[MOAB-dev] r4064 - MOAB/trunk/src/io

[kraftche at cae.wisc.edu]

Author: kraftche
Date: 2010-07-21 17:30:04 -0500 (Wed, 21 Jul 2010)
New Revision: 4064

Added:
   MOAB/trunk/src/io/ReadHDF5Dataset.cpp
   MOAB/trunk/src/io/ReadHDF5Dataset.hpp
Modified:
   MOAB/trunk/src/io/Makefile.am
   MOAB/trunk/src/io/ReadHDF5.cpp
   MOAB/trunk/src/io/ReadHDF5.hpp
Log:
use complex hyperslabs to avoid many read calls to HDF5 library for fragmented data

Modified: MOAB/trunk/src/io/Makefile.am
===================================================================
--- MOAB/trunk/src/io/Makefile.am	2010-07-21 22:29:24 UTC (rev 4063)
+++ MOAB/trunk/src/io/Makefile.am	2010-07-21 22:30:04 UTC (rev 4064)
@@ -23,7 +23,12 @@
 
 if HDF5_FILE
   libmoabio_la_LIBADD += mhdf/libmhdf.la
-  MOAB_HDF5_SRCS = ReadHDF5.cpp ReadHDF5.hpp WriteHDF5.cpp WriteHDF5.hpp
+  MOAB_HDF5_SRCS = ReadHDF5.cpp \
+                   ReadHDF5.hpp \
+                   ReadHDF5Dataset.hpp \
+                   ReadHDF5Dataset.cpp \
+                   WriteHDF5.cpp \
+                   WriteHDF5.hpp
   AM_CPPFLAGS += -I$(srcdir)/mhdf/include
 else
   MOAB_HDF5_SRCS = 

Modified: MOAB/trunk/src/io/ReadHDF5.cpp
===================================================================
--- MOAB/trunk/src/io/ReadHDF5.cpp	2010-07-21 22:29:24 UTC (rev 4063)
+++ MOAB/trunk/src/io/ReadHDF5.cpp	2010-07-21 22:30:04 UTC (rev 4064)
@@ -51,6 +51,7 @@
 #include <functional>
 
 #include "IODebugTrack.hpp"
+#include "ReadHDF5Dataset.hpp"
 
 namespace moab {
 
@@ -1031,7 +1032,6 @@
   mhdf_Status status;
   const int dim = fileInfo->nodes.vals_per_ent;
   Range range;
-  IODebugTrack debug_track(debugTrack, "NodeCoords");
   
   if (node_file_ids.empty())
     return MB_SUCCESS;
@@ -1054,79 +1054,54 @@
 
   EntityHandle handle;
   std::vector<double*> arrays(dim);
-  rval = readUtil->get_node_coords( dim, (int)node_file_ids.size(), 0, handle, arrays );
+  const size_t num_nodes = node_file_ids.size();
+  rval = readUtil->get_node_coords( dim, (int)num_nodes, 0, handle, arrays );
   if (MB_SUCCESS != rval)
   {
     mhdf_closeData( filePtr, data_id, &status );
     return error(rval);
   }