[svn-r620] Changes since 19980825

----------------------

./MANIFEST
./src/H5R.c		[NEW]
./src/H5Rprivate.h	[NEW]
./src/H5Rpublic.h	[NEW]
./src/Makefile.in
./src/hdf5.h
./test/ragged.c		[NEW]
	Preliminary support for 2d ragged arrays for Mark Miller and
	Jim Reus.  Not fully implemented yet. The test is not actually
	part of `make test' because we still have some memory problems.

./src/H5E.c
./src/H5Epublic.h
	Added H5E_RAGGED as a major error number.

./bin/release
	Checks the MANIFEST file against `svf ls' on systems that have
	it.

./bin/trace
	Fixed a bug that caused arguments of type `void *x[]' to not
	be handled.

./src/H5.c
	Removed unused variables and changed a couple types to
	fix compiler warnings.

	Added tracing support for ragged array object ID's and arrays
	of pointers.

./src/H5D.c
	H5Dcreate() will complain if either of the property lists are
	invalid (instead of using the default).

./src/H5D.c
./src/H5Dprivate.h
	Split H5Dget_space() into an API and internal function so it
	can be called from the new ragged array layer.

./src/H5Fistore.c
	Fixed warnings about unsigned vs. signed comparisons.

./src/H5Flow.c
	Fixed a warning about a variable being shadowed in the MPI-IO
	stuff.

./src/H5Iprivate.h
./src/H5Ipublic.h
	Added the H5_RAGGED atom group.

./src/H5Shyper.c
	Fixed some freeing-free-memory errors that resulted when
	certain arrays were freed but the pointers were left in the
	data structures.  I simply set the pointers to null after they
	were freed.

./src/H5Sprivate.h
./src/H5Sselect.c
	Split the H5Sselect_hyperslab() function into an API and a
	private function so it could be called from the ragged array
	layer.

	Added H5S_SEL_ERROR and H5S_SEL_N to the switch statements to
	get rid or compiler warnings.

./src/H5Tconv.c
	Removed a misleading comment.

./test/bittests.c
	Fixed a warning about a printf().

./test/cmpd_dset.c
	Fixed warnings about unused variables because of test #11
	being commented out.

./bin/trace
	Shortened the right margin for the output to allow room for
	the `);' at the end of the TRACE() macros.

1 files changed, 1075 insertions, 0 deletions

diff --git a/src/H5R.c b/src/H5R.c
new file mode 100644
index 0000000..02c4e25
--- /dev/null
+++ b/src/H5R.c
@@ -0,0 +1,1075 @@
+/*
+ * Copyright © 1998 NCSA
+ *                  All rights reserved.
+ *
+ * Programmer:  Robb Matzke <matzke@llnl.gov>
+ *              Tuesday, August 25, 1998
+ *
+ * Purpose:	A ragged array package layered on top of other HDF5 objects.
+ *		This was originally implemented on the HDF5 API but has been
+ *		moved under the API so it meshes better with other objects,
+ *		is somewhat faster, and has better debugging support.
+ *
+ * Note:	This file implementes a two dimensional array where each row
+ *		of the array is a different length (a.k.a., ragged array). It
+ *		is intended for applications where the distribution of row
+ *		lengths is such that most rows near an average length with
+ *		only a few rows that are significantly shorter or longer. The
+ *		raw data is split among two datasets `raw' and `over': the
+ *		`raw' dataset is a 2d chunked dataset whose width is large
+ *		enough to hold most of the rows and the `over' dataset is a
+ *		heap that stores the end of rows that overflow the first
+ *		dataset.  A third dataset called `meta' contains one record
+ *		for each row and describes what elements (if any) overflow
+ *		the `raw' dataset and where they are stored in the `over'
+ *		dataset.  All three datasets are contained in a single group
+ *		whose name is the name of the ragged array.
+ */
+#include <H5Rprivate.h>
+
+#include <H5private.h>
+#include <H5Eprivate.h>
+#include <H5Iprivate.h>
+#include <H5MMprivate.h>
+#include <H5Pprivate.h>
+
+typedef struct H5R_meta_t {
+    hsize_t	nelmts;		/*num elements in row			*/
+    hssize_t	offset;		/*offset into overflow array		*/
+    hsize_t	nover;		/*allocated size in overflow array	*/
+} H5R_meta_t;
+
+struct H5R_t {
+    H5D_t	*meta;		/*ragged meta data array		*/
+    H5D_t	*raw;		/*fixed-width raw data			*/
+    H5D_t	*over;		/*overflow data				*/
+};
+
+#define PABLO_MASK	H5R_mask
+static hbool_t interface_initialize_g = FALSE;
+#define INTERFACE_INIT H5R_init_interface
+static herr_t H5R_init_interface(void);
+static void H5R_term_interface(void);
+static H5T_t *H5R_meta_type_g = NULL;
+
+static herr_t H5R_fix_overflow(H5R_t *ra, H5T_t *type, H5R_meta_t *meta,
+			       hsize_t nelmts, void *buf);
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5R_init_interface
+ *
+ * Purpose:	Initialize the interface.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5R_init_interface(void)
+{
+    herr_t	ret_value = SUCCEED;
+    H5T_t	*type = NULL;
+    
+    FUNC_ENTER(H5R_init_interface, FAIL);
+
+    /* The atom group */
+    if ((ret_value=H5I_init_group(H5_RAGGED, H5I_RAGGED_HASHSIZE, 0,
+				  (herr_t(*)(void*))H5R_close))>=0) {
+	ret_value = H5_add_exit(H5R_term_interface);
+    }
+
+    /* The meta dataset type */
+    if (NULL==(type=H5T_create(H5T_COMPOUND, sizeof(H5R_meta_t))) ||
+	H5T_insert(type, "nelmts", HOFFSET(H5R_meta_t, nelmts),
+		   0, NULL, NULL, H5I_object(H5T_NATIVE_HSIZE_g))<0 ||
+	H5T_insert(type, "offset", HOFFSET(H5R_meta_t, offset),
+		   0, NULL, NULL, H5I_object(H5T_NATIVE_HSSIZE_g))<0 ||
+	H5T_insert(type, "nover", HOFFSET(H5R_meta_t, nover),
+		   0, NULL, NULL, H5I_object(H5T_NATIVE_HSIZE_g))) {
+	HRETURN_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		      "unable to define ragged array meta type");
+    }
+    H5R_meta_type_g = type;
+    
+    FUNC_LEAVE(ret_value);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5R_term_interface
+ *
+ * Purpose:	Terminate the ragged array interface.
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+H5R_term_interface(void)
+{
+    H5I_destroy_group(H5_RAGGED);
+    H5T_close(H5R_meta_type_g);
+    H5R_meta_type_g = NULL;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5Rcreate
+ *
+ * Purpose:	Create a new ragged array with the specified name.  A ragged
+ *		array is implemented as a group containing three datasets.
+ *		The dataset `raw' is a fixed width dataset which will hold
+ *		the majority of the data.  The dataset `over' is a one
+ *		dimensional heap which will hold the end of rows which are
+ *		too long to fit in `raw'.  Finally, the `meta' dataset
+ *		contains information about the `over' array.  All elements of
+ *		the ragged array are stored with the same data type.
+ *
+ *		The property list PLIST_ID  should contain information about
+ *		chunking. The chunk width will determine the width of the
+ *		`raw' dataset while the chunk length should be such that the
+ *		total chunk size is reasonably large (I/O will be performed
+ *		in units of chunks).  If the PLIST_ID doesn't have a chunk
+ *		size defined (e.g., H5P_DEFAULT) then this function will fail.
+ *
+ * Return:	Success:	A ragged array ID.
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+hid_t
+H5Rcreate(hid_t loc_id, const char *name, hid_t type_id, hid_t plist_id)
+{
+    H5R_t		*ra=NULL;
+    H5G_t		*loc=NULL;
+    H5T_t		*type=NULL;
+    const H5D_create_t	*plist=NULL;
+    hid_t		ret_value=FAIL;
+    
+    FUNC_ENTER(H5Rcreate, FAIL);
+    H5TRACE4("i","isii",loc_id,name,type_id,plist_id);
+
+    /* Check args */
+    if (NULL==(loc=H5G_loc(loc_id))) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
+    }
+    if (!name || !*name) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name given");
+    }
+    if (H5_DATATYPE!=H5I_group(type_id) ||
+	NULL==(type=H5I_object(type_id))) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
+    }
+    if (H5P_DEFAULT==plist_id) {
+	plist = &H5D_create_dflt;
+    } else if (H5P_DATASET_CREATE!=H5P_get_class(plist_id) ||
+	       NULL==(plist=H5I_object(plist_id))) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL,
+		      "not a dataset creation property list");
+    }
+    if (H5D_CHUNKED!=plist->layout) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
+		      "property list must define a chunked storage layout");
+    }
+    if (2!=plist->layout) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
+		      "chunked storage is not two dimensional");
+    }
+    
+    /* Do the real work */
+    if (NULL==(ra=H5R_create(loc, name, type, plist))) {
+	HRETURN_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		      "unable to create ragged array");
+    }
+
+    /* Register the new dataset to get an ID for it */
+    if ((ret_value=H5I_register(H5_RAGGED, ra))<0) {
+	H5R_close(ra);
+	HRETURN_ERROR(H5E_RAGGED, H5E_CANTREGISTER, FAIL,
+		      "unable to register ragged array");
+    }
+
+    FUNC_LEAVE(ret_value);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5R_create
+ *
+ * Purpose:	Create a new ragged array implemented as a group.
+ *
+ * Return:	Success:	Pointer to the new ragged array.
+ *
+ *		Failure:	NULL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+H5R_t *
+H5R_create(H5G_t *loc, const char *name, H5T_t *type, const H5D_create_t *dcpl)
+{
+    H5R_t		*ra = NULL;
+    H5G_t		*grp = NULL;
+    H5S_t		*space = NULL;
+    hsize_t		cur_dims[2];
+    hsize_t		max_dims[2];
+    H5R_t		*ret_value=NULL;
+    H5D_create_t	d1_dcpl;
+    
+    FUNC_ENTER(H5R_create, NULL);
+
+    /* Check args */
+    assert(loc);
+    assert(name && *name);
+    assert(type);
+    assert(dcpl);
+    assert(H5D_CHUNKED==dcpl->layout);
+
+    /* Create the data struct */
+    if (NULL==(ra=H5MM_calloc(sizeof(H5R_t)))) {
+	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL,
+		    "memory allocation failed for ragged array struct");
+    }
+
+    /* Create the group to contain the arrays */
+    if (NULL==(grp=H5G_create(loc, name, 0))) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to create container group");
+    }
+
+    /* The raw data array */
+    cur_dims[0] = 0;
+    max_dims[0] = H5S_UNLIMITED;
+    cur_dims[1] = max_dims[1] = dcpl->chunk_size[1];
+    if (NULL==(space=H5S_create(H5S_SIMPLE)) ||
+	H5S_set_extent_simple(space, 2, cur_dims, max_dims)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to define raw dataset extents");
+    }
+    if (NULL==(ra->raw=H5D_create(grp, "raw", type, space, dcpl))) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to create raw dataset");
+    }
+    if (H5S_close(space)<0) {
+	space = NULL;
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to close raw dataset extents");
+    }
+    space = NULL;
+    
+    /* The overflow data array */
+    cur_dims[0] = 0;
+    max_dims[0] = H5S_UNLIMITED;
+    if (NULL==(space=H5S_create(H5S_SIMPLE)) ||
+	H5S_set_extent_simple(space, 1, cur_dims, max_dims)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to define overflow dataset extents");
+    }
+    d1_dcpl = *dcpl;
+    d1_dcpl.chunk_ndims = 1;
+    d1_dcpl.chunk_size[0] = dcpl->chunk_size[0]*dcpl->chunk_size[1];
+    if (NULL==(ra->over=H5D_create(grp, "over", type, space, &d1_dcpl))) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to create overflow dataset");
+    }
+    if (H5S_close(space)<0) {
+	space = NULL;
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to close overflow dataset extents");
+    }
+    space = NULL;
+    
+    /* The meta data array */
+    cur_dims[0] = 0;
+    max_dims[0] = H5S_UNLIMITED;
+    if (NULL==(space=H5S_create(H5S_SIMPLE)) ||
+	H5S_set_extent_simple(space, 1, cur_dims, max_dims)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to define meta dataset extents");
+    }
+    d1_dcpl.chunk_size[0] = MAX(1,
+				(dcpl->chunk_size[0]*dcpl->chunk_size[1]*
+				 H5T_get_size(type))/
+				H5T_get_size(H5R_meta_type_g));
+    if (NULL==(ra->meta=H5D_create(grp, "meta", H5R_meta_type_g, space,
+				   &d1_dcpl))) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to create meta dataset");
+    }
+    if (H5S_close(space)<0) {
+	space = NULL;
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to close meta dataset extents");
+    }
+    space = NULL;
+
+    /* Close the group -- we no longer need it */
+    if (H5G_close(grp)<0) {
+	grp = NULL;
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to close ragged array group");
+    }
+    grp = NULL;
+    ret_value = ra;
+
+ done:
+    if (!ret_value) {
+	if (grp) H5G_close(grp);
+	if (space) H5S_close(space);
+	if (ra) {
+	    if (ra->raw) H5D_close(ra->raw);
+	    if (ra->over) H5D_close(ra->over);
+	    if (ra->meta) H5D_close(ra->meta);
+	    H5MM_xfree(ra);
+	}
+    }
+    FUNC_LEAVE(ret_value);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5Ropen
+ *
+ * Purpose:	Opens an existing ragged array.  The name of the array should
+ *		be the same that was used when the array was created; that is,
+ *		the name of the group which implements the array.
+ *		
+ * Return:	Success:	An array ID
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+hid_t
+H5Ropen(hid_t loc_id, const char *name)
+{
+    H5G_t	*loc=NULL;
+    H5R_t	*ra=NULL;
+    hid_t	ret_value=FAIL;
+    
+    FUNC_ENTER(H5Ropen, FAIL);
+    H5TRACE2("i","is",loc_id,name);
+
+    /* Check args */
+    if (NULL==(loc=H5G_loc(loc_id))) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
+    }
+    if (!name || !*name) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name given");
+    }
+
+    /* The real work */
+    if (NULL==(ra=H5R_open(loc, name))) {
+	HRETURN_ERROR(H5E_RAGGED, H5E_CANTOPENOBJ, FAIL,
+		      "unable to open ragged array");
+    }
+
+    /* Turn it into an atom */
+    if ((ret_value=H5I_register(H5_RAGGED, ra))<0) {
+	H5R_close(ra);
+	HRETURN_ERROR(H5E_RAGGED, H5E_CANTREGISTER, FAIL,
+		      "unable to register ragged array");
+    }
+
+    FUNC_LEAVE(ret_value);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5R_open
+ *
+ * Purpose:	Open a ragged array.  The name of the array is the same as
+ *		the group that implements the array.
+ *
+ * Return:	Success:	Ptr to a new ragged array object.
+ *
+ *		Failure:	NULL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+H5R_t *
+H5R_open(H5G_t *loc, const char *name)
+{
+    H5R_t	*ra = NULL;
+    H5R_t	*ret_value = NULL;
+    H5G_t	*grp=NULL;
+    
+    FUNC_ENTER(H5R_open, NULL);
+
+    /* Check arguments */
+    assert(loc);
+    assert(name && *name);
+
+    /* Create the struct */
+    if (NULL==(ra=H5MM_calloc(sizeof(H5R_t)))) {
+	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL,
+		    "memory allocation failed for ragged array struct");
+    }
+
+    /* Open the containing group */
+    if (NULL==(grp=H5G_open(loc, name))) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTOPENOBJ, NULL,
+		    "unable to open container group");
+    }
+
+    /* Open the datasets */
+    if (NULL==(ra->raw=H5D_open(grp, "raw")) ||
+	NULL==(ra->over=H5D_open(grp, "over")) ||
+	NULL==(ra->meta=H5D_open(grp, "meta"))) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTOPENOBJ, NULL,
+		    "unable to open one or more component datasets");
+    }
+
+    /* Close group */
+    if (H5G_close(grp)<0) {
+	grp = NULL;
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, NULL,
+		    "unable to close container group");
+    }
+    grp = NULL;
+    ret_value = ra;
+    
+ done:
+    if (!ret_value) {
+	if (grp) H5G_close(grp);
+	if (ra) {
+	    if (ra->raw) H5D_close(ra->raw);
+	    if (ra->over) H5D_close(ra->over);
+	    if (ra->meta) H5D_close(ra->meta);
+	    H5MM_xfree(ra);
+	}
+    }
+    FUNC_LEAVE(ret_value);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5Rclose
+ *
+ * Purpose:	Close a ragged array.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Rclose(hid_t array_id)
+{
+    H5R_t	*ra=NULL;
+    
+    FUNC_ENTER(H5Rclose, FAIL);
+    H5TRACE1("e","i",array_id);
+
+    /* Check args */
+    if (H5_RAGGED!=H5I_group(array_id) ||
+	NULL==(ra=H5I_object(array_id))) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a ragged array");
+    }
+    
+    /*
+     * Decrement the counter on the array.  It will be freed if the count
+     * reaches zero.
+     */
+    if (H5I_dec_ref(array_id) < 0) {
+	HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to free");
+    }
+    
+    FUNC_LEAVE(SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5R_close
+ *
+ * Purpose:	Close a ragged array
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5R_close(H5R_t *ra)
+{
+    FUNC_ENTER(H5R_close, FAIL);
+
+    assert(ra);
+    if ((ra->raw && H5D_close(ra->raw)<0) ||
+	(ra->over && H5D_close(ra->over)<0) ||
+	(ra->meta && H5D_close(ra->meta)<0)) {
+	HRETURN_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		      "unable to close one or more component datasets");
+    }
+    HDmemset(ra, 0, sizeof(H5R_t));
+    H5MM_xfree(ra);
+
+    FUNC_LEAVE(SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5Rwrite
+ *
+ * Purpose:	Write a contiguous set of rows to a ragged array beginning at
+ *		row number START_ROW and continuing for NROWS rows.  Each row
+ *		of the ragged array contains SIZE[] elements of type TYPE_ID
+ *		and each row is stored in a buffer pointed to by BUF[].
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Rwrite(hid_t array_id, hssize_t start_row, hsize_t nrows,
+	 hid_t type_id, hsize_t size[/*nrows*/], void *buf[/*nrows*/])
+{
+    H5R_t	*ra=NULL;
+    H5T_t	*type=NULL;
+    hsize_t	i;
+    
+    FUNC_ENTER(H5Rwrite, FAIL);
+    H5TRACE6("e","iHshi*[a2]h*[a2]x",array_id,start_row,nrows,type_id,size,
+             buf);
+
+    /* Check args */
+    if (H5_RAGGED!=H5I_group(array_id) ||
+	NULL==(ra=H5I_object(array_id))) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a ragged array");
+    }
+    if (H5_DATATYPE!=H5I_group(type_id) ||
+	NULL==(type=H5I_object(type_id))) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
+    }
+    if (nrows>0 && !size) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no size array");
+    }
+    if (nrows>0 && !buf) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer array");
+    }
+    for (i=0; i<nrows; i++) {
+	if (size[i]>0 && !buf[i]) {
+	    HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
+			  "one or more buffer points are null");
+	}
+    }
+    
+    /* Do the work */
+    if (H5R_write(ra, start_row, nrows, type, size, buf)<0) {
+	HRETURN_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL,
+		      "unable to write to ragged array");
+    }
+
+    FUNC_LEAVE(SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5R_write
+ *
+ * Purpose:	Write a contiguous set of rows to a ragged array beginning at
+ *		row number START_ROW and continuing for NROWS rows.  Each row
+ *		of the ragged array contains SIZE[] elements of type TYPE_ID
+ *		and each row is stored in a buffer pointed to by BUF[].
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5R_write(H5R_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type,
+	  hsize_t size[], void *buf[])
+{
+    herr_t	ret_value=FAIL;
+    H5R_meta_t	*meta = NULL;
+    H5S_t	*mf_space=NULL;		/*meta file data space		*/
+    H5S_t	*mm_space=NULL;		/*meta memory data space	*/
+    H5S_t	*rf_space=NULL;		/*raw data file space		*/
+    H5S_t	*rm_space=NULL;		/*raw data memory space		*/
+    hsize_t	meta_cur_size;		/*current meta data nelmts	*/
+    hsize_t	meta_read_size;		/*amount to read		*/
+    hsize_t	raw_cur_size[2];	/*raw data current size		*/
+    hssize_t	hs_offset[2];		/*hyperslab offset		*/
+    hsize_t	hs_size[2];		/*hyperslab size		*/
+    uint8	*raw_buf=NULL;		/*raw buffer			*/
+    size_t	type_size;		/*size of the TYPE argument	*/
+    hsize_t	i;
+    
+    FUNC_ENTER(H5R_write, FAIL);
+
+    /* Check args */
+    assert(ra);
+    assert(type);
+    assert(0==nrows || size);
+    assert(0==nrows || buf);
+    if (0==nrows) HRETURN(SUCCEED);
+    type_size = H5T_get_size(type);
+
+    /* Get the meta data */
+    if (NULL==(mf_space=H5D_get_space(ra->meta)) ||
+	H5S_extent_dims(mf_space, &meta_cur_size, NULL)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		    "unable to get current meta data extents");
+    }
+    if ((hsize_t)start_row>=meta_cur_size) {
+	meta_read_size = 0;
+    } else {
+	meta_read_size = MIN(nrows, meta_cur_size-(hsize_t)start_row);
+    }
+    if (NULL==(mm_space=H5S_create(H5S_SIMPLE)) ||
+	H5S_set_extent_simple(mm_space, 1, &meta_read_size, NULL)<0 ||
+	H5S_select_hyperslab(mf_space, H5S_SELECT_SET, &start_row, NULL,
+			     &meta_read_size, NULL)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		    "unable to set meta data selection");
+    }
+    if (NULL==(meta=H5MM_malloc(nrows*sizeof(H5R_meta_t)))) {
+	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL,
+		    "memory allocation failed for meta data");
+    }
+    if (H5D_read(ra->meta, H5R_meta_type_g, mm_space, mf_space,
+		 &H5D_xfer_dflt, meta)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL,
+		    "unable to read meta data");
+    }
+    HDmemset(meta+meta_read_size, 0,
+	     (nrows-meta_read_size)*sizeof(H5R_meta_t));
+
+    /* Write the part of the data that will fit in the raw dataset */
+    if (NULL==(rf_space=H5D_get_space(ra->raw)) ||
+	H5S_extent_dims(rf_space, raw_cur_size, NULL)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		    "unable to determine current raw data extents");
+    }
+    if (NULL==(raw_buf=H5MM_malloc(nrows*raw_cur_size[1]*type_size))) {
+	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL,
+		    "unable to allocate buffer for raw data");
+    }
+    for (i=0; i<nrows; i++) {
+	size_t nbytes = MIN(size[i], raw_cur_size[1])*type_size;
+	HDmemcpy(raw_buf+i*raw_cur_size[1]*type_size, buf[i], nbytes);
+	HDmemset(raw_buf+i*raw_cur_size[1]*type_size+nbytes, 0,
+		 raw_cur_size[1]*type_size-nbytes);
+    }
+    if ((hsize_t)start_row+nrows>raw_cur_size[0]) {
+	raw_cur_size[0] = (hsize_t)start_row + nrows;
+	if (H5D_extend(ra->raw, raw_cur_size)<0) {
+	    HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+			"unable to extend raw dataset");
+	}
+    }
+    hs_offset[0] = start_row;
+    hs_offset[1] = 0;
+    hs_size[0] = nrows;
+    hs_size[1] = raw_cur_size[1];
+    if (NULL==(rm_space=H5S_create(H5S_SIMPLE)) ||
+	H5S_set_extent_simple(rm_space, 2, hs_size, NULL)<0 ||
+	H5S_select_hyperslab(rf_space, H5S_SELECT_SET,
+			     hs_offset, NULL, hs_size, NULL)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		    "unable to set meta data selection");
+    }
+    if (H5D_write(ra->raw, type, rm_space, rf_space, &H5D_xfer_dflt,
+		  raw_buf)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL,
+		    "unable to write raw data");
+    }
+    
+    /* Update the meta data */
+    for (i=0; i<nrows; i++) {
+	if (size[i]>raw_cur_size[1]) {
+	    H5R_fix_overflow(ra, type, meta+i, size[i]-raw_cur_size[1],
+			     (uint8*)(buf[i])+raw_cur_size[1]);
+	}
+	meta[i].nelmts = size[i];
+    }
+    
+    /* Extend and write the new meta data */
+    if ((hsize_t)start_row+nrows>meta_cur_size) {
+	meta_cur_size = (hsize_t)start_row+nrows;
+	if (H5D_extend(ra->meta, &meta_cur_size)<0) {
+	    HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+			"unable to extend meta dataset");
+	}
+    }
+    if (H5S_set_extent_simple(mm_space, 1, &nrows, NULL)<0 ||
+	H5S_select_hyperslab(mf_space, H5S_SELECT_SET, &start_row, NULL,
+			     &nrows, NULL)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		    "unable to set meta data selection");
+    }
+    if (H5D_write(ra->meta, H5R_meta_type_g, mm_space, mf_space,
+		  &H5D_xfer_dflt, meta)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL,
+		    "unable to write meta data");
+    }
+    
+    ret_value = SUCCEED;
+ done:
+    H5MM_xfree(meta);
+    H5MM_xfree(raw_buf);
+    if (mm_space) H5S_close(mm_space);
+    if (mf_space) H5S_close(mf_space);
+    if (rm_space) H5S_close(rm_space);
+    if (rf_space) H5S_close(rf_space);
+	
+    FUNC_LEAVE(ret_value);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5R_fix_overflow
+ *
+ * Purpose:	Updates the overflow information for a row.  This is where
+ *		the heap management comes into play.  The NELMTS is the
+ *		number of elements that overflow into the heap and BUF is a
+ *		pointer to those elements.  The first part of the row has
+ *		already been written to the raw dataset.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, August 26, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5R_fix_overflow(H5R_t *ra, H5T_t *type, H5R_meta_t *meta, hsize_t nelmts,
+		 void *buf)
+{
+    H5S_t	*of_space=NULL;		/*overflow file space		*/
+    H5S_t	*om_space=NULL;		/*overflow memory space		*/
+    hsize_t	cur_size;		/*num elmts in overflow dataset	*/
+    herr_t	ret_value=FAIL;		/*return value			*/
+    
+    FUNC_ENTER(H5R_fix_overflow, FAIL);
+    
+    assert(ra);
+    assert(meta);
+    assert(buf);
+
+    if (nelmts==meta->nover) {
+	/* The space is already allocated -- do nothing */
+	
+    } else if (nelmts<meta->nover) {
+	/* Too much space is allocated -- free the extra */
+#ifndef LATER
+	/*
+	 * For now we don't worry about reclaiming space.  But we remember
+	 * the original amount allocated to allow the row to grow again up to
+	 * that amount.
+	 */
+#endif
+	
+    } else if (meta->nover>0) {
+	/* Space is allocated but we need more */
+#ifndef LATER
+	/*
+	 * For now we'll just reallocate space at the end of the overflow
+	 * dataset, but eventually we'll want to move the smallest of the
+	 * current overflow, the previous overflow, or the following overflow
+	 * region to the end of the file and be careful to reclaim space.
+	 */
+	if (NULL==(of_space=H5D_get_space(ra->over)) ||
+	    H5S_extent_dims(of_space, &cur_size, NULL)<0) {
+	    HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+			"unable to get overflow dataset extents");
+	}
+	meta->offset = (hssize_t)cur_size;
+	meta->nover = nelmts;
+	cur_size += nelmts;
+	if (H5D_extend(ra->over, &cur_size)<0) {
+	    HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+			"unable to extend overflow dataset");
+	}
+#endif
+	
+    } else {
+	/* No space is allocated */
+	assert(nelmts>0);
+	if (NULL==(of_space=H5D_get_space(ra->over)) ||
+	    H5S_extent_dims(of_space, &cur_size, NULL)<0) {
+	    HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+			"unable to get overflow dataset extents");
+	}
+	meta->offset = (hssize_t)cur_size;
+	meta->nover = nelmts;
+	cur_size += nelmts;
+	if (H5D_extend(ra->over, &cur_size)<0) {
+	    HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+			"unable to extend overflow dataset");
+	}
+    }
+
+    /* Write the data */
+    if (nelmts>0) {
+	if (!of_space && NULL==(of_space=H5D_get_space(ra->over))) {
+	    HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+			"unable to get overflow dataset extents");
+	}
+	if (NULL==(om_space=H5S_create(H5S_SIMPLE)) ||
+	    H5S_set_extent_simple(om_space, 1, &nelmts, NULL)<0 ||
+	    H5S_select_hyperslab(of_space, H5S_SELECT_SET, &(meta->offset),
+				 NULL, &nelmts, NULL)<0) {
+	    HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+			"unable to set overflow selection");
+	}
+	if (H5D_write(ra->over, type, om_space, of_space, &H5D_xfer_dflt,
+		      buf)<0) {
+	    HGOTO_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL,
+			"unable to write to overflow dataset");
+	}
+    }
+    
+    ret_value = SUCCEED;
+    
+ done:
+    if (of_space) H5S_close(of_space);
+    if (om_space) H5S_close(om_space);
+    if (ret_value<0) {
+	meta->offset = 0;
+	meta->nover = 0;
+    }
+    FUNC_LEAVE(ret_value);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5Rread
+ *
+ * Purpose:	Reads the contents of one or more rows of a ragged array
+ *		pointed to by ARRAY_ID.  The rows to read begin at row
+ *		START_ROW and continue for NROWS rows with all raw data
+ *		converted to type TYPE_ID.
+ *
+ *		The caller must allocate the SIZE[] and BUF[] arrays but
+ *		memory for the data can be allocated by either the caller or
+ *		the library.  In the former case the caller should initialize
+ *		the BUF[] array with pointers to valid memory and the SIZE[]
+ *		array with the lengths of the buffers.  In the latter case
+ *		the caller should initialize BUF[] with null pointers (the
+ *		input value of SIZE[] is irrelevant in this case) and the
+ *		library will allocate memory for each row by calling malloc().
+ *
+ * Return:	Success:	SUCCEED.  The values of the SIZE[] array will
+ *				be the true length of each row.  If a row is
+ *				longer than the caller-allocated length then
+ *				SIZE[] will contain the true length of the
+ *				row although not all elements of that row
+ *				will be stored in the buffer.
+ *
+ *		Failure:	FAIL.  The BUF[] array will contain it's
+ *				original pointers (null or otherwise)
+ *				although the caller-supplied buffers may have
+ *				been modified. The SIZE[] array may also be
+ *				modified.
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 25, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Rread(hid_t array_id, hssize_t start_row, hsize_t nrows,
+	hid_t type_id, hsize_t size[/*nrows*/], void *buf[/*nrows*/])
+{
+    H5R_t	*ra=NULL;
+    H5T_t	*type=NULL;
+    
+    FUNC_ENTER(H5Rread, FAIL);
+    H5TRACE6("e","iHshi*[a2]h*[a2]x",array_id,start_row,nrows,type_id,size,
+             buf);
+
+    /* Check args */
+    if (H5_RAGGED!=H5I_group(array_id) ||
+	NULL==(ra=H5I_object(array_id))) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a ragged array");
+    }
+    if (H5_DATATYPE!=H5I_group(type_id) ||
+	NULL==(type=H5I_object(type_id))) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
+    }
+    if (nrows>0 && !size) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no size array");
+    }
+    if (nrows>0 && !buf) {
+	HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer array");
+    }
+    
+    /* Do the work */
+    if (H5R_read(ra, start_row, nrows, type, size, buf)<0) {
+	HRETURN_ERROR(H5E_RAGGED, H5E_READERROR, FAIL,
+		      "unable to read ragged array");
+    }
+
+    FUNC_LEAVE(SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5R_read
+ *
+ * Purpose:	Reads (part of) a ragged array.  See H5Rread() for details.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, August 26, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5R_read(H5R_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type,
+	 hsize_t size[], void *buf[])
+{
+    herr_t	ret_value=FAIL;
+    H5R_meta_t	*meta = NULL;
+    H5S_t	*mf_space=NULL;		/*meta file data space		*/
+    H5S_t	*mm_space=NULL;		/*meta memory data space	*/
+    H5S_t	*rf_space=NULL;		/*raw data file space		*/
+    H5S_t	*rm_space=NULL;		/*raw data memory space		*/
+    hsize_t	meta_cur_size;		/*current meta data nelmts	*/
+    hsize_t	meta_read_size;		/*amount of meta data to read	*/
+    hsize_t	raw_cur_size[2];	/*raw data current size		*/
+    hsize_t	raw_read_size;		/*amount of raw data to read	*/
+    hssize_t	hs_offset[2];		/*hyperslab offset		*/
+    hsize_t	hs_size[2];		/*hyperslab size		*/
+    uint8	*raw_buf=NULL;		/*raw buffer			*/
+    size_t	type_size;		/*size of the TYPE argument	*/
+    hsize_t	i;
+
+    FUNC_ENTER(H5R_read, FAIL);
+
+    /* Check args */
+    assert(ra);
+    assert(type);
+    assert(0==nrows || size);
+    assert(0==nrows || buf);
+    if (0==nrows) HRETURN(SUCCEED);
+    type_size = H5T_get_size(type);
+
+    /* Read from the raw dataset */
+    if (NULL==(rf_space=H5D_get_space(ra->raw)) ||
+	H5S_extent_dims(rf_space, raw_cur_size, NULL)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		    "unable to determine current raw data extents");
+    }
+    if ((hsize_t)start_row>=raw_cur_size[0]) {
+	raw_read_size = 0;
+    } else {
+	raw_read_size = MIN(nrows, raw_cur_size[0]-(hsize_t)start_row);
+    }
+    
+	
+	       
+
+
+
+
+    /* Get the meta data */
+    if (NULL==(meta=H5MM_malloc(nrows*sizeof(H5R_meta_t)))) {
+	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL,
+		    "memory allocation failed for meta data");
+    }
+    if (NULL==(mf_space=H5D_get_space(ra->meta)) ||
+	H5S_extent_dims(mf_space, &meta_cur_size, NULL)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		    "unable to get current meta data extents");
+    }
+    if ((hsize_t)start_row>=meta_cur_size) {
+	meta_read_size = 0;
+    } else {
+	meta_read_size = MIN(nrows, meta_cur_size-(hsize_t)start_row);
+    }
+    if (NULL==(mm_space=H5S_create(H5S_SIMPLE)) ||
+	H5S_set_extent_simple(mm_space, 1, &meta_read_size, NULL)<0 ||
+	H5S_select_hyperslab(mf_space, H5S_SELECT_SET, &start_row, NULL,
+			     &meta_read_size, NULL)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
+		    "unable to set meta data selection");
+    }
+    if (H5D_read(ra->meta, H5R_meta_type_g, mm_space, mf_space,
+		 &H5D_xfer_dflt, meta)<0) {
+	HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL,
+		    "unable to read meta data");
+    }
+    HDmemset(meta+meta_read_size, 0,
+	     (nrows-meta_read_size)*sizeof(H5R_meta_t));
+
+
+    HGOTO_ERROR(H5E_RAGGED, H5E_UNSUPPORTED, FAIL,
+		"not implemented yet");
+    
+ done:
+    FUNC_LEAVE(ret_value);
+}
+