From 5198f82b59784e37a34405f60634760b455f7b0e Mon Sep 17 00:00:00 2001
From: guj <jgu@lbl.gov>
Date: Tue, 13 Jun 2017 10:30:07 -0700
Subject: [PATCH] This fixes #117
---
examples/heatTransfer/write/IO_ph5.cpp | 99 ++++++++++++++++++-
.../adios2/toolkit/interop/hdf5/HDF5Common.h | 2 +
2 files changed, 96 insertions(+), 5 deletions(-)
diff --git a/examples/heatTransfer/write/IO_ph5.cpp b/examples/heatTransfer/write/IO_ph5.cpp
index 674b53887..0aa921e58 100644
--- a/examples/heatTransfer/write/IO_ph5.cpp
+++ b/examples/heatTransfer/write/IO_ph5.cpp
@@ -34,9 +34,13 @@ public:
hid_t h5Type, const hsize_t *shape, const hsize_t *offset,
const hsize_t *count);
+ void applyMetadataCacheEviction();
+ void WriteSimpleWithChunking(const std::string &varName, int dimSize, const void *data,
+ hid_t h5Type, const hsize_t *shape, const hsize_t *offset,
+ const hsize_t *count);
int m_CurrentTimeStep;
unsigned int m_TotalTimeSteps;
-
+ bool m_Chunking;
private:
hid_t m_FilePropertyListId;
hid_t m_FileId;
@@ -44,7 +48,7 @@ private:
};
HDF5NativeWriter::HDF5NativeWriter(const std::string &fileName)
-: m_CurrentTimeStep(0), m_TotalTimeSteps(0)
+ : m_CurrentTimeStep(0), m_TotalTimeSteps(0), m_Chunking(false)
{
m_FilePropertyListId = H5Pcreate(H5P_FILE_ACCESS);
@@ -59,6 +63,8 @@ HDF5NativeWriter::HDF5NativeWriter(const std::string &fileName)
throw std::runtime_error("Unable to open " + fileName + " for reading");
}
+ applyMetadataCacheEviction();
+
std::string ts0 = "/TimeStep0";
m_GroupId = H5Gcreate2(m_FileId, ts0.c_str(), H5P_DEFAULT, H5P_DEFAULT,
@@ -67,10 +73,32 @@ HDF5NativeWriter::HDF5NativeWriter(const std::string &fileName)
{
throw std::runtime_error("HDF5: Unable to create group " + ts0);
}
+
+ std::string prefix = "chunking";
+ if(fileName.substr(0, prefix.size()) == prefix) {
+ m_Chunking = true;
+ }
}
HDF5NativeWriter::~HDF5NativeWriter() { Close(); }
+void HDF5NativeWriter::applyMetadataCacheEviction()
+{
+#ifdef NEVER
+ /*
+ see https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2011-February/004201.html
+ John said the code below worked for the paper but not anymore after updates
+ */
+ H5AC_cache_config_t mdc_config;
+ mdc_config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
+ H5Pget_mdc_config(m_FilePropertyListId, &mdc_config);
+ mdc_config.evictions_enabled = 0; // FALSE
+ mdc_config.incr_mode = H5C_incr__off;
+ mdc_config.decr_mode = H5C_decr__off;
+ H5Pset_mdc_config(m_FilePropertyListId, &mdc_config);
+#endif
+}
+
void HDF5NativeWriter::Close()
{
if (m_FileId < 0)
@@ -138,8 +166,11 @@ void HDF5NativeWriter::WriteScalar(const std::string &varName, const void *data,
hid_t filespaceID = H5Screate(H5S_SCALAR);
hid_t dsetID = H5Dcreate(m_GroupId, varName.c_str(), h5Type, filespaceID,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ hid_t plistID = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plistID, H5FD_MPIO_COLLECTIVE);
+
herr_t status =
- H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
+ H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, plistID, data);
H5Sclose(filespaceID);
H5Dclose(dsetID);
@@ -183,6 +214,58 @@ void HDF5NativeWriter::WriteSimple(const std::string &varName, int dimSize,
H5Pclose(plistID);
}
+void HDF5NativeWriter::WriteSimpleWithChunking(const std::string &varName, int dimSize,
+ const void *data, hid_t h5Type,
+ const hsize_t *shape, const hsize_t *offset,
+ const hsize_t *count)
+{
+ CheckWriteGroup();
+ hid_t fileSpace = H5Screate_simple(dimSize, shape, NULL);
+
+ hid_t dsetPid = H5Pcreate(H5P_DATASET_CREATE);
+ H5Pset_chunk(dsetPid, dimSize, count);
+
+ size_t bytes = H5Tget_size (h5Type);
+ for (int i=0; i<dimSize; i++) {
+ bytes *= count[i];
+ }
+ hid_t access_plistid = H5Pcreate(H5P_DATASET_ACCESS);
+ H5Pset_chunk_cache(access_plistid, 101, bytes, 1);
+
+ hid_t dsetID = H5Dcreate(m_GroupId, varName.c_str(), h5Type, fileSpace,
+ H5P_DEFAULT, dsetPid, access_plistid);
+
+ hid_t memSpace = H5Screate_simple(dimSize, count, NULL);
+
+ // Select hyperslab
+ fileSpace = H5Dget_space(dsetID);
+ H5Sselect_hyperslab(fileSpace, H5S_SELECT_SET, offset, NULL, count, NULL);
+
+ // Create property list for collective dataset write.
+
+ hid_t plistID = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plistID, H5FD_MPIO_COLLECTIVE);
+
+ herr_t status;
+
+ status = H5Dwrite(dsetID, h5Type, memSpace, fileSpace, plistID, data);
+
+ if (status < 0)
+ {
+ // error
+ std::cerr << " Write failed. " << std::endl;
+ }
+
+ H5Dclose(dsetID);
+ H5Sclose(fileSpace);
+ H5Sclose(memSpace);
+ H5Pclose(plistID);
+
+ H5Pclose(dsetPid);
+ H5Pclose(access_plistid);
+
+}
+
//
//
std::shared_ptr<HDF5NativeWriter> h5writer;
@@ -224,8 +307,14 @@ void IO::write(int step, const HeatTransfer &ht, const Settings &s,
std::vector<hsize_t> offset = {s.offsx, s.offsy};
std::vector<hsize_t> count = {s.ndx, s.ndy};
- h5writer->WriteSimple("T", 2, ht.data_noghost().data(), H5T_NATIVE_DOUBLE,
- dims.data(), offset.data(), count.data());
+ if (h5writer->m_Chunking) {
+ h5writer->WriteSimpleWithChunking("T", 2, ht.data_noghost().data(), H5T_NATIVE_DOUBLE,
+ dims.data(), offset.data(), count.data());
+ } else {
+ h5writer->WriteSimple("T", 2, ht.data_noghost().data(), H5T_NATIVE_DOUBLE,
+ dims.data(), offset.data(), count.data());
+ }
+
h5writer->WriteScalar("gndy", &(s.gndy), H5T_NATIVE_UINT);
h5writer->WriteScalar("gndx", &(s.gndx), H5T_NATIVE_UINT);
diff --git a/source/adios2/toolkit/interop/hdf5/HDF5Common.h b/source/adios2/toolkit/interop/hdf5/HDF5Common.h
index 84151a2ec..546587a70 100644
--- a/source/adios2/toolkit/interop/hdf5/HDF5Common.h
+++ b/source/adios2/toolkit/interop/hdf5/HDF5Common.h
@@ -20,6 +20,8 @@
#include "adios2/ADIOSTypes.h"
#include "adios2/core/Variable.h"
+#include <stdexcept> // for Intel Compiler
+
namespace adios
{
namespace interop
--
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