From 833ff6fbb4dcc548ede3209485eab49f059f5310 Mon Sep 17 00:00:00 2001
From: guj <jgu@lbl.gov>
Date: Fri, 12 May 2017 14:07:50 -0700
Subject: [PATCH] new heatTransfer IO with adios2/hdf5
---
examples/heatTransfer/write/IO_ph5_adios2.cpp | 18 ++++++-------
source/adios2/engine/hdf5/HDF5WriterP.cpp | 27 ++++++++++---------
source/adios2/engine/hdf5/HDF5WriterP.h | 2 +-
3 files changed, 25 insertions(+), 22 deletions(-)
diff --git a/examples/heatTransfer/write/IO_ph5_adios2.cpp b/examples/heatTransfer/write/IO_ph5_adios2.cpp
index a4b37c5dc..abed29d13 100644
--- a/examples/heatTransfer/write/IO_ph5_adios2.cpp
+++ b/examples/heatTransfer/write/IO_ph5_adios2.cpp
@@ -24,7 +24,7 @@ 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);
+ // adios::ADIOS adios(comm, adios::Verbose::INFO, false);
ad = new adios::ADIOS(comm, adios::Verbose::INFO, false);
// Define method for engine creation
@@ -36,7 +36,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
// 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
+ // Allow an extra thread for data processing
const std::string aggregatorsParam("Aggregators=" +
std::to_string((s.nproc + 1) / 2));
@@ -56,7 +56,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
// 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}));
+ {s.ndx, s.ndy}));
// add transform to variable
// adios::Transform tr = adios::transform::BZIP2( );
@@ -72,7 +72,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
IO::~IO()
{
h5writer->Close();
- //delete ad;
+ // delete ad;
}
void IO::write(int step, const HeatTransfer &ht, const Settings &s,
@@ -86,8 +86,8 @@ void IO::write(int step, const HeatTransfer &ht, const Settings &s,
// 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);
+ // 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
@@ -100,12 +100,12 @@ void IO::write(int step, const HeatTransfer &ht, const Settings &s,
above.
Default memspace is always the full selection.
*/
- //adios::SelectionBoundingBox memspace =
+ // adios::SelectionBoundingBox memspace =
// adios::SelectionBoundingBox({1, 1}, {s.ndx, s.ndy});
- //varT->SetMemorySelection(memspace);
+ // varT->SetMemorySelection(memspace);
h5writer->Write<double>(*varT, ht.data_noghost().data());
- //h5writer->Write(*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);
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.cpp b/source/adios2/engine/hdf5/HDF5WriterP.cpp
index 6969c4a40..acd523fec 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.cpp
+++ b/source/adios2/engine/hdf5/HDF5WriterP.cpp
@@ -23,7 +23,7 @@ HDF5Writer::HDF5Writer(ADIOS &adios, const std::string name,
: Engine(adios, "HDF5Writer", name, accessMode, mpiComm,
method, /*debugMode, cores,*/
" HDF5Writer constructor (or call to ADIOS Open).\n")
- //m_Buffer(m_DebugMode)
+// m_Buffer(m_DebugMode)
{
Init();
}
@@ -256,17 +256,20 @@ 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;
+ 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;
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.h b/source/adios2/engine/hdf5/HDF5WriterP.h
index d4c4d217e..3ab1b970e 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();
--
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