Merge pull request #133 from guj/hdf5

This fixes #117

examples/heatTransfer/write/IO_ph5.cpp

@@ -34,8 +34,14 @@ 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;
@@ -44,7 +50,7 @@ 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 +65,8 @@ 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 +75,35 @@ 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 +171,10 @@ 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);
-    herr_t status =
-        H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
+    hid_t plistID = H5Pcreate(H5P_DATASET_XFER);
+    H5Pset_dxpl_mpio(plistID, H5FD_MPIO_COLLECTIVE);
+
+    herr_t status = H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, plistID, data);
 
     H5Sclose(filespaceID);
     H5Dclose(dsetID);
@@ -183,6 +218,57 @@ 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 +310,19 @@ 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);
 

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