOS1Reader::InquireVariable(const std::string &variableName,
const bool readIn) // not yet implemented
{
return nullptr;
}
Variable<char> *
-BPFileReader::InquireVariableChar(const std::string &variableName,
+ADIOS1Reader::InquireVariableChar(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<char>(variableName, readIn);
}
Variable<unsigned char> *
-BPFileReader::InquireVariableUChar(const std::string &variableName,
+ADIOS1Reader::InquireVariableUChar(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<unsigned char>(variableName, readIn);
}
Variable<short> *
-BPFileReader::InquireVariableShort(const std::string &variableName,
+ADIOS1Reader::InquireVariableShort(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<short>(variableName, readIn);
}
Variable<unsigned short> *
-BPFileReader::InquireVariableUShort(const std::string &variableName,
+ADIOS1Reader::InquireVariableUShort(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<unsigned short>(variableName, readIn);
}
-Variable<int> *BPFileReader::InquireVariableInt(const std::string &variableName,
+Variable<int> *ADIOS1Reader::InquireVariableInt(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<int>(variableName, readIn);
}
Variable<unsigned int> *
-BPFileReader::InquireVariableUInt(const std::string &variableName,
+ADIOS1Reader::InquireVariableUInt(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<unsigned int>(variableName, readIn);
}
Variable<long int> *
-BPFileReader::InquireVariableLInt(const std::string &variableName,
+ADIOS1Reader::InquireVariableLInt(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<long int>(variableName, readIn);
}
Variable<unsigned long int> *
-BPFileReader::InquireVariableULInt(const std::string &variableName,
+ADIOS1Reader::InquireVariableULInt(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<unsigned long int>(variableName, readIn);
}
Variable<long long int> *
-BPFileReader::InquireVariableLLInt(const std::string &variableName,
+ADIOS1Reader::InquireVariableLLInt(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<long long int>(variableName, readIn);
}
Variable<unsigned long long int> *
-BPFileReader::InquireVariableULLInt(const std::string &variableName,
+ADIOS1Reader::InquireVariableULLInt(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<unsigned long long int>(variableName, readIn);
}
Variable<float> *
-BPFileReader::InquireVariableFloat(const std::string &variableName,
+ADIOS1Reader::InquireVariableFloat(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<float>(variableName, readIn);
}
Variable<double> *
-BPFileReader::InquireVariableDouble(const std::string &variableName,
+ADIOS1Reader::InquireVariableDouble(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<double>(variableName, readIn);
}
Variable<long double> *
-BPFileReader::InquireVariableLDouble(const std::string &variableName,
+ADIOS1Reader::InquireVariableLDouble(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<long double>(variableName, readIn);
}
Variable<std::complex<float>> *
-BPFileReader::InquireVariableCFloat(const std::string &variableName,
+ADIOS1Reader::InquireVariableCFloat(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<std::complex<float>>(variableName, readIn);
}
Variable<std::complex<double>> *
-BPFileReader::InquireVariableCDouble(const std::string &variableName,
+ADIOS1Reader::InquireVariableCDouble(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<std::complex<double>>(variableName, readIn);
}
Variable<std::complex<long double>> *
-BPFileReader::InquireVariableCLDouble(const std::string &variableName,
+ADIOS1Reader::InquireVariableCLDouble(const std::string &variableName,
const bool readIn)
{
return InquireVariableCommon<std::complex<long double>>(variableName,
@@ -149,31 +150,34 @@ BPFileReader::InquireVariableCLDouble(const std::string &variableName,
}
VariableCompound *
-BPFileReader::InquireVariableCompound(const std::string &variableName,
+ADIOS1Reader::InquireVariableCompound(const std::string &variableName,
const bool readIn)
{
return nullptr;
}
-void BPFileReader::Close(const int transportIndex) {}
+void ADIOS1Reader::Close(const int transportIndex) {}
// PRIVATE
-void BPFileReader::Init()
+void ADIOS1Reader::Init()
{
if (m_DebugMode == true)
{
if (m_AccessMode != "r" && m_AccessMode != "read")
throw std::invalid_argument(
- "ERROR: BPFileReader doesn't support access mode " +
+ "ERROR: ADIOS1Reader doesn't support access mode " +
m_AccessMode +
- ", in call to ADIOS Open or BPFileReader constructor\n");
+ ", in call to ADIOS Open or ADIOS1Reader constructor\n");
}
-
+ InitParameters();
InitTransports();
}
-void BPFileReader::InitTransports() // maybe move this?
+void ADIOS1Reader::InitParameters() {}
+
+void ADIOS1Reader::InitTransports()
{
+
if (m_DebugMode == true)
{
if (TransportNamesUniqueness() == false)
@@ -188,43 +192,10 @@ void BPFileReader::InitTransports() // maybe move this?
for (const auto ¶meters : m_Method.m_TransportParameters)
{
auto itTransport = parameters.find("transport");
- if (itTransport->second == "file" || itTransport->second == "File")
+ if (itTransport->second == "file" || itTransport->second == "File" ||
+ itTransport->second == "bp" || itTransport->second == "BP")
{
- auto itLibrary = parameters.find("library");
- if (itLibrary == parameters.end() ||
- itLibrary->second == "POSIX") // use default POSIX
- {
- auto file = std::make_shared<transport::FileDescriptor>(
- m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "FILE*" ||
- itLibrary->second == "stdio.h")
- {
- auto file = std::make_shared<transport::FilePointer>(
- m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "fstream" ||
- itLibrary->second == "std::fstream")
- {
- auto file = std::make_shared<transport::FStream>(m_MPIComm,
- m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "MPI-IO")
- {
- }
- else
- {
- if (m_DebugMode == true)
- throw std::invalid_argument(
- "ERROR: file transport library " + itLibrary->second +
- " not supported, in " + m_Name + m_EndMessage);
- }
+ read_method = ADIOS_READ_METHOD_BP;
}
else
{