[MOAB-dev] r5298 - in MOAB/trunk: . src src/io src/moab src/parallel test test/parallel

[tautges at mcs.anl.gov]

Author: tautges
Date: 2012-01-10 03:59:12 -0600 (Tue, 10 Jan 2012)
New Revision: 5298

Added:
   MOAB/trunk/src/io/WriteDamsel.cpp
   MOAB/trunk/src/io/WriteDamsel.hpp
   MOAB/trunk/src/moab/Error.hpp
   MOAB/trunk/test/coords_connect_iterate.cpp
Removed:
   MOAB/trunk/src/Error.hpp
Modified:
   MOAB/trunk/RELEASE_NOTES
   MOAB/trunk/configure.ac
   MOAB/trunk/src/AEntityFactory.cpp
   MOAB/trunk/src/BitTag.cpp
   MOAB/trunk/src/Core.cpp
   MOAB/trunk/src/DenseTag.cpp
   MOAB/trunk/src/DenseTag.hpp
   MOAB/trunk/src/Makefile.am
   MOAB/trunk/src/MeshTag.cpp
   MOAB/trunk/src/ReadUtil.cpp
   MOAB/trunk/src/ReaderWriterSet.cpp
   MOAB/trunk/src/SequenceManager.cpp
   MOAB/trunk/src/SetIterator.cpp
   MOAB/trunk/src/SparseTag.cpp
   MOAB/trunk/src/TagInfo.cpp
   MOAB/trunk/src/TypeSequenceManager.cpp
   MOAB/trunk/src/VarLenDenseTag.cpp
   MOAB/trunk/src/VarLenSparseTag.cpp
   MOAB/trunk/src/WriteUtil.cpp
   MOAB/trunk/src/WriteUtil.hpp
   MOAB/trunk/src/io/Makefile.am
   MOAB/trunk/src/moab/Core.hpp
   MOAB/trunk/src/moab/Interface.hpp
   MOAB/trunk/src/moab/WriteUtilIface.hpp
   MOAB/trunk/src/parallel/ParallelComm.cpp
   MOAB/trunk/src/parallel/ReadParallel.cpp
   MOAB/trunk/src/parallel/ReadParallel.hpp
   MOAB/trunk/test/MBTest.cpp
   MOAB/trunk/test/Makefile.am
   MOAB/trunk/test/TestTypeSequenceManager.cpp
   MOAB/trunk/test/parallel/mbparallelcomm_test.cpp
Log:
2 big additions: 
1) adding coords_iterate and connect_iterate, which allow direct access
to coordinate and connectivity arrays for blocks of entity handles, similar to tag_iterate
providing access to dense tag memory.  

2) And, adding initial implementation of Damsel writer, supporting a project on parallel I/O.
This isn't actually instantiated anywhere, but at least it compiles (if you have the damsel.h
being developed for the Damsel API).

This commit also moves access to Error class to query_interface.

The ..._iterate functions are tested in coords_connect_iterate auto test.

Specific changes:
- implementing another interface available through Interface::query_interface, for Error object
associated with instance; allows reporting of errors through Interface's error handling
- in Core::delete_entities(EntityHandle*, ...), implemented this function on the array in order,
instead of putting the entities into a range and calling range-based variant; when entity array
contains e.g. hexes and vertices used by those hexes, this function failed, because actually deleting
entities is deferred until after the call to AEntityFactory::update_adjacencies, which itself fails
for vertices if there are still entities that use them.
- implemented WriteUtil::gather_entities, which basically gathers all entities in the model or
entity set array and puts them in a range
- implemented DenseTag::get_array(EntitySequence*, ...), which gets read-only tag storage for a whole sequence,
instead of for specific handle
- removed function Core::get_error_handler(), since that's now accessed through query_interface

Passes make check in serial and parallel.



Modified: MOAB/trunk/RELEASE_NOTES
===================================================================
--- MOAB/trunk/RELEASE_NOTES	2012-01-06 22:09:11 UTC (rev 5297)
+++ MOAB/trunk/RELEASE_NOTES	2012-01-10 09:59:12 UTC (rev 5298)
@@ -1,8 +1,10 @@
 Version 4.5: (in progress)
 * ITAPS: added iMesh_stepIter, iMesh_tagIterate, iMesh_createTagWithOptions (see iMesh_extensions.h)
 * More partitioning options for structured mesh (see ScdInterface::compute_partition functions, and doc/metadata_info.doc)
+* Error class exposed in API, and query_interface now supports getting access to the moab::Core member of that class.
+* Added Interface::coords_iterate and Interface::connect_iterate, analogous to tag_iterate (allows direct access to
+  coordinate and connectivity memory for blocks of entity handles)
 
-
 Version 4.1:
 * Structured mesh API (see src/moab/ScdInterface.hpp)
 * Parallel read of netcdf-based .nc files using pnetcdf (see doc/metadata_info.pdf)

Modified: MOAB/trunk/configure.ac
===================================================================
--- MOAB/trunk/configure.ac	2012-01-06 22:09:11 UTC (rev 5297)
+++ MOAB/trunk/configure.ac	2012-01-10 09:59:12 UTC (rev 5298)
@@ -402,6 +402,23 @@
 
 
 ################################################################################
+#                             DAMSEL OPTIONS
+################################################################################
+
+old_LDFLAGS="$LDFLAGS"
+LDFLAGS="$LDFLAGS $HDF5_LDFLAGS"
+FATHOM_CHECK_DAMSEL
+LDFLAGS="$old_LDFLAGS"
+if test "xno" != "x$HAVE_DAMSEL"; then
+  AM_CPPFLAGS="$AM_CPPFLAGS -DAMSEL_FILE"
+fi
+AM_CONDITIONAL(DAMSEL_FILE, [test "xno" != "x$HAVE_DAMSEL"])
+AM_CPPFLAGS="$DAMSEL_CPPFLAGS $AM_CPPFLAGS"
+EXPORT_LDFLAGS="$DAMSEL_LDFLAGS $EXPORT_LDFLAGS"
+AC_SUBST(DAMSEL_LIBS)
+
+
+################################################################################
 #                             NetCDF OPTIONS
 ################################################################################
 

Modified: MOAB/trunk/src/AEntityFactory.cpp
===================================================================
--- MOAB/trunk/src/AEntityFactory.cpp	2012-01-06 22:09:11 UTC (rev 5297)
+++ MOAB/trunk/src/AEntityFactory.cpp	2012-01-10 09:59:12 UTC (rev 5298)
@@ -19,7 +19,7 @@