diff --git a/examples/heatTransfer/write/CMakeLists.txt b/examples/heatTransfer/write/CMakeLists.txt
index 763a151aa2206afee7aa56a95e05be48744cb2fb..7144a8e7720987406c27e6bbf61c2e31f7a0b4a7 100644
--- a/examples/heatTransfer/write/CMakeLists.txt
+++ b/examples/heatTransfer/write/CMakeLists.txt
@@ -52,4 +52,25 @@ if(ADIOS_USE_MPI)
${MPI_C_LIBRARIES} ${HDF5_C_LIBRARIES}
)
endif()
+
+ if(ADIOS_USE_HDF5)
+ find_package(MPI COMPONENTS C REQUIRED)
+
+ add_executable(heatTransfer_write_a2h5
+ main.cpp
+ HeatTransfer.cpp
+ Settings.cpp
+ IO_ph5_adios2.cpp
+ )
+
+ target_include_directories(heatTransfer_write_a2h5
+ PRIVATE ${MPI_C_INCLUDE_PATH}
+ )
+ #target_link_libraries(heatTransfer_write_a2h5
+ # ${MPI_C_LIBRARIES}
+ #)
+ target_link_libraries(heatTransfer_write_a2h5 PUBLIC adios2)
+
+ endif()
+
endif()
diff --git a/examples/heatTransfer/write/IO_ph5_adios2.cpp b/examples/heatTransfer/write/IO_ph5_adios2.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a4b37c5dc466eba83a2d60a2f1918ecdd421adef
--- /dev/null
+++ b/examples/heatTransfer/write/IO_ph5_adios2.cpp
@@ -0,0 +1,120 @@
+/*
+ * 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 <string>
+
+#include <adios2.h>
+
+static int rank_saved;
+adios::ADIOS *ad = nullptr;
+std::shared_ptr<adios::Engine> h5writer;
+adios::Variable<double> *varT = nullptr;
+adios::Variable<unsigned int> *varGndx = nullptr;
+
+IO::IO(const Settings &s, MPI_Comm comm)
+{
+ rank_saved = s.rank;
+ m_outputfilename = s.outputfile + ".h5";
+ //adios::ADIOS adios(comm, adios::Verbose::INFO, false);
+ ad = new adios::ADIOS(comm, adios::Verbose::INFO, false);
+
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
+
+ adios::Method &h5writerSettings = ad->DeclareMethod("output");
+ if (!h5writerSettings.IsUserDefined())
+ {
+ // if not defined by user, we can change the default settings
+ // BPFileWriter is the default engine
+ h5writerSettings.SetEngine("HDF5Writer");
+ // Allow an extra thread for data processing
+
+ const std::string aggregatorsParam("Aggregators=" +
+ std::to_string((s.nproc + 1) / 2));
+ h5writerSettings.SetParameters("have_metadata_file=yes",
+ aggregatorsParam);
+ }
+
+ // ad->DefineScalar<unsigned int>("gndx", true);
+ varGndx = &(ad->DefineVariable<unsigned int>("gndx"));
+ ad->DefineVariable<unsigned int>("gndy");
+
+ // define T as 2D global array
+ varT = &(ad->DefineArray<double>(
+ "T",
+ // Global dimensions
+ {s.gndx, s.gndy},
+ // starting offset of the local array in the global space
+ {s.offsx, s.offsy},
+ // local size, could be defined later using SetSelection()
+ {s.ndx, s.ndy}));
+
+ // add transform to variable
+ // adios::Transform tr = adios::transform::BZIP2( );
+ // varT.AddTransform( tr, "" );
+ // varT.AddTransform( tr,"accuracy=0.001" ); // for ZFP
+
+ h5writer = ad->Open(m_outputfilename, "w", comm, h5writerSettings);
+
+ if (h5writer == nullptr)
+ throw std::ios_base::failure("ERROR: failed to open ADIOS h5writer\n");
+}
+
+IO::~IO()
+{
+ h5writer->Close();
+ //delete ad;
+}
+
+void IO::write(int step, const HeatTransfer &ht, const Settings &s,
+ MPI_Comm comm)
+{
+#if 1
+
+ /* 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::SelectionBoundingBox sel({s.offsx, s.offsy}, {s.ndx, s.ndy});
+ //varT->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::SelectionBoundingBox memspace =
+ // adios::SelectionBoundingBox({1, 1}, {s.ndx, s.ndy});
+ //varT->SetMemorySelection(memspace);
+
+ h5writer->Write<double>(*varT, ht.data_noghost().data());
+ //h5writer->Write(*varT, ht.data_noghost().data());
+ h5writer->Write<unsigned int>(*varGndx, s.gndx);
+ h5writer->Write<unsigned int>("gndy", s.gndy);
+
+ h5writer->Advance();
+
+#else
+
+ h5writer->Write<double>(*varT, ht.data_noghost().data());
+ h5writer->Advance();
+
+#endif
+}
diff --git a/examples/hello/hdf5Writer/helloHDF5Writer.cpp b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
index adf524928bfcd4d68e3c20f47f77360839e26331..cc1b7bd3f7c9fe6aad29a6887179fe0d27e78117 100644
--- a/examples/hello/hdf5Writer/helloHDF5Writer.cpp
+++ b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
@@ -73,17 +73,16 @@ int main(int argc, char *argv[])
try
{
// Define variable and local size
- auto &ioMyInts =
- adios.DefineArray<int>("myInts", {intCountDim1, intDim2}, {4, 3},
- {intOffsetDim1, intOffsetDim2});
+ auto &ioMyInts = adios.DefineArray<int>("myInts", {4, 3},
+ {intOffsetDim1, intOffsetDim2}, {intCountDim1, intDim2});
auto &ioMyDoubles = adios.DefineArray<double>(
- "myDoubles", {doubleVCount}, {Nx}, {doubleVOffset});
+ "myDoubles", {Nx}, {doubleVOffset}, {doubleVCount});
auto &ioMyCFloats = adios.DefineArray<std::complex<float>>(
- "myCFloats", {complexCount}, {3}, {complexOffset});
+ "myCFloats", {3}, {complexOffset}, {complexCount});
auto &ioMyCDoubles = adios.DefineArray<std::complex<double>>(
- "myCDoubles", {complexCount}, {3}, {complexOffset});
+ "myCDoubles", {3}, {complexOffset}, {complexCount});
auto &ioMyCLongDoubles = adios.DefineArray<std::complex<long double>>(
- "myCLongDoubles", {complexCount}, {3}, {complexOffset});
+ "myCLongDoubles", {3}, {complexOffset}, {complexCount});
// Define method for engine creation, it is basically straight-forward
// parameters
diff --git a/source/adios2/engine/hdf5/HDF5Common.cpp b/source/adios2/engine/hdf5/HDF5Common.cpp
index e2a9c521ee6b08d50094910ea43e85920d395350..d628689c7d6a3b380e1b782f6ed331cd473fe2b9 100644
--- a/source/adios2/engine/hdf5/HDF5Common.cpp
+++ b/source/adios2/engine/hdf5/HDF5Common.cpp
@@ -162,6 +162,10 @@ void HDF5Common::Close()
H5Fclose(m_FileId);
m_FileId = -1;
m_GroupId = -1;
+
+ H5Tclose(m_DefH5TypeComplexFloat);
+ H5Tclose(m_DefH5TypeComplexDouble);
+ H5Tclose(m_DefH5TypeComplexLongDouble);
}
void HDF5Common::Advance()
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.cpp b/source/adios2/engine/hdf5/HDF5WriterP.cpp
index d4f036a1b321c2310efb451d343382264db23c92..6969c4a40138bd44924dd75ddc206bdf50b9d0c0 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.cpp
+++ b/source/adios2/engine/hdf5/HDF5WriterP.cpp
@@ -22,8 +22,8 @@ HDF5Writer::HDF5Writer(ADIOS &adios, const std::string name,
const Method &method)
: Engine(adios, "HDF5Writer", name, accessMode, mpiComm,
method, /*debugMode, cores,*/
- " HDF5Writer constructor (or call to ADIOS Open).\n"),
- m_Buffer(m_DebugMode)
+ " HDF5Writer constructor (or call to ADIOS Open).\n")
+ //m_Buffer(m_DebugMode)
{
Init();
}
@@ -256,6 +256,19 @@ void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
int dimSize = std::max(variable.m_Shape.size(), variable.m_Count.size());
+ if (dimSize == 0) {
+ // scalar
+ hid_t filespaceID = H5Screate(H5S_SCALAR);
+ hid_t dsetID = H5Dcreate(m_H5File.m_GroupId, variable.m_Name.c_str(), h5Type, filespaceID,
+ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ herr_t status = H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, values);
+
+ H5Sclose (filespaceID);
+ H5Dclose (dsetID);
+
+ return;
+ }
+
std::vector<hsize_t> dimsf, count, offset;
for (int i = 0; i < dimSize; i++)
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.h b/source/adios2/engine/hdf5/HDF5WriterP.h
index 21151a18ab648cab1b8d389436a13dfb3518c3ef..d4c4d217e4afd56fc392eba8d68acf481febfe7a 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.h
+++ b/source/adios2/engine/hdf5/HDF5WriterP.h
@@ -91,7 +91,7 @@ public:
private:
///< heap capsule, contains data and metadata buffers
- capsule::STLVector m_Buffer;
+ //capsule::STLVector m_Buffer;
void Init();