added coordinate attribute to H5Block

.gitattributes

@@ -9,8 +9,6 @@
 /NEWS -text
 /README -text
 /autogen.sh -text
-/config.guess -text
-/config.sub -text
 /configure-crayxt -text
 /configure.ac -text
 /depcomp -text
@@ -79,6 +77,7 @@ test/H5test.cc -text
 test/H5testF.f -text
 test/H5testFpar.F90 -text
 test/Makefile.am -text
+test/coords.F90 -text
 test/params.h -text
 test/read.c -text
 test/test.c -text

.gitignore

@@ -0,0 +1,13 @@
+/Makefile.in
+/aclocal.m4
+/autom4te.cache
+/build
+/config.h.in
+/configure
+doc/Makefile.in
+/ltmain.sh
+/m4
+src/H5PartF.h
+src/Makefile.in
+test/Makefile.in
+tools/Makefile.in

AUTHORS

@@ -8,4 +8,4 @@ John Shalf (NERSC/LBNL)
 Cristina Siegerist (NERSC/LBNL)
 Mark Howison (NERSC/LBNL)
 
-Please use h5part@lists.psi.ch for communicaion.
+Please use h5part@lists.psi.ch for communication.

Makefile.am

@@ -1,5 +1,3 @@
-# Trial by Antino Kim
-# Top level Makefile.am
 ACLOCAL_AMFLAGS=-I m4
 
 SUBDIRS = \

NEWS

@@ -1,3 +1,24 @@
+#### 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.

autogen.sh

@@ -1,54 +1,48 @@
 #!/bin/sh
 # Run this to generate all the initial makefiles, etc.
 
+ACLOCAL_FLAGS="-I m4 $ACLOCAL_FLAGS"
+LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
+AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
+
+LIBTOOLIZE=`which libtoolize`
+if [ "$LIBTOOLIZE" = "" ]; then
+        LIBTOOLIZE=`which glibtoolize`
+fi
+if [ "$LIBTOOLIZE" = "" ]; then
+        echo "libtoolize not found" 1>&2
+        exit 1
+fi
+
 echo "+ making misc files ..."
 touch NEWS README AUTHORS ChangeLog
 echo
-echo
+$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
+	echo "libtoolize failed"
+	exit 1
+}
 echo
 echo "+ running aclocal ..."
 aclocal $ACLOCAL_FLAGS || {
-  echo
+	echo "aclocal failed - check that all needed development files are present on system"
-  echo "aclocal failed - check that all needed development files are present on system"
+	exit 1
-  exit 1
 }
 echo
-echo
-echo
 echo "+ running autoheader ... "
 autoheader || {
-  echo
+	echo "autoheader failed"
-  echo "autoheader failed"
+	exit 1
-  exit 1
 }
 echo
-echo
-echo
-echo "+ running libtoolize ... "
-libtoolize --force || {
-  echo
-  echo "libtoolize failed"
-  exit 1
-}
-echo
-echo
-echo
 echo "+ running autoconf ... "
 autoconf || {
-  echo
+	echo "autoconf failed"
-  echo "autoconf failed"
+	exit 1
-  exit 1
 }
 echo
-echo
-echo
 echo "+ running automake ... "
-automake -a -c --foreign || {
+automake $AUTOMAKE_FLAGS || {
-  echo
+	echo "automake failed"
-  echo "automake failed"
+	exit 1
-  exit 1
 }
-echo
-echo
-echo
 

configure.ac

@@ -1,6 +1,6 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5Part], [1.6.3], [h5part@lists.psi.ch], H5Part)
+AC_INIT([H5Part], [1.6.6], [h5part@lists.psi.ch], H5Part)
 
 # Ensure that a recent enough version of Autoconf is being used. 
 # If the version of Autoconf being used to create configure is earlier than version, 
@@ -54,20 +54,6 @@ AC_ARG_WITH(
 	[path to HDF5 installation [default=""]])],
 	[HDF5PATH=$withval], [HDF5PATH=""])
 
-###############################################################################
-################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-###############################################################################
-
-SAVE_CC=$CC
-SAVE_CXX=$CXX
-SAVE_FC=$FC
-SAVE_CFLAGS=$CFLAGS
-SAVE_CXXFLAGS=$CXXFLAGS
-SAVE_FFLAGS=$FFLAGS
-SAVE_INCLUDES=$INCLUDES
-SAVE_LDFLAGS=$LDFLAGS
-SAVE_LIBS=$LIBS
-
 ###############################################################################
 ############### PATH SERACH FUNCTION - to be used later... ####################
 ###############################################################################
@@ -316,48 +302,6 @@ AC_TYPE_SSIZE_T
 AC_FUNC_MALLOC
 AC_CHECK_FUNCS([memset pow strchr strdup])
 
-
-###############################################################################
-################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-###############################################################################
-
-#if there was an external input for the variable...
-if test -n "$SAVE_CC"; then
-	CC="$SAVE_CC"
-fi
-
-if test -n "$SAVE_CXX"; then
-	CXX="$SAVE_CXX"
-fi
-
-if test -n "$SAVE_FC"; then
-	FC="$SAVE_FC"
-fi
-
-if test -n "$SAVE_CFLAGS"; then
-	CFLAGS="$SAVE_CFLAGS"
-fi
-
-if test -n "$SAVE_CXXFLAGS"; then
-	CFLAGS="$SAVE_CXXFLAGS"
-fi
-
-if test -n "$SAVE_FFLAGS"; then
-	FFLAGS="$SAVE_FFLAGS"
-fi
-
-if test -n "$SAVE_INCLUDES"; then
-	INCLUDES="$SAVE_INCLUDES"
-fi
-
-if test -n "$SAVE_LDFLAGS"; then
-	LDFLAGS="$SAVE_LDFLAGS"
-fi
-
-if test -n "$SAVE_LIBS"; then
-	LIBS="$SAVE_LIBS"
-fi
-
 ###############################################################################
 ############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
 ###############################################################################

doc/Doxyfile

@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 PROJECT_NAME           = H5Part
-PROJECT_NUMBER         = 1.6.1
+PROJECT_NUMBER         = 1.6.6
 OUTPUT_DIRECTORY       = ./ReferencePages
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English

src/H5Block.c

@@ -269,17 +269,16 @@ static h5part_int64_t
 _allgather (
 	const H5PartFile *f		/*!< IN: file handle */
 	) {
-	struct H5BlockPartition *partition = &f->block->user_layout[f->myproc];
 	struct H5BlockPartition *layout = f->block->user_layout;
 
 	MPI_Datatype    partition_m;
 	size_t n = sizeof (struct H5BlockPartition) / sizeof (h5part_int64_t);
 
 	MPI_Type_contiguous ( n, MPI_LONG_LONG, &partition_m );
-	  MPI_Type_commit ( &partition_m );
+	MPI_Type_commit ( &partition_m );
 
-	MPI_Allgather ( partition, 1, partition_m, layout, 1, partition_m,
+	MPI_Allgather ( MPI_IN_PLACE, 0, MPI_DATATYPE_NULL,
-			f->comm );
+			layout, 1, partition_m, f->comm );
 
 	return H5PART_SUCCESS;
 }
@@ -2010,6 +2009,250 @@ H5Block3dSetFieldSpacing (
 		3 );
 }
 
+/*!
+  \ingroup h5block_attrib
+
+  Get the explicit list of X coordinates for field \c field_name in the current
+  time step. The coordinates are read into the 1D array \c coords which has
+  length \c coords_len.
+
+  By convention, the \c coords array should have the same length as the X
+  dimension of the field, and a warning will be printed if they differ.
+
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dGetFieldXCoords(
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	h5part_float64_t *coords,		/*!< OUT: X coordinates */
+	const h5part_int64_t coords_len		/*!< IN: length of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockGetFieldXCoords" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->i_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
+		    (long long)coords_len, (long long)b->i_max + 1);
+
+	return _read_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_XCOORD_NAME,
+		coords );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Set an explicit list of X coordinates for field \c field_name in the current
+  time step. The coordinates are a 1D array of floating point values with
+  dimension \c coords_len.
+
+  By convention, the \c coords array should have the same length as the X
+  dimension of the field, and a warning will be printed if not.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dSetFieldXCoords (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const h5part_float64_t *coords,		/*!< IN: X coordinates */
+	const h5part_int64_t coords_len		/*!< IN: number of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockSetFieldXCoords" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->i_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
+		    (long long)coords_len, (long long)b->i_max + 1);
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_XCOORD_NAME,
+		(const hid_t)H5PART_FLOAT64, 
+		coords,
+		coords_len
+		 );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Get the explicit list of Y coordinates for field \c field_name in the current
+  time step. The coordinates are read into the 1D array \c coords which has
+  length \c coords_len.
+
+  By convention, the \c coords array should have the same length as the Y
+  dimension of the field, and a warning will be printed if they differ.
+
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dGetFieldYCoords(
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	h5part_float64_t *coords,		/*!< OUT: Y coordinates */
+	const h5part_int64_t coords_len		/*!< IN: length of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockGetFieldYCoords" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->j_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match Y dimension (%lld)",
+		    (long long)coords_len, (long long)b->j_max + 1);
+
+	return _read_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_YCOORD_NAME,
+		coords );
+}
+
+
+/*!
+  \ingroup h5block_attrib
+
+  Set an explicit list of Y coordinates for field \c field_name in the current
+  time step. The coordinates are a 1D array of floating point values with
+  dimension \c coords_len.
+
+  By convention, the \c coords array should have the same length as the Y
+  dimension of the field, and a warning will be printed if not.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dSetFieldYCoords (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const h5part_float64_t *coords,		/*!< IN: Y coordinates */
+	const h5part_int64_t coords_len		/*!< IN: number of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockSetFieldYCoords" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->j_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
+		    (long long)coords_len, (long long)b->j_max + 1);
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_YCOORD_NAME,
+		(const hid_t)H5PART_FLOAT64, 
+		coords,
+		coords_len
+		 );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Get the explicit list of Z coordinates for field \c field_name in the current
+  time step. The coordinates are read into the 1D array \c coords which has
+  length \c coords_len.
+
+  By convention, the \c coords array should have the same length as the Z
+  dimension of the field, and a warning will be printed if they differ.
+
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dGetFieldZCoords(
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	h5part_float64_t *coords,		/*!< OUT: Z coordinates */
+	const h5part_int64_t coords_len		/*!< IN: length of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockGetFieldZCoords" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->k_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match Z dimension (%lld)",
+		    (long long)coords_len, (long long)b->k_max + 1);
+
+	return _read_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_ZCOORD_NAME,
+		coords );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Set an explicit list of Z coordinates for field \c field_name in the current
+  time step. The coordinates are a 1D array of floating point values with
+  dimension \c coords_len.
+
+  By convention, the \c coords array should have the same length as the Z
+  dimension of the field, and a warning will be printed if not.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dSetFieldZCoords (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const h5part_float64_t *coords,		/*!< IN: Z coordinates */
+	const h5part_int64_t coords_len		/*!< IN: number of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockSetFieldZCoords" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->k_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
+		    (long long)coords_len, (long long)b->k_max  + 1);
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_ZCOORD_NAME,
+		(const hid_t)H5PART_FLOAT64, 
+		coords,
+		coords_len
+		 );
+}
+
 /*!
   \ingroup h5block_model
 

src/H5Block.f90

@@ -232,4 +232,69 @@ INTEGER*8 FUNCTION h5bl_3d_set_field_origin ( filehandle, name, x, y, z )
     REAL*8, INTENT(IN) :: z
 END FUNCTION
   
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dGetFieldXCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_get_field_xcoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(OUT) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dSetFieldXCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_set_field_xcoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(IN) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dGetFieldYCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_get_field_ycoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(OUT) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dSetFieldYCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_set_field_ycoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(IN) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dGetFieldZCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_get_field_zcoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(OUT) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dSetFieldZCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_set_field_zcoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(IN) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
 

src/H5Block.h

@@ -13,6 +13,9 @@ extern "C" {
 
 #define H5BLOCK_FIELD_ORIGIN_NAME	"__Origin__"
 #define H5BLOCK_FIELD_SPACING_NAME	"__Spacing__"
+#define H5BLOCK_FIELD_XCOORD_NAME	"__X_Coordinates__"
+#define H5BLOCK_FIELD_YCOORD_NAME	"__Y_Coordinates__"
+#define H5BLOCK_FIELD_ZCOORD_NAME	"__Z_Coordinates__"
 
 /*! 
   Interface for block structured field data.
@@ -138,6 +141,54 @@ H5Block3dSetFieldSpacing (
 	const h5part_float64_t z_spacing
 	);
 
+h5part_int64_t
+H5Block3dGetFieldXCoords (
+	H5PartFile *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dSetFieldXCoords (
+	H5PartFile *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dGetFieldYCoords (
+	H5PartFile *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dSetFieldYCoords (
+	H5PartFile *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dGetFieldZCoords (
+	H5PartFile *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dSetZCoords (
+	H5PartFile *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
 h5part_int64_t
 H5BlockWriteFieldAttrib (
 	H5PartFile *f,

src/H5BlockF.c

@@ -68,6 +68,24 @@
 #define h5bl_3d_get_field_origin F77NAME (				\
 					h5bl_3d_get_field_origin_,	\
 					H5BL_3D_GET_FIELD_origin )
+#define h5bl_3d_get_field_xcoords F77NAME (				\
+					h5bl_3d_get_field_xcoords_,	\
+					H5BL_3D_GET_FIELD_XCOORDS )
+#define h5bl_3d_set_field_xcoords F77NAME (				\
+					h5bl_3d_set_field_xcoords_,	\
+					H5BL_3D_SET_FIELD_XCOORDS )
+#define h5bl_3d_get_field_ycoords F77NAME (				\
+					h5bl_3d_get_field_ycoords_,	\
+					H5BL_3D_GET_FIELD_YCOORDS )
+#define h5bl_3d_set_field_ycoords F77NAME (				\
+					h5bl_3d_set_field_ycoords_,	\
+					H5BL_3D_SET_FIELD_YCOORDS )
+#define h5bl_3d_get_field_zcoords F77NAME (				\
+					h5bl_3d_get_field_zcoords_,	\
+					H5BL_3D_GET_FIELD_ZCOORDS )
+#define h5bl_3d_set_field_zcoords F77NAME (				\
+					h5bl_3d_set_field_zcoords_,	\
+					H5BL_3D_SET_FIELD_ZCOORDS )
 #endif
 
 h5part_int64_t
@@ -447,3 +465,123 @@ h5bl_3d_set_field_origin (
 	free ( field_name2 );
 	return herr;
 }
+
+h5part_int64_t
+h5bl_3d_set_field_xcoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dSetFieldXCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_get_field_xcoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dGetFieldXCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_set_field_ycoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dSetFieldYCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_get_field_ycoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dGetFieldYCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_set_field_zcoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dSetFieldZCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_get_field_zcoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dGetFieldZCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}

src/H5BlockReadWriteF.c

@@ -57,7 +57,7 @@ h5bl_3d_read_scalar_field_r8 (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block3dWriteScalarFieldFloat64 (
+	h5part_int64_t herr = H5Block3dReadScalarFieldFloat64 (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );
@@ -161,7 +161,7 @@ h5bl_3d_read_scalar_field_r4 (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block3dWriteScalarFieldFloat32 (
+	h5part_int64_t herr = H5Block3dReadScalarFieldFloat32 (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );
@@ -265,7 +265,7 @@ h5bl_3d_read_scalar_field_i8 (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block3dWriteScalarFieldInt64 (
+	h5part_int64_t herr = H5Block3dReadScalarFieldInt64 (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );
@@ -369,7 +369,7 @@ h5bl_3d_read_scalar_field_i4 (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block3dWriteScalarFieldInt32 (
+	h5part_int64_t herr = H5Block3dReadScalarFieldInt32 (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );

src/H5MultiBlock.c

@@ -567,10 +567,10 @@ _halo_exchange_buffers (
 	ibufsize = (int)bufsize;
 	if ( (h5part_int64_t)ibufsize != bufsize ) return HANDLE_MPI_INT64_ERR;
 
-	send_buffer = malloc ( bufsize );
+	send_buffer = (char*) malloc ( bufsize );
 	if ( send_buffer == NULL ) return HANDLE_H5PART_NOMEM_ERR;
 
-	recv_buffer = malloc ( bufsize );
+	recv_buffer = (char*) malloc ( bufsize );
 	if ( recv_buffer == NULL ) return HANDLE_H5PART_NOMEM_ERR;
 
 	/* forward */

src/H5Part.c

@@ -291,15 +291,15 @@ _H5Part_open_file (
 
 	if ( align != 0 ) {
 		_H5Part_print_info (
-			"Setting HDF5 alignment to %ld bytes",
+			"Setting HDF5 alignment to %lld bytes with threshold at half that many bytes",
-			align );
+			(long long)align );
-		if (H5Pset_alignment ( f->access_prop, 0, align ) < 0) {
+		if (H5Pset_alignment ( f->access_prop, align/2, align ) < 0) {
 			HANDLE_H5P_SET_FAPL_ERR;
 			goto error_cleanup;
 		}
 		_H5Part_print_info (
-			"Setting HDF5 meta block to %ld bytes",
+			"Setting HDF5 meta block to %lld bytes",
-			align );
+			(long long)align );
 		if (H5Pset_meta_block_size ( f->access_prop, align ) < 0) {
 			HANDLE_H5P_SET_FAPL_ERR;
 			goto error_cleanup;
@@ -1314,6 +1314,9 @@ _H5Part_normalize_h5_type (
 		if ( size==8 ) {
 			return H5PART_INT64;
 		}
+	  	else if ( size==4 ) {
+			return H5PART_INT32;
+		}
 	  	else if ( size==1 ) {
 			return H5PART_CHAR;
 		}
@@ -1343,9 +1346,7 @@ _H5Part_read_attrib (
 	) {
 
 	herr_t herr;
-	h5part_int64_t h5err;
 	hid_t attrib_id;
-	hid_t space_id;
 	hid_t type_id;
 
 #ifdef H5PART_HAVE_HDF5_18
@@ -1361,15 +1362,9 @@ _H5Part_read_attrib (
 	type_id = H5Aget_type ( attrib_id );
 	if ( type_id < 0 ) return HANDLE_H5A_GET_TYPE_ERR;
 
-	space_id = H5Aget_space ( attrib_id );
-	if ( space_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR;
-
 	herr = H5Aread ( attrib_id, type_id, attrib_value );
 	if ( herr < 0 ) return HANDLE_H5A_READ_ERR;
 
-	herr = H5Sclose ( space_id );
-	if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
-
 	herr = H5Tclose ( type_id );
 	if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR;
 
@@ -2086,9 +2081,6 @@ _H5Part_iteration_operator2 (
 	void *operator_data		/*!< [in,out] data passed to the iterator */
 	) {
 
-  struct _iter_op_data *data = (struct _iter_op_data*)operator_data;
-  herr_t herr = 0;
-
   switch (linfo->type) {
     case H5L_TYPE_HARD: {
 
@@ -2332,7 +2324,11 @@ _H5Part_get_object_name (
 	data.len = (size_t)len_obj_name;
 
 #ifdef H5PART_HAVE_HDF5_18
-	hid_t child_id = H5Gopen ( group_id, group_name, H5P_DEFAULT );
+	hid_t child_id = H5Gopen ( group_id, group_name
+#ifndef H5_USE_16_API
+		, H5P_DEFAULT
+#endif
+		);
 	if ( child_id < 0 ) return child_id;
  	herr = H5Literate ( child_id, H5_INDEX_NAME, H5_ITER_INC, 0,
  			_H5Part_iteration_operator2, &data );
@@ -2855,9 +2851,9 @@ _set_view_indices (
 	herr = _reset_view ( f );
 	if ( herr < 0 ) return herr;
 
-	if ( indices == NULL || nelems <= 0 ) {
+	if ( indices == NULL || nelems < 0 ) {
 		_H5Part_print_warn (
-			"View indices array is null or size is <= 0: reseting view." );
+			"View indices array is null or size is < 0: reseting view." );
 		return H5PART_SUCCESS;
 	}
 
@@ -3210,7 +3206,6 @@ _read_data (
 				"elements selected (%lld) than are available "
 				"in memory (%lld).",
 				name2, (long long)nread, (long long)nmem );
-			memspace_id == H5S_ALL;
 		}
 	}
 

src/H5Part.f90

@@ -115,9 +115,10 @@ END FUNCTION
 !! - \c vfd_mpiposix - use the HDF5 MPI-POSIX virtual file driver
 !! - \c vfd_mpio_ind - use MPI-IO in indepedent mode
 !!
+!! See \ref H5PartOpenFileParallelAlign
 !! \return 0 on success or error code
 !<
-INTEGER*8 FUNCTION h5pt_openr_par_align ( filename, mpi_communicator, align )
+INTEGER*8 FUNCTION h5pt_openr_par_align ( filename, mpi_communicator, align, flags )
     CHARACTER(LEN=*), INTENT(IN) :: filename    !< the filename to open for reading
     INTEGER, INTENT(IN) :: mpi_communicator     !< the MPI_Communicator used by the program
     INTEGER*8, INTENT(IN) :: align              !< alignment value in bytes

src/H5Part.h

@@ -16,10 +16,10 @@ extern "C" {
 #include "H5MultiBlock.h"
 #endif
 
-#define H5PART_VER_STRING	"1.6.3"
+#define H5PART_VER_STRING	"1.6.6"
 #define H5PART_VER_MAJOR	1
 #define H5PART_VER_MINOR	6
-#define H5PART_VER_RELEASE	3
+#define H5PART_VER_RELEASE	6
 
 /* error values */
 #define H5PART_SUCCESS		0

src/H5PartPrivate.h

@@ -116,6 +116,24 @@ _H5Part_write_attrib (
 	const hsize_t attrib_nelem
 	);
 
+h5part_int64_t
+_H5Part_write_file_attrib (
+	H5PartFile *f,
+	const char *name,
+	const hid_t type,
+	const void *value,
+	const hsize_t nelem
+	);
+
+h5part_int64_t
+_H5Part_write_step_attrib (
+	H5PartFile *f,
+	const char *name,
+	const hid_t type,
+	const void *value,
+	const hsize_t nelem
+	);
+
 h5part_int64_t
 _H5Part_get_attrib_info (
 	hid_t id,

src/generate-h5bl-readwrite.py

@@ -214,7 +214,7 @@ h5bl_#DIM#d_read_scalar_field_#TYPE_F90_ABV# (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block#DIM#dWriteScalarField#TYPE_ABV# (
+	h5part_int64_t herr = H5Block#DIM#dReadScalarField#TYPE_ABV# (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );

test/Makefile.am

@@ -22,6 +22,6 @@ test_LDADD   =  ../src/libH5Part.la
 testf_SOURCES = testf.F90
 testf_LDADD   =  ../src/libH5PartF.la
 
-clean: clean-am
+clean-local:
-	rm -f *.h5
+	$(RM) -f *.h5
 

test/coords.F90

@@ -0,0 +1,97 @@
+program H5BlockCoordsTest
+  implicit none
+
+#ifdef PARALLEL_IO
+  include 'mpif.h'
+#endif
+  include 'H5PartF.h'
+
+#ifdef PARALLEL_IO
+  integer :: ierr, comm
+#endif
+  integer*8 :: file_id, status, i
+  real*8, allocatable :: r8buf(:,:,:), r8buf3(:,:,:,:), coords(:)
+  real*8 :: x, y, z
+
+#ifdef PARALLEL_IO
+  call MPI_INIT(ierr)
+  comm = MPI_COMM_WORLD
+#endif
+
+  ! this enables level 4 ("debug") messages to be
+  ! printed by the H5Part library
+  ! (4_8 is the literal for an integer*8 with value 4)
+  status = h5pt_set_verbosity_level (4_8)
+
+  ! open the a file called 'test.h5' in parallel for writing
+#ifdef PARALLEL_IO
+  file_id = h5pt_openw_par_align ('test.h5', comm, 1048576_8, "vfd_mpiposix")
+#else
+  file_id = h5pt_openw_align ('test.h5', 1048576_8, "vfd_mpiposix")
+#endif
+
+  status = h5bl_define3dlayout(file_id, 1_8, 30_8, 1_8, 30_8, 1_8, 30_8)
+
+  ! in the Fortran API, steps start at 1
+  status = h5pt_setstep (file_id, 1_8)
+
+  ! create fake data
+  allocate(r8buf(30,30,30))
+  allocate(r8buf3(30,30,30,3))
+  allocate(coords(30))
+  x = 1.0
+  y = 2.0
+  z = 3.0
+
+  ! write the data
+  status = h5bl_3d_write_scalar_field_r8(file_id, "x", r8buf(1,1,1))
+  status = h5bl_3d_set_field_origin(file_id, "x", x, y, z)
+  status = h5bl_3d_set_field_spacing(file_id, "x", x, y, z)
+
+  status = h5bl_3d_write_3dvector_field_r8(file_id, "v", r8buf3(1,1,1,1), r8buf3(1,1,1,2), r8buf3(1,1,1,3))
+  status = h5bl_3d_set_field_origin(file_id, "v", x, y, z)
+  status = h5bl_3d_set_field_spacing(file_id, "v", x, y, z)
+
+  ! create fake coordinates
+  do i = 1, 30
+    coords(i) = 3*i
+  enddo
+  status = h5bl_3d_set_field_xcoords(file_id, "v", coords, 30_8)
+  do i = 1, 30
+    coords(i) = 3*i + 1
+  enddo
+  status = h5bl_3d_set_field_ycoords(file_id, "v", coords, 30_8)
+  do i = 1, 30
+    coords(i) = 3*i + 2
+  enddo
+  status = h5bl_3d_set_field_zcoords(file_id, "v", coords, 30_8)
+
+  ! read fake coordinates
+  do i = 1, 30
+    coords(i) = -1
+  enddo
+  status = h5bl_3d_get_field_xcoords(file_id, "v", coords, 30_8)
+  write(*, *) coords
+  !write(*, "I3") ( coords(i), i=1, 30 )
+  do i = 1, 30
+    coords(i) = -1
+  enddo
+  status = h5bl_3d_get_field_ycoords(file_id, "v", coords, 30_8)
+  write(*, *) coords
+  !write(*, "I3") ( coords(i), i=1, 30 )
+  do i = 1, 30
+    coords(i) = -1
+  enddo
+  status = h5bl_3d_get_field_zcoords(file_id, "v", coords, 30_8)
+  write(*, *) coords
+  !write(*, "I3") ( coords(i), i=1, 30 )
+
+  ! close the file
+  status = h5pt_close (file_id)
+
+#ifdef PARALLEL_IO
+  call MPI_FINALIZE(ierr)
+#endif
+
+end program H5BlockCoordsTest
+

test/read.c

@@ -1,3 +1,4 @@
+#include <string.h>
 #include <H5Part.h>
 
 #include "testframe.h"

test/testframe.c

@@ -536,7 +536,7 @@ TestPrintf(const char *format, ...)
     int nproc;
     MPI_Comm_rank(MPI_COMM_WORLD, &nproc);
     if ( nproc == 0 || VERBOSE_HI ) {
-	char *format2 = malloc(strlen(format)+8);
+	char *format2 = (char*)malloc(strlen(format)+8);
 	sprintf(format2, "[%d] %s", nproc, format);
 	va_start(arglist, format);
 	ret_value = vprintf(format2, arglist);
@@ -570,7 +570,7 @@ TestErrPrintf(const char *format, ...)
     int nproc;
     MPI_Comm_rank(MPI_COMM_WORLD, &nproc);
     if ( nproc == 0 || VERBOSE_HI ) {
-	char *format2 = malloc(strlen(format)+8);
+	char *format2 = (char*)malloc(strlen(format)+8);
 	sprintf(format2, "[%d] %s", nproc, format);
 	va_start(arglist, format);
 	ret_value = vfprintf(stderr, format2, arglist);
@@ -661,7 +661,7 @@ test_open_objects(H5PartFile *file, int max_objects)
 				"at line %4d in %s\n", nopen, max_objects,
 				(int)__LINE__, __FILE__ );
 
-		hid_t *list = malloc(sizeof(hid_t)*nopen);
+		hid_t *list = (hid_t)malloc(sizeof(hid_t)*nopen);
 		H5Fget_obj_ids(file->file, H5F_OBJ_ALL, nopen, list);
 
                 H5O_info_t info;

test/testframe.h

@@ -6,6 +6,8 @@
 #ifndef _H5PART_TESTFRAME_H_
 #define _H5PART_TESTFRAME_H_
 
+#include <string.h>
+
 #ifdef PARALLEL_IO
 #define OPEN(file,mode) \
     H5PartOpenFileParallel(file,mode,MPI_COMM_WORLD)