new updated

.gitattributes

@@ -520,6 +520,7 @@ test/H5Fed/tetmesh_write.c -text
 test/H5Fed/tetmesh_write1.c -text
 test/H5Fed/tetmesh_write2.c -text
 test/H5Fed/tetmesh_write_tags.c -text
+test/H5Fed/trimesh_2gnuplot.c -text
 test/H5Fed/trimesh_adjacencies.c -text
 test/H5Fed/trimesh_read.c -text
 test/H5Fed/trimesh_write.c -text
@@ -565,6 +566,8 @@ tools/h5hutcc.in -text
 tools/h5pAttrib.cc -text
 tools/h5pToGNUplot.cc -text
 tools/homdynToH5p.cc -text
+tools/vtk2h5grid/Makefile.am -text
+tools/vtk2h5grid/vtk2h5grid.cc -text
 visit_plugins/databases/H5Part/.depend -text
 visit_plugins/databases/H5Part/Makefile -text
 visit_plugins/databases/H5Part/README.txt -text

.gitignore

@@ -77,4 +77,6 @@ test/h5u_test
 tools/.deps
 tools/Makefile
 tools/Makefile.in
+tools/h5PartDcToVtk
+tools/h5PartSurfaceToVtk
 tools/h5hutcc

NEWS

@@ -0,0 +1,407 @@
+#### H5PART 1.99.10 ###########################################################
+
+Bugfixes in the malloc wrappers
+
+Converter from vtk to H5hut added.
+
+Bugfixes in the autotools files.
+
+#### H5PART 1.99.9 ############################################################
+
+Bugfix in option parsing in tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk
+
+tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk removed from list of tools
+to be compiled. These tools should be moved to another repository anyway.
+
+#### H5PART 1.99.8 ############################################################
+
+Bugfixes
+
+#### H5PART 1.99.7 ############################################################
+
+Linking problem on Linux fixed
+
+#### H5PART 1.99.6 ############################################################
+
+
+#### H5PART 1.99.5 ############################################################
+#### H5PART 1.99.4 ############################################################
+#### H5PART 1.99.3 ############################################################
+#### H5PART 1.99.2 ############################################################
+#### H5PART 1.99.1 ############################################################
+#### H5PART 1.99 ############################################################
+
+Renamed type: 
+    H5PartFile -> h5_file_t
+    h5part_int64_t -> h5_int64_t
+
+Renamed functions:
+    
+
+#### H5PART 1.6.6 ############################################################
+
+Fixed typo (Write instead of Read) in the h5bl_3d_read_scalar_field* Fortran
+interface.
+
+Added missing type normalization for int32 type.
+
+Rewrite of h5pAttrib tool.
+
+#### H5PART 1.6.5 ############################################################
+
+Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.
+
+#### H5PART 1.6.4 ############################################################
+
+Fixed bug where H5PartSetViewIndices was not setting an empty view when the
+number of elements is 0.
+
+Set a threshold on the HDF5 alignment parameter so that small metadata writes
+are not aligned, which causes large gaps in the file.
+
+#### H5PART 1.6.3 ############################################################
+
+New build system uses libtool and can build shared libraries.
+
+Fixed a bug that incorrectly identifies the number of selected points in a view
+when using H5PartSetViewIndices.
+
+Fixed bug in Fortran test reported by several people, as well as several
+incorrect views set in the C test that were causing segfaults.
+
+Fixed name mismatches in the Fortran interface, and an off-by-one indexing
+problem.
+
+#### H5PART 1.6.2 ############################################################
+
+Removed H5PartSetViewEmpty
+--------------------------
+
+An empty view can now be selected with:
+H5PartSetNumParticles(file, 0);
+
+Bug Fixes to Attribute Calls in Fortran API
+-------------------------------------------
+
+Fixed a problem where attribute values were reverting to zero.
+
+#### H5PART 1.6.1 ############################################################
+
+Chunking in the H5Part API
+--------------------------
+
+There is now an H5Part equivalent H5PartSetChunkSize to the existing
+H5BlockDefine3DChunkDims call. Both of these calls enable the chunking
+mechanism in the underlying HDF5 layer. Chunking is used in combination
+with the aligned open calls to pad datasets to alignment multiples
+on disk.
+
+All Steps Available on Write
+----------------------------
+
+Previously, existing steps in a file were only accessible in read-only mode.
+Now, all steps are available in all modes, including write-truncate and
+write-append. Thus, it is now possible to overwrite existing data in write
+mode. To help alert the user to this possibility, a warning is issued every
+time an existing dataset is written to. Warnings can be printed by setting
+the verbosity to H5PART_VERB_WARN or higher.
+
+New Throttling Routine
+----------------------
+
+Previously, a throttle factor of N meant that for P processors, the total
+number of P writes were divided into N batches of P/N writes.
+
+To better accommodate round-robin lustre striping, the new policy is to
+execute P/N batches of N writes. Thus, matching N to the number of stripes
+results in the desirable 1-1 matching of writers to stripes.
+
+Other Fixes
+-----------
+
+* The configure script should correctly detect PGI compilers now.
+* There was a small memory leak in the Fortran file open calls.
+* There was a compile error with HDF5 1.6.x due to a missing assignment.
+
+#### H5PART 1.6 ##############################################################
+
+Updated Documentation
+---------------------
+
+The Fortran API has been added to the doxygen documentation. Most entries have
+a reference to their respective C API call.
+
+Regression Test Suite
+---------------------
+
+The test subdirectory has been reorganized to include a systematic series
+of regression tests of common use cases for the API. The goal is to have both
+complete coverage of the API (every call is exercised) and testing of some
+unlikely or unsuspected values and cases.
+
+Currently, the C test covers the entire H5Part API and the Fortran test is
+still in development.
+
+Benchmark Utilities
+-------------------
+
+Two benchmarking utilities, H5PartBench and H5BlockBench, have been added to
+the tools collection. Both require the parallel library and have functionality
+and syntax similar to the IOR benchmark:
+
+  http://sourceforge.net/projects/ior-sio/
+
+File Mode Flags
+---------------
+
+Previously, the only flags used were H5PART_READ, H5PART_WRITE, and
+H5PART_APPEND, and these were mutually exclusive. Additional flags have been
+added to select the underlying virtual file driver (VFD) that HDF5 uses in
+parallel mode and to accommodate the lustre filesystem:
+
+H5PART_VFD_MPIPOSIX (use the MPI-POSIX driver, which bypasses MPI-IO)
+H5PART_VFD_MPIIO_IND (use MPI-IO in independent mode)
+H5PART_FS_LUSTRE (activate H5P tunings for the lustre stripe size)
+
+These flags can be specified using the typical bitwise OR method, e.g.
+
+  char flag = H5PART_WRITE | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE;
+
+will select write mode with these two additional options.
+
+The parallel library now defaults to using the MPI-IO collective mode driver
+(previously it used independent mode). The collective buffering algorithm in
+the Cray XT4/5 environment has been substantially improved in the last year,
+and defaulting to collective mode allows us to take advantage of these
+improvements automatically.
+
+There are also new open calls H5PartOpenAlign and H5PartOpenParallelAlign that
+take an additional 'alignment' value. This value is passed to HDF5 and used to
+pad out objects so that they align to filesystem boundaries. For instance, it
+would make sense to use the stripe size as the alignment value when writing to
+a lustre filesystem.
+
+Unified 'View' Model
+--------------------
+
+Views are now supported in both read and write mode (previously only supported
+in read mode). It is possible to specify non-sensical views: you could for
+instance specify a read view that is larger than the dataset on disk. Or you
+could create a write view that is larger than the data in memory. In those
+cases, you will encounter an error when you try to perform a read or write
+operation on a dataset.
+
+There are two new methods for selecting views. H5PartSetNumParticlesStrided
+selects a view with $n$ particles per processor, but such that the data in
+memory is expected to have a 'stride' factor. For instance, if you have
+particle data with fields $x$ and $y$ and a single array with entries
+$x1,y1,x2,y2...$, then the stride factor is 2. Striding works for both reads
+and writes and only affects the view of memory: individual fields are still
+stored as individual arrays on disk.
+
+The second new method is H5PartSetViewIndices, which allows for point
+selections of datasets. You can pass a list of indices for the points you
+want to select. This is useful, for instance, when interfacing with FastBit
+to perform queries that select a small subset of non-contiguous particles.
+
+Because views are now supported on write, it is possible to write a dataset
+using multiple 'passes' or to leave some values unwritten.
+
+Also, all views are now *inclusive*, so that a view of (0,9) corresponds
+to the 10 items 0, 1, 2, ... 9.
+
+Internal Handling of Dataspaces
+-------------------------------
+
+H5PartSetNumParticles and H5PartSetNumParticlesStrided now share the same
+HDF5 dataspace state in the H5PartFile struct with the calls that modify
+the view (H5PartSetView etc.). Previously, the memory and disk dataspaces
+were regenerated from the view on every read access, which was unnecessary.
+
+Autogeneration of API Calls
+---------------------------
+
+Python scripts have been added to automatically generate read/write call
+variants for different data types.
+
+Renamed Fortran Include
+-----------------------
+
+The automake system no longer greps the *F90.inc files to generate an include
+called 'H5Part.inc'. Instead, the *F90.inc files have been renamed to *.f90,
+and awk is used to generate an 'H5PartF.h' file (the same naming convention
+as in MPI's 'mpif.h').
+
+The change to *.f90 was necessary to facilitate integration of the Fortran
+API into doxygen. Note that the *.f90 files will not compile, nor can they
+be included directly. Simply use
+
+  include 'H5PartF.h'
+
+in your Fortran code to include all the definitions for Fortran H5Part/H5Block
+calls.
+
+64 Char Limit on Dataset Names
+------------------------------
+
+Previously, a user could overrun internal buffers for dataset names. Now, a
+fixed limit of 64 chars is imposed. Dataset names that are longer than this are
+truncated and a warning is printed. We expect that most users are using
+short canonical names like x, px, id, etc.
+
+Changes to Existing API
+-----------------------
+
+The H5BlockGetFieldInfo and H5BlockGetFieldInfoByName calls now both include
+a parameter for the 'type' of the field.
+
+
+#### H5PART 1.4 ##############################################################
+
+Error Handling
+--------------
+ Now all functions, in which an error could occure, are returning a
+value. This value is either a 64bit integer or a pointer.
+
+ A negative 64bit integer as result indicates an error. Values >= 0
+indicates successfull execution.   This is similiar to the convention
+used in UNIX system calls, but we do not return -1 but the error
+number (which is always negative).
+
+ For functions returning a pointer the NULL-pointer is used to indicate
+an error. You can call the function H5PartGetErrno() to get the error
+number.  For the time being there is no strerror(3) or perror(3)
+equivalent. 
+
+
+API Changes
+-----------
+ There are several changes in the API of H5Part. The biggest change is
+a side-effect of the implementation of strict error handling.  The
+impact to the existing C/C++ code is very small.  But now you *can*
+and *should* implement some kind of error handling.  The simplest
+error handling is to set an error handler which aborts the program as
+soon as an error occured.
+
+ The next "biggest" change is the use of H5Part types instead of "long
+long" and "double". The replacement of "long long" is "h5part_int64_t"
+and for "double" "h5part_float64_t". This change has now effect in
+Fortran.  
+
+ In some functions the argument type changed from "int" to
+"h5part_int64_t". Since on most systems "int" is a 32bit integer,
+calls to these functions must be adapted to the new API. In C/C++ the
+compiler will complain about it. But in Fortran you will *not* get an
+error message.So, you must check your Fortran code carefully.
+
+ Changes in detail (not listed are functions where only the return
+type changed from any to "h5part_int64_t"):
+
+	New API					Changes to old API
+
+	h5part_int64_t				void
+	H5PartSetNumParticles (
+		H5PartFile *f,
+		h5part_int64_t nparticles	long long
+		);
+
+	h5part_int64_t				int
+	H5PartWriteDataFloat64 (
+		H5PartFile *f,
+		char *name, 
+		h5part_float64_t *dta		double
+		);
+
+	h5part_int64_t				int
+	H5PartWriteDataInt64 (
+		H5PartFile *f,
+		char *name,
+		h5part_int64_t *dta		long long
+		);
+
+	h5part_int64_t				void
+	H5PartSetStep (
+		H5PartFile *f,
+		h5part_int64_t step		int
+		);
+
+	h5part_int64_t				void
+	H5PartSetView (
+		H5PartFile *f,
+		h5part_int64_t start,		long long
+		h5part_int64_t end		long long
+		);
+
+	h5part_int64_t				int
+	H5PartGetView (
+		H5PartFile *f,
+		h5part_int64_t *start,		long long
+		h5part_int64_t *end		long long
+		);
+
+	h5part_int64_t				int
+	H5PartReadDataFloat64 (
+		H5PartFile *f,
+		char *name,
+		h5part_float64_t *dta		double
+		);
+
+	h5part_int64_t				int
+	H5PartReadDataInt64 (
+		H5PartFile *f,
+		char *name,
+		h5part_int64_t *dta		long long
+		);
+    
+	h5part_int64_t				void
+	H5PartReadParticleStep (		
+		H5PartFile *f,
+		h5part_int64_t step,		int
+		h5part_float64_t *x,		double
+		h5part_float64_t *y,		double
+		h5part_float64_t *z,		double
+		h5part_float64_t *px,		double
+		h5part_float64_t *py,		double
+		h5part_float64_t *pz,		double
+		h5part_int64_t *id		long long
+		);
+
+New functions:
+
+	h5part_int64_t
+	H5PartSetVerbosityLevel (
+		unsigned int
+		);
+
+	h5part_int64_t
+	H5PartSetErrorHandler ( 
+		h5part_error_handler handler
+		);
+
+	h5part_int64_t
+	H5PartGetErrno (
+		void
+		);
+
+	h5part_int64_t
+	H5PartDefaultErrorHandler (
+		const char *funcname,
+		const h5part_int64_t eno,
+		const char *fmt,
+		...
+		);
+
+	h5part_int64_t
+	H5PartAbortErrorHandler (
+		const char *funcname,
+		const h5part_int64_t eno,
+		const char *fmt,
+		...
+		);
+
+Removed functions:
+
+	int
+	H5PartFileIsValid (
+		H5PartFile *f
+		);

configure.ac

@@ -49,6 +49,13 @@ AC_ARG_ENABLE(
 	[Compile the MPI/IO interface [default=no]])],
 	[USE_PARALLEL=$enableval])
 
+AC_ARG_ENABLE(
+	[vtkconverter],
+	[AS_HELP_STRING([--enable-vtkconverter],
+	[Compile the vtk to H5hut converter for grids [default=no]])],
+	[ENABLE_VTKCONVERTER=$enableval])
+AM_CONDITIONAL([ENABLE_VTKCONVERTER], [test "$ENABLE_VTKCONVERTER" = "yes"])
+
 AC_ARG_WITH(
 	[hdf5],
 	[AC_HELP_STRING([--with-hdf5],
@@ -67,6 +74,12 @@ AC_ARG_WITH(
 	[path to lustre user API [default=""]])],
 	[LUSTREPATH=$withval], [LUSTREPATH=""])
 
+AC_ARG_WITH(
+	[vtk],
+	[AS_HELP_STRING([--with-vtk],
+	[path to VTK installation [default=""]])],
+	[VTK_PREFIX=$withval], [VTK_PREFIX=""])
+
 ###############################################################################
 ############### PATH SERACH FUNCTION - to be used later... ####################
 ###############################################################################
@@ -108,6 +121,16 @@ AC_CANONICAL_HOST
 
 AC_PROG_MAKE_SET
 
+AC_MSG_CHECKING([if debug is enabled])
+
+if test "X$USE_DEBUG" = "Xyes"; then
+    AC_MSG_RESULT([yes])
+    CFLAGS="$CFLAGS -g"
+    FFLAGS="$FFLAGS -g"
+else
+    AC_MSG_RESULT([no])
+fi
+
 # Determine a C/C++ compiler to use. 
 # If CC is not already set in the environment, check for gcc and cc, then
 # for other C compilers. 
@@ -181,16 +204,6 @@ AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
 ######################## CONFIGURE LINE OPTIONS ###############################
 ###############################################################################
 
-AC_MSG_CHECKING([if debug is enabled])
-
-if test "X$USE_DEBUG" = "Xyes"; then
-    AC_MSG_RESULT([yes])
-    CFLAGS="$CFLAGS -g"
-    FFLAGS="$FFLAGS -g"
-else
-    AC_MSG_RESULT([no])
-fi
-
 ############################ fortran enabled ##################################
 AC_MSG_CHECKING([if C interface enabled])
 if test "X$USE_C" = "Xyes"; then
@@ -199,7 +212,7 @@ if test "X$USE_C" = "Xyes"; then
 	LIB_C="libH5hutC.la"
 	BUILD_LIBS="$BUILD_LIBS libH5hutC"
 	BUILD_TESTS="$BUILD_TESTS h5u_test h5b_test"
-	BUILD_TOOLS="$BUILD_TOOLS h5hutcc h5PartDcToVtk h5PartSurfaceToVtk"
+	BUILD_TOOLS="$BUILD_TOOLS h5hutcc"
 fi
 
 ############################ fortran enabled ##################################
@@ -320,7 +333,7 @@ if test -z "$HDF5ROOT"; then
 	exit 1
 fi
 
-INCLUDES="$INCLUDES -I$HDF5ROOT/include"
+AM_CPPFLAGS="$AM_CPPFLAGS -I$HDF5ROOT/include"
 LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
 LIBS="$LIBS -lhdf5"
 
@@ -357,13 +370,23 @@ if test -z "$LUSTREROOT"; then
 	AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
 else
         CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
-        INCLUDES="$INCLUDES -I$LUSTREROOT/usr/include"
+        AM_CPPFLAGS=="$AM_CPPFLAGS -I$LUSTREROOT/usr/include"
         LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
         LIBS="$LIBS -llustreapi"
 fi
 
 LIBS="$LIBS -lz -lm"
 
+###############################################################################
+# TOOLS
+AC_MSG_CHECKING([if we have to compile the VTK to H5hut grid converter])
+if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
+	AC_MSG_RESULT([yes])
+        # :TODO: add test whether we can compile/link a prog with vtk
+else
+	AC_MSG_RESULT([no])
+fi
+
 ###############################################################################
 ############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
 ###############################################################################
@@ -378,7 +401,7 @@ AC_SUBST(HDF5ROOT)
 AC_SUBST(LUSTREROOT)
 AC_SUBST(CFLAGS)
 AC_SUBST(FFLAGS)
-AC_SUBST(INCLUDES)
+AC_SUBST(AM_CPPFLAGS)
 AC_SUBST(LDFLAGS)
 AC_SUBST(LIBS)
 AC_SUBST(UNDERSCORE_H)
@@ -400,6 +423,7 @@ AC_CONFIG_FILES([
         test/H5Fed/Makefile
 	tools/Makefile
 	tools/h5hutcc
+        tools/vtk2h5grid/Makefile
 ])
 
 AC_OUTPUT

src/C++/Makefile.am

@@ -3,7 +3,7 @@ CC = @CC@
 CXX = @CXX@
 
 LIBS = @LIBS@
-INCLUDES = -I../include @INCLUDES@
+AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
 
 OBJEXT = o
 

src/C/Makefile.am

@@ -2,7 +2,7 @@
 
 OBJEXT=o
 
-INCLUDES = -I../include @INCLUDES@
+AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
 
 # What to build... Will be determined by configure script.
 lib_LTLIBRARIES = @LIB_C@

src/Fortran/H5Block_F.c

@@ -116,7 +116,9 @@ h5bl_3d_getview (
 		      k_start, k_end);
 	H5_API_RETURN (h5b_3d_get_view (
 			       fh,
-			       i_start, i_end, j_start, j_end, k_start, k_end ));
+			       (h5_size_t*)i_start, (h5_size_t*)i_end,
+			       (h5_size_t*)j_start, (h5_size_t*)j_end,
+			       (h5_size_t*)k_start, (h5_size_t*)k_end ));
 }
 
 h5_err_t
@@ -142,7 +144,9 @@ h5bl_3d_getreducedview (
 		      k_start, k_end);
 	H5_API_RETURN(h5b_3d_get_reduced_view (
 		fh,
-		i_start, i_end, j_start, j_end, k_start, k_end ));
+		(h5_size_t*)i_start, (h5_size_t*)i_end,
+		(h5_size_t*)j_start, (h5_size_t*)j_end,
+		(h5_size_t*)k_start, (h5_size_t*)k_end ));
 }
 
 h5_int64_t

src/Fortran/H5Part_F.c

@@ -155,14 +155,14 @@ h5pt_setview (
 h5_err_t
 h5pt_setview_indices (
 	const h5_int64_t *f,
-	const h5_int64_t *indices,
+	const h5_int64_t * const indices,
 	const h5_int64_t *nelem
 	) {
 
 	h5_file_t *fh = h5_filehandlefor2c(f);
 	H5_API_ENTER (h5_err_t, "f=%p, indices=%p, nelem=%lld",
 				fh, indices, (long long)*nelem);
-	H5_API_RETURN(h5u_set_view_indices ( fh, indices, *nelem ));
+	H5_API_RETURN(h5u_set_view_indices ( fh, (const h5_size_t*const)indices, *nelem ));
 }
 
 h5_err_t

src/Fortran/H5_F.c

@@ -51,25 +51,6 @@
 
 #endif
 
-static h5_int32_t
-_flagsfor2c (
-	char * flags
-	) {
-
-	h5_int32_t fbits = 0x00;
-
-	flags = strtok ( flags, "," );
-	while ( flags != NULL ) {
-		if ( strcmp ( flags, "vfd_mpiposix" ) == 0 )
-				fbits |= H5_VFD_MPIPOSIX;
-		else if ( strcmp ( flags, "vfd_independent" ) == 0 )
-				fbits |= H5_VFD_INDEPENDENT;
-		flags = strtok ( NULL, "," );
-	}
-
-	return fbits;
-}
-
 /* open/close interface */
 h5_err_t
 h5_openr (
@@ -79,7 +60,7 @@ h5_openr (
 
 	H5_API_ENTER (h5_err_t, "name='%s', l_name=%d", name, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_file_t* f = h5_open_file ( name2, H5_O_RDONLY, 0 );
+	h5_file_t* f = h5_open_file ( name2, H5_O_RDONLY, 0, 0 );
 	free ( name2 );
 	H5_API_RETURN((h5_int64_t)(size_t)f);
 }
@@ -92,7 +73,7 @@ h5_openw (
 
 	H5_API_ENTER (h5_err_t, "name='%s', l_name=%d", name, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_file_t* f = h5_open_file ( name2, H5_O_WRONLY, 0 );
+	h5_file_t* f = h5_open_file ( name2, H5_O_WRONLY, 0, 0 );
 	free ( name2 );
 	H5_API_RETURN((h5_int64_t)(size_t)f);
 }
@@ -105,7 +86,7 @@ h5pt_opena (
 
 	H5_API_ENTER (h5_err_t, "name='%s', l_name=%d", name, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_file_t* f = h5_open_file ( name2, H5_O_APPEND, 0 );
+	h5_file_t* f = h5_open_file ( name2, H5_O_APPEND, 0, 0 );
 	free ( name2 );
 	H5_API_RETURN((h5_int64_t)(size_t)f);
 }

src/Fortran/Makefile.am

@@ -2,7 +2,7 @@
 
 OBJEXT=o
 
-INCLUDES = -I../include @INCLUDES@
+AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
 
 F90_FILES =     	H5.f90 \
 			H5_attribs.f90 \

src/h5core/Makefile.am

@@ -2,7 +2,7 @@
 
 OBJEXT=o
 
-INCLUDES = -I../include @INCLUDES@
+AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
 
 EXTRA_HEADERS =					\
 	../include/h5core/h5_attach.h		\

src/h5core/h5_attach.c

@@ -274,7 +274,7 @@ h5_get_attachment (
 	// write file
 	if (f->myproc == 0) {
 		int fd;
-		if ((fd = open (fname, O_WRONLY|O_CREAT|O_TRUNC)) < 0) {
+		if ((fd = open (fname, O_WRONLY|O_CREAT|O_TRUNC, 0600)) < 0) {
 			H5_CORE_API_LEAVE (
 				h5_error (
 					H5_ERR_H5,

src/h5core/h5t_retrieve.c

@@ -310,3 +310,22 @@ h5t_get_vertex_coords_by_id (
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
 
+h5_err_t
+h5t_get_neighbor_indices (
+	h5t_mesh_t* const m,
+	h5_loc_id_t entity_id,
+	h5_loc_idx_t* neighbor_indices
+	) {
+	H5_CORE_API_ENTER (h5_err_t,
+			   "m=%p, entity_id=%llu, neighbor_indices=%p",
+			   m,
+			   (long long unsigned)entity_id,
+			   neighbor_indices);
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (entity_id);
+	h5_loc_idx_t* indices = h5tpriv_get_loc_elem_neighbor_indices (m, elem_idx);
+	int num_facets = h5tpriv_ref_elem_get_num_facets (m);
+	for (int i = 0; i < num_facets; i++) {
+		neighbor_indices[i] = indices[i];
+	}
+	H5_CORE_API_RETURN (H5_SUCCESS);
+}

src/h5core/h5t_store.c

@@ -245,6 +245,9 @@ h5t_end_store_elems (
 	H5_CORE_API_ENTER (h5_err_t, "m=%p", m);
 
 	m->num_elems[m->leaf_level] = m->last_stored_eid+1;
+        if (m->leaf_level == 0) {
+                m->num_leaf_elems[0] = m->num_elems[0];
+        }
 
 	/* assign global indices to new indices */
 	TRY (assign_glb_elem_indices (m));

src/include/H5Fed_retrieve.h

@@ -173,6 +173,19 @@ H5FedGetVertexIndicesOfEntity (
 	H5_API_RETURN (h5t_get_vertex_indices_of_entity (m, entity_id, vertex_indices));
 }
 
+static inline h5_err_t
+H5FedGetNeighborIndicesOfElement (
+	h5t_mesh_t* const m,
+	h5_loc_id_t entity_id,
+	h5_loc_idx_t* neighbor_indices
+	) {
+	H5_API_ENTER (h5_err_t,
+		      "m=%p, entity_id=%lld, neighbor_indices=%p",
+		      m, (long long)entity_id, neighbor_indices);
+	H5_API_RETURN (h5t_get_neighbor_indices (m, entity_id, neighbor_indices));
+}
+
+
 #ifdef __cplusplus
 }
 #endif

src/include/h5core/h5_syscall.h

@@ -19,11 +19,11 @@ h5_alloc (
 	void* ptr,
 	const size_t size
 	) {
-	MALLOC_WRAPPER_ENTER (void_p, "ptr=%p, size=%lu", ptr, size); 
+	MALLOC_WRAPPER_ENTER (void_p, "ptr=%p, size=%zu", ptr, size); 
 	ptr = realloc (ptr, size);
 	if (ptr == NULL) {
 		MALLOC_WRAPPER_LEAVE (
-			(void_p)h5_error (H5_ERR_NOMEM, "Out of memory."));
+			(void_p)(uintptr_t)h5_error (H5_ERR_NOMEM, "Out of memory."));
 	}
 	MALLOC_WRAPPER_RETURN (ptr);
 }
@@ -37,7 +37,7 @@ h5_calloc (
 	void* ptr = calloc (count, size);
 	if (ptr == NULL) {
 		MALLOC_WRAPPER_LEAVE (
-			(void_p)h5_error (H5_ERR_NOMEM, "Out of memory."));
+			(void_p)(uintptr_t)h5_error (H5_ERR_NOMEM, "Out of memory."));
 	}
 	MALLOC_WRAPPER_RETURN (ptr);
 }
@@ -62,7 +62,7 @@ h5_strdup (
 	char_p s2 = (char_p)h5_calloc (1, strlen (s1)+1 );
 	if (s2 == NULL) {
 		MALLOC_WRAPPER_LEAVE (
-			(char_p)h5_error (H5_ERR_NOMEM, "Out of memory."));
+			(char_p)(uintptr_t)h5_error (H5_ERR_NOMEM, "Out of memory."));
 	}
 	MALLOC_WRAPPER_RETURN (strcpy (s2, s1));
 }

src/include/h5core/h5t_retrieve.h

@@ -78,6 +78,8 @@ h5t_get_vertex_coords_by_index (h5t_mesh_t* const, h5_loc_idx_t, h5_float64_t[3]
 h5_err_t
 h5t_get_vertex_coords_by_id (h5t_mesh_t* const, h5_loc_id_t, h5_float64_t[3]);
 
+h5_err_t
+h5t_get_neighbor_indices (h5t_mesh_t* const, h5_loc_id_t, h5_loc_idx_t*);
 #ifdef __cplusplus
 }
 #endif

test/H5Fed/Makefile.am

@@ -4,7 +4,7 @@ OBJEXT = o
 
 AM_LDFLAGS = -L../../src/lib @LDFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@
-INCLUDES = -I../../src/include @INCLUDES@
+AM_CPPFLAGS = -I../../src/include @AM_CPPFLAGS@
 
 noinst_PROGRAMS =				\
 		tetmesh_write			\
@@ -16,6 +16,7 @@ noinst_PROGRAMS =				\
 		tetmesh_read_tags		\
 		trimesh_read			\
 		trimesh_write			\
+		trimesh_2gnuplot		\
 		trimesh_adjacencies		\
 		trimesh_write_dunetest
 
@@ -28,12 +29,13 @@ EXTRA_DIST =					\
 		tetmesh_read.c			\
 		tetmesh_read_tags.c		\
 		tetmesh_write.c			\
-		tetmesh_write1.c			\
+		tetmesh_write1.c		\
 		tetmesh_write2.c		\
 		tetmesh_write_tags.c		\
 		trimesh_adjacencies.c		\
 		trimesh_read.c			\
 		trimesh_write.c			\
+		trimesh_2gnuplot.c		\
 		trimesh_write_dunetest.c
 
 #		map_tet2globalid.c \

test/H5Fed/trimesh_2gnuplot.c

@@ -0,0 +1,101 @@
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "H5hut.h"
+#if defined (PARALLEL_IO)
+#include <mpi.h>
+#endif
+
+#define H5FedGetNumLeafElementsTotal H5FedGetNumElementsTotal
+/*
+  Traverse elements and output coordinates
+ */
+static h5_err_t
+traverse_elems (
+	h5t_mesh_t* const m
+	) {
+	/* get number of elements we have to expect */
+	h5_size_t num_elems_expect = H5FedGetNumLeafElementsTotal (m);
+
+	/* get iterator for co-dim 0 */
+	h5t_iterator_t* iter = H5FedBeginTraverseEntities (m, 0);
+
+	/* iterate over all co-dim 0 entities, i.e. elements */
+	h5_loc_id_t local_id;
+	h5_size_t num_elems = 0;
+	while ((local_id = H5FedTraverseEntities (iter)) >= 0) {
+		h5_loc_id_t local_vids[4];
+		H5FedGetVertexIndicesOfEntity (m, local_id, local_vids);
+
+		printf ("# cell %llx\n", (long long unsigned)local_id );
+		h5_float64_t P[3];
+		for (int i = 0; i < 3; i++) {
+			H5FedGetVertexCoordsByIndex (m, local_vids[i], P);
+			printf (" %8.6f %8.6f\n", P[0], P[1]);
+		}
+		H5FedGetVertexCoordsByIndex (m, local_vids[0], P);
+		printf (" %8.6f %8.6f\n", P[0], P[1]);
+		printf ("\n");
+		num_elems++;
+	}
+
+	/* done */
+	H5FedEndTraverseEntities (iter);
+
+	/* report error if we got a different number then expected */
+	if (num_elems != num_elems_expect) {
+		fprintf (stderr, "!!! Got %lld elements, but expected %lld.\n",
+			 (long long)num_elems, (long long)num_elems_expect);
+		exit(1);
+	}
+	return H5_SUCCESS;
+}
+
+int
+main (
+	int argc,
+	char* argv[]
+	) {
+
+#if defined (PARALLEL_IO)
+	MPI_Comm comm = MPI_COMM_WORLD;
+	MPI_Init (&argc, &argv);
+#else
+	MPI_Comm comm = 0;
+#endif
+	if (argc < 2 || argc > 3) {
+		fprintf (stderr, "Usage: %s FILE [LEVEL]\n", argv[0]);
+		exit (42);
+	}
+
+	/* abort program on error, so we don't have to handle them */
+	H5SetErrorHandler (H5AbortErrorhandler);
+	H5SetVerbosityLevel (0);
+
+	/* open file and get number of meshes */
+	h5_file_t* f = H5OpenFile (argv[1], H5_O_RDONLY, comm);
+	h5t_mesh_t*  m;
+	H5FedOpenTriangleMeshByIndex (f, 0, &m);
+	int num_levels = H5FedGetNumLevels (m);
+	int level = num_levels-1;
+	if (argc >= 3) {
+		level = atoi (argv[2]);
+	}
+	if (level >= num_levels || level < 0) {
+		fprintf (stderr, "level %d out of range\n", level);
+		goto done;
+	}
+	H5FedSetLevel (m, level);
+	traverse_elems (m);
+
+
+done:
+	H5FedCloseMesh (m);
+	H5CloseFile (f);
+
+#if defined (PARALLEL_IO)
+	MPI_Finalize ();
+#endif
+
+	return 0;
+}

test/Makefile.am

@@ -5,7 +5,7 @@ SUBDIRS = H5Fed
 
 OBJEXT=o
 
-INCLUDES = -I../src/include @INCLUDES@
+AM_CPPFLAGS = -I../src/include @AM_CPPFLAGS@
 
 noinst_PROGRAMS = @BUILD_TESTS@
 

tools/Makefile.am

@@ -1,11 +1,15 @@
 # tools level Makefile.am
 
-OBJEXT=o
+SUBDIRS =
+
+if ENABLE_VTKCONVERTER
+SUBDIRS +=	vtk2h5grid
+endif
 
 AM_LDFLAGS = -L../src/lib @LDFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@
 
-INCLUDES = -I../src/include @INCLUDES@
+AM_CPPFLAGS = -I../src/include @AM_CPPFLAGS@
 
 # What to build... make install will place these files in the $(prefix)/bin directory.
 bin_PROGRAMS = @BUILD_TOOLS@

tools/h5PartDcToVtk.cc

@@ -167,7 +167,7 @@ int get_option(int argc, const char **argv, const char *opts, const struct long_
     }
   else
     {
-      register char *cp;    /* pointer into current token */
+      register const char *cp;    /* pointer into current token */
 
       /* short command line option */
       opt_opt = argv[opt_ind][sp];
@@ -312,7 +312,7 @@ int main(int argc, const char *argv[])
    
   string ifn = string(input_name) + string(".h5");
 
-  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, NULL);
+  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, 0);
    
   if( h5file == NULL ) {
     fprintf(stdout, "unable to open file %s\n", input_name);

tools/h5PartSurfaceToVtk.cc

@@ -176,7 +176,7 @@ int get_option(int argc, const char **argv, const char *opts, const struct long_
     }
   else
     {
-      register char *cp;    /* pointer into current token */
+      register const char *cp;    /* pointer into current token */
 
       /* short command line option */
       opt_opt = argv[opt_ind][sp];
@@ -336,7 +336,7 @@ int main(int argc, const char *argv[])
    
   string ifn = string(input_name) + string(".h5");
    
-  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, NULL);
+  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, 0);
      
   if( h5file == NULL ) {
     fprintf(stdout, "unable to open file %s\n", input_name);

tools/vtk2h5grid/Makefile.am

@@ -0,0 +1,16 @@
+AM_CPPFLAGS = -I${abs_top_builddir}/src/include -Wno-deprecated
+FFLAGS += -cpp $(AM_CPPFLAGS)
+LDFLAGS += -L${abs_top_builddir}/src/lib
+
+LDADD = 
+
+LDADD += -lH5hut -lH5hutC -lvtkCommon -lvtkIO
+
+
+bin_PROGRAMS = 
+
+bin_PROGRAMS += vtk2h5grid
+vtk2h5grid_SOURCES = vtk2h5grid.cc
+
+distclean-local:
+	$(RM) *~

tools/vtk2h5grid/vtk2h5grid.cc

@@ -0,0 +1,204 @@
+#include <sys/stat.h>
+#include <stdio.h>
+#include <stdarg.h>
+#include <getopt.h>
+#include <errno.h>
+
+#include <map>
+
+
+#include <vtkSmartPointer.h>
+#include <vtkExtractEdges.h>
+#include "vtkUnstructuredGrid.h"
+#include "vtkUnstructuredGridReader.h"
+
+#include "H5hut.h"
+
+const char* version = "0.1.0";
+int convert_boundary = 1;
+int convert_volume = 0;
+const struct option longopts[] = {
+        {"version",     no_argument, 0,                 'v'},
+        {"help",        no_argument, 0,                 'h'},
+        {"boundary",    no_argument, &convert_boundary, 1},
+        {"volume",      no_argument, &convert_volume,   1},
+        {"no-boundary", no_argument, &convert_boundary, 0},
+        {"no-volume",   no_argument, &convert_volume,   0},
+        {0,0,0,0},
+};
+
+typedef std::map<int, size_t> IdMap;
+
+static void
+usage (
+        char* cmd
+        ) {
+        std::cout << std::endl << "Usage: " << std::endl;
+        std::cout << "  " << cmd << " [OPTIONS] FILE..." << std::endl << std::endl;
+        std::cout << "Options:" << std::endl;
+        std::cout << "  --(no-)boundary   do (not) convert boundary triangles." << std::endl;
+        std::cout << "                    default is yes" << std::endl;
+        std::cout << "  --(no-)volume     do (not) convert volume mesh." << std::endl;
+        std::cout << "                    default is no" << std::endl;
+        std::cout << std::endl;
+        exit (1);
+}
+
+static void
+print_version (
+        char* cmd
+        ) {
+        std::cout << "Version: " << cmd << " " << version << std::endl;
+        exit (1);
+}
+
+static int
+init (
+        int argc,
+        char* argv[]
+        ) {
+        int index;
+        int iarg = 0;
+
+        //turn off getopt error message
+        opterr = 1; 
+
+        while(iarg != -1) {
+                iarg = getopt_long(argc, argv, "vh?", longopts, &index);
+
+                switch (iarg) {
+                case 'h':
+                case '?':
+                        usage (argv[0]);
+                        break;
+
+                case 'v':
+                        print_version (argv[0]);
+                        break;
+                }
+        }
+        return argc - optind;
+}
+
+void
+convert_vtk2h5grid (
+        vtkUnstructuredGrid* vtk_grid,
+        h5t_mesh_t* h5_grid,
+        int cell_type
+        ) {
+        IdMap idmap;
+        vtkIdType num_vtk_cells = vtk_grid->GetNumberOfCells ();
+        vtkIdType num_vtk_pts = vtk_grid->GetNumberOfPoints ();
+        h5_loc_idx_t (*cells)[4] = new h5_loc_idx_t[num_vtk_cells][4];
+        int h5_cell_idx = 0;
+        int h5_vertex_idx = 0;
+        H5FedBeginStoreVertices (h5_grid, num_vtk_pts);
+        for (vtkIdType vtk_cell_id = 0; vtk_cell_id < num_vtk_cells; vtk_cell_id++) {
+                if (vtk_grid->GetCellType (vtk_cell_id) != cell_type) 
+                        continue;
+                
+                vtkIdType num_pts;
+                vtkIdType* pts;
+                vtk_grid->GetCellPoints (vtk_cell_id, num_pts, pts);
+                for (vtkIdType i = 0; i < num_pts; i++) {
+                        IdMap::iterator it = idmap.find (pts[i]);
+                        if (it == idmap.end ()) {
+                                // add point to H5hut mesh
+                                double pt[3];
+                                vtk_grid->GetPoint (pts[i], pt);
+                                H5FedStoreVertex (h5_grid, -1, pt);
+                                // map pt index in vtk file to pt index in H5hut file
+                                idmap.insert (IdMap::value_type (pts[i], h5_vertex_idx));
+                                cells[h5_cell_idx][i] = h5_vertex_idx++;
+                        } else {
+                                cells[h5_cell_idx][i] = it->second;
+                        }
+                }
+                h5_cell_idx++;
+        }
+        H5FedEndStoreVertices (h5_grid);
+        int num_h5_vertices = h5_vertex_idx;
+        int num_h5_cells = h5_cell_idx;
+        cout << "  number of points in mesh: " << num_h5_vertices << endl;
+        cout << "  number of cells in mesh:  " << num_h5_cells << endl;
+        // add cells to H5hut file
+        H5FedBeginStoreElements (h5_grid, num_h5_cells);
+        for (int i = 0; i < num_h5_cells; i++) {
+                H5FedStoreElement (h5_grid, cells[i]);
+        }
+        H5FedEndStoreElements (h5_grid);
+        delete cells;
+}
+
+h5_err_t
+H5Errorhandler (
+	const char* fmt,
+	va_list ap
+	) {
+	vfprintf (stderr, fmt, ap);
+        exit (42);
+	return -2;
+}
+
+int
+main (
+        int argc,
+        char* argv[]
+        ) {
+
+        argc = init (argc, argv);
+        if (argc == 0) {
+                std::cout << "No file(s) to convert?!" << std::endl;
+                usage (argv[0]);
+        }
+        argv += optind;
+        H5SetErrorHandler (H5Errorhandler);
+        for (int i = 0; i < argc; i++) {
+                std::string vtk_filename = argv[i];
+                std::string h5grid_filename = vtk_filename.substr (0, vtk_filename.find_last_of ('.')) + ".h5";
+                struct stat st;
+                if (stat (vtk_filename.c_str(), &st) < 0) {
+                        perror (vtk_filename.c_str());
+                        exit (1);
+                }
+                if (!(st.st_mode & S_IRUSR)) {
+                        std::cerr << vtk_filename << ": not readable" << std::endl;
+                        exit (1);
+                }
+                if (stat (h5grid_filename.c_str(), &st) == 0) {
+                        std::cerr << h5grid_filename << ": already exits" << std::endl;
+                        exit (1);
+                }
+                if (errno != ENOENT) {
+                        perror (h5grid_filename.c_str());
+                        exit (1);
+                }
+                std::cout << vtk_filename << ": converting ...." << std::endl;
+
+                // read vtk file
+                vtkSmartPointer<vtkUnstructuredGridReader> reader =
+                        vtkSmartPointer<vtkUnstructuredGridReader>::New ();
+                reader->SetFileName (vtk_filename.c_str ());
+                reader->Update ();
+                vtkUnstructuredGrid* vtk_grid = reader->GetOutput ();
+
+                // open new H5hut file
+                h5_file_t* f = H5OpenFile (h5grid_filename.c_str(), H5_O_WRONLY, 0);
+
+                h5t_mesh_t* h5_grid;
+                if (convert_boundary) {
+                        // add boundary mesh
+                        H5FedAddTriangleMesh (f, "0", &h5_grid);
+                        convert_vtk2h5grid (vtk_grid, h5_grid, VTK_TRIANGLE);
+                        H5FedCloseMesh (h5_grid);
+                }
+                if (convert_volume) {
+                        // add volume mesh
+                        H5FedAddTetrahedralMesh (f, "0", &h5_grid);
+                        convert_vtk2h5grid (vtk_grid, h5_grid, VTK_TETRA);
+                        H5FedCloseMesh (h5_grid);
+                }
+                H5CloseFile (f);
+        }
+        return 0;
+}