[svn-r129] Changes since 19970916

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

./config/depend.in
	Fixed backslashes in sed script because the H5Gnode.c
	dependency info was disappearing.  You'll have to rerun
	config.status to rebuild the Makefiles unless you use gnu
	make.

./config/conclude.in
	Also removes emacs backup files, TAGS, and svf backup files.

./config/linux
	Grouped gcc flags and added provisions for debugging vs. production.

./html/H5.format.html
	Updated messages 0x0008, 0x0009, and 0x000A.

./html/storage.html
	Documentation describing storage schemes.

./src/Makefile.in
./test/Makefile.in
	New source files.

./src/H5A.c
./src/H5Apublic.h
./src/H5C.c
	Changed VOIDP to void* in a couple places.

./src/H5AC.c
./src/H5ACprivate.h
./src/H5B.c
./src/H5Bprivate.h
./src/H5G.c
./src/H5Gnode.c
./src/H5Gprivate.h
./src/H5H.c
./src/H5O.c
	Removed `const' from some variables because H5G_node_found() wanted
	to modify it's udata argument. Removing const there caused it
	to cascade to these other locations.

./src/H5AC.c
./src/H5ACprivate.h
./src/H5B.c
./src/H5Gnode.c
./src/H5Gstab.c
./src/H5H.c
./src/H5O.c
	Added an extra argument to H5AC_find_f() and H5AC_protect(). This
	arg gets passed to the load() method.  Also added an extra
	argument to the H5AC_find() macro.

./src/H5B.c
./src/H5Bprivate.h
./src/H5Gnode.c
	Extra argument passed to the sizeof_rkey() method.

./src/H5Fprivate.c
./src/H5Fistore.c (new)
	Added indexed I/O operations.

./src/H5G.c
./src/H5Gnode.c
./src/H5Gprivate.h
	Beginning to add H5G_open/close and related bug fixes.

./src/H5Oprivate.h
./src/H5Oistore.c (new)
	Added the H5O_ISTORE messsage (0x0008) for indexed storage of
	objects.

./src/H5private.h
	Added extra braces around both sides of the FUNC_ENTER() and
	FUNC_LEAVE() macros so FUNC_ENTER() can appear before
	declarations or after executable statements the second case is
	used by H5G_namei() to initialize output arguments to sane
	values before FUNC_ENTER() might return failure.

		int f ()
		{
		   int decl1;
		   printf ("This happens before FUNC_ENTER()\n");
		   FUNC_ENTER (...);
		   int another_declaration;

./src/H5B.c
./src/H5Bprivate.h
./src/H5Gnode.c
	Extra arguments for key encoding and decoding.

./src/H5E.c
./src/H5Epublic.h
./src/H5Fistore.c
./src/H5Oistore.c
./src/H5Oprivate.h
	Indexed, chunked, sparse storage (not ready for general consumption
	yet).

./src/H5V.c		(new)
./src/H5Vprivate.h	(new)
./test/hyperslab.c	(new)
	Vector, array, and hyperslab functions.

./src/H5B.c
./src/H5Bprivate.h
./src/H5Fistore.c
./src/H5Gnode.c
./src/H5V.c
./src/H5Vprivate.h
./test/hyperslab.c
	Added functionality for indexed storage.

./src/H5F.c
	Fixed problems with seek optimizing.  Recommend we disable it
	until we can implement it in the file/address class since all
	of HDF5 must be aware of it.

./src/H5O.c
	Fixed comeent speling erorr :-)

./MANIFEST
	Added new files.

./config/conclude.in
	Added the word `Testing' to the test cases.  So if a test
	program is called hyperslab then the make output will contain
	the line `Testing hyperslab'.

./config/linux
	The default file I/O library is Posix section 2 on my linux
	machine so I can do some I/O performance testing.

./src/H5C.c
./src/H5Cprivate.h
./src/H5Cpublic.h
	Added ability to set size of indexed-storage B-tree.

./src/H5D.c
./src/H5E.c
./src/H5Epublic.h
./src/H5F.c
./src/H5Fprivate.h
./src/H5G.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5Gpublic.h
./src/H5Gshad.c
./src/H5Gstab.c
./test/stab.c
	Changed `directory' to `group' in numerous places.

./src/H5private.h
	The FILELIB constant can be set on the compile command-line.

./src/istore.c		     NEW
	Tests for indexed storage.

3 files changed, 462 insertions, 11 deletions

diff --git a/test/Makefile.in b/test/Makefile.in
index 8a7d4f0..d2cbe3a 100644
--- a/test/Makefile.in
+++ b/test/Makefile.in
@@ -10,18 +10,38 @@
 CPPFLAGS=-I. -I../src @CPPFLAGS@
 
 # These are our main targets:
-PROGS=testhdf5
+PROGS=testhdf5 hyperslab istore
 TESTS=$(PROGS)
 
-# Source and object files for programs...
-PROG_SRC=testhdf5.c tfile.c theap.c tmeta.c tohdr.c tstab.c th5t.c th5p.c th5d.c
+# Source and object files for programs...  The PROG_SRC list contains all the
+# source files and is used for things like dependencies, archiving, etc.  The
+# other source lists are for the individual tests, the files of which may
+# overlap with other tests.
+PROG_SRC=testhdf5.c tfile.c theap.c tmeta.c tohdr.c tstab.c th5t.c th5p.c    \
+         th5d.c hyperslab.c istore.c
 PROG_OBJ=$(PROG_SRC:.c=.o)
 
+TESTHDF5_SRC=testhdf5.c tfile.c theap.c tmeta.c tohdr.c tstab.c th5t.c       \
+	     th5p.c th5d.c
+TESTHDF5_OBJ=$(TESTHDF5_SRC:.c=.o)
+
+HYPERSLAB_SRC=hyperslab.c
+HYPERSLAB_OBJ=$(HYPERSLAB_SRC:.c=.o)
+
+ISTORE_SRC=istore.c
+ISTORE_OBJ=$(ISTORE_SRC:.c=.o)
+
 # Private header files (not to be installed)...
 PRIVATE_HDR=testhdf5.h
 
 # How to build the programs...
-testhdf5: $(PROG_OBJ) ../src/libhdf5.a
-	$(CC) $(CFLAGS) -o $@ $(PROG_OBJ) ../src/libhdf5.a $(LIBS)
+testhdf5: $(TESTHDF5_OBJ) ../src/libhdf5.a
+	$(CC) $(CFLAGS) -o $@ $(TESTHDF5_OBJ) ../src/libhdf5.a $(LIBS)
+
+hyperslab: $(HYPERSLAB_OBJ) ../src/libhdf5.a
+	$(CC) $(CFLAGS) -o $@ $(HYPERSLAB_OBJ) ../src/libhdf5.a $(LIBS)
+
+istore: $(ISTORE_OBJ) ../src/libhdf5.a
+	$(CC) $(CFLAGS) -o $@ $(ISTORE_OBJ) ../src/libhdf5.a $(LIBS)
 
 @CONCLUDE@
diff --git a/test/istore.c b/test/istore.c
new file mode 100644
index 0000000..9f6fa1f
--- /dev/null
+++ b/test/istore.c
@@ -0,0 +1,431 @@
+/*
+ * Copyright (C) 1997 NCSA
+ *                    All rights reserved.
+ *
+ * Programmer: 	Robb Matzke <matzke@llnl.gov>
+ *             	Wednesday, October 15, 1997
+ *
+ * Purpose:	Tests various aspects of indexed raw data storage.
+ */
+#include <H5private.h>
+#include <H5Fprivate.h>
+#include <H5Gprivate.h>
+#include <H5MMprivate.h>
+#include <H5Oprivate.h>
+#include <H5Vprivate.h>
+
+#define FILENAME	"istore.h5"
+
+#define AT() printf ("   at %s:%d in %s()...\n",			    \
+		     __FILE__, __LINE__, __FUNCTION__);
+   
+
+
+/*-------------------------------------------------------------------------
+ * Function:	print_array
+ *
+ * Purpose:	Prints the values in an array
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Friday, October 10, 1997
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+print_array (uint8 *array, size_t nx, size_t ny, size_t nz)
+{
+   int		i, j, k;
+
+   for (i=0; i<nx; i++) {
+      if (nz>1) {
+	 printf ("i=%d:\n", i);
+      } else {
+	 printf ("%03d:", i);
+      }
+      
+      for (j=0; j<ny; j++) {
+	 if (nz>1) printf ("%03d:", j);
+	 for (k=0; k<nz; k++) {
+	    printf (" %3d", *array++);
+	 }
+	 if (nz>1) printf ("\n");
+      }
+      printf ("\n");
+   }
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function:	new_object
+ *
+ * Purpose:	Creates a new object that refers to a indexed storage of raw
+ *		data.  No raw data is stored.
+ *
+ * Return:	Success:	Handle to a new open object.
+ *
+ *		Failure:	NULL, error message printed.
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, October 15, 1997
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static H5G_entry_t *
+new_object (H5F_t *f, const char *name, size_t ndims)
+{
+   H5G_entry_t	*handle = NULL;
+   H5O_istore_t	istore;
+   intn		i;
+   
+   /* Create the object symbol table entry and header */
+   if (NULL==(handle=H5G_create (f, name, 64))) {
+      puts ("*FAILED*");
+      if (!isatty (1)) {
+	 AT ();
+	 printf ("   H5G_create (f, name=\"%s\") = NULL\n", name);
+      }
+      return NULL;
+   }
+
+   /* Add the indexed-storage message */
+   memset (&istore, 0, sizeof istore);
+   istore.ndims = ndims;
+   for (i=0; i<ndims; i++) istore.alignment[i] = 2;
+
+   if (H5O_modify (f, H5O_NO_ADDR, handle, H5O_ISTORE, H5O_NEW_MESG,
+		   &istore)<0) {
+      printf ("*FAILED*\n");
+      if (!isatty (1)) {
+	 AT();
+	 printf ("   H5G_modify istore message failure\n");
+      }
+      return NULL;
+   }
+
+   return handle;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	test_create
+ *
+ * Purpose:	Creates a named object that refers to indexed storage of raw
+ *		data.  No raw data is stored.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, October 15, 1997
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+test_create (H5F_t *f, const char *prefix)
+{
+   H5G_entry_t	*handle = NULL;
+   intn		i;
+   char		name[256];
+   
+   printf ("%-70s", "Testing istore create");
+   fflush (stdout);
+
+   for (i=1; i<=H5O_ISTORE_NDIMS; i++) {
+      sprintf (name, "%s_%02d", prefix, i);
+      if (NULL==(handle=new_object (f, name, i))) return FAIL;
+      H5G_close (f, handle);
+   }
+
+   puts (" PASSED");
+   return SUCCEED;
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function:	test_extend
+ *
+ * Purpose:	Creates an empty object and then writes to it in such a way
+ *		as to always extend the object's domain.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, October 15, 1997
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+test_extend (H5F_t *f, const char *prefix,
+	     size_t nx, size_t ny, size_t nz)
+{
+   H5G_entry_t	*handle = NULL;
+   int		i, j, k, ndims, ctr;
+   uint8	*buf=NULL, *check=NULL, *whole=NULL;
+   char		dims[64], s[256], name[256];
+   size_t	offset[3];
+   size_t	max_corner[3];
+   size_t	size[3];
+   size_t	whole_size[3];
+   H5O_istore_t	istore;
+
+   if (!nz) {
+      if (!ny) {
+	 ndims = 1;
+	 ny = nz = 1;
+	 sprintf (dims, "%d", nx);
+      } else {
+	 ndims = 2;
+	 nz = 1;
+	 sprintf (dims, "%dx%d", nx, ny);
+      }
+   } else {
+      ndims = 3;
+      sprintf (dims, "%dx%dx%d", nx, ny, nz);
+   }
+
+
+   sprintf (s, "Testing istore extend: %s", dims);
+   printf ("%-70s", s);
+   fflush (stdout);
+   buf = H5MM_xmalloc (nx*ny*nz);
+   check = H5MM_xmalloc (nx*ny*nz);
+   whole = H5MM_xcalloc (nx*ny*nz, 1);
+
+   /* Build the new empty object */
+   sprintf (name, "%s_%s", prefix, dims);
+   if (NULL==(handle=new_object (f, name, ndims))) {
+      if (!isatty (1)) {
+	 AT ();
+	 printf ("   Cannot create %d-d object `%s'\n", ndims, name);
+      }
+      goto error;
+   }
+   if (NULL==H5O_read (f, H5O_NO_ADDR, handle, H5O_ISTORE, 0, &istore)) {
+      puts ("*FAILED*");
+      if (!isatty (1)) {
+	 AT ();
+	 printf ("   Unable to read istore message\n");
+      }
+      goto error;
+   }
+   if (ndims!=istore.ndims) {
+      puts ("*FAILED*");
+      if (!isatty (1)) {
+	 AT ();
+	 printf ("   Header read error: istore.ndims != %d\n", ndims);
+      }
+      goto error;
+   }
+
+   whole_size[0] = nx;
+   whole_size[1] = ny;
+   whole_size[2] = nz;
+   max_corner[0] = 0;
+   max_corner[1] = 0;
+   max_corner[2] = 0;
+
+   for (ctr=0; H5V_vector_lt (ndims, max_corner, whole_size); ctr++) {
+
+      /* Size and location */
+      if (0==ctr) {
+	 offset[0] = offset[1] = offset[2] = 0;
+	 size[0] = size[1] = size[2] = 1;
+      } else {
+	 for (i=0; i<ndims; i++) {
+	    if (ctr % ndims == i) {
+	       offset[i] = max_corner[i];
+	       size[i] = 1;
+	       if (offset[i]+size[i]>whole_size[i]) continue;
+	    } else {
+	       offset[i] = 0;
+	       size[i] = max_corner[i];
+	    }
+	 }
+      }
+
+#if 0
+      if (0==ctr) printf ("\n");
+      printf ("   Insert: ctr=%d, corner=(%d", ctr, offset[0]);
+      if (ndims>1) printf (",%d", offset[1]);
+      if (ndims>2) printf (",%d", offset[2]);
+      printf ("), size=(%d", size[0]);
+      if (ndims>1) printf (",%d", size[1]);
+      if (ndims>2) printf (",%d", size[2]);
+      printf (")\n");
+#endif
+      
+      /* Fill the source array */
+      memset (buf, 128+ctr, size[0]*size[1]*size[2]);
+
+      /* Write to disk */
+      if (H5F_istore_write (f, &istore, offset, size, buf)<0) {
+	 puts ("*FAILED*");
+	 if (!isatty (1)) {
+	    AT ();
+	    printf ("   Write failed: ctr=%d\n", ctr);
+	 }
+	 goto error;
+      }
+
+      /* Read from disk */
+      memset (check, 0xff, size[0]*size[1]*size[2]);
+      if (H5F_istore_read (f, &istore, offset, size, check)<0) {
+	 puts ("*FAILED*");
+	 if (!isatty (1)) {
+	    AT ();
+	    printf ("   Read failed: ctr=%d\n", ctr);
+	 }
+	 goto error;
+      }
+      if (memcmp (buf, check, size[0]*size[1]*size[2])) {
+	 puts ("*FAILED*");
+	 if (!isatty (1)) {
+	    AT ();
+	    printf ("   Read check failed: ctr=%d\n", ctr);
+	    printf ("   Wrote:\n");
+	    print_array (buf, size[0], size[1], size[2]);
+	    printf ("   Read:\n");
+	    print_array (buf, size[0], size[1], size[2]);
+	 }
+	 goto error;
+      }
+      
+      /* Write to `whole' buffer for later checking */
+      H5V_hyper_copy (ndims, size,
+		      whole_size, offset, whole,	/*dst*/
+		      size, H5V_ZERO, buf);		/*src*/
+
+      /* Update max corner */
+      for (i=0; i<ndims; i++) {
+	 max_corner[i] = MAX (max_corner[i], offset[i]+size[i]);
+      }
+   }
+
+   /* Update the object header */
+   H5O_modify (f, H5O_NO_ADDR, handle, H5O_ISTORE, 0, &istore);
+
+
+   /* Now read the entire array back out and check it */
+   memset (buf, 0xff, nx*ny*nz);
+   if (H5F_istore_read (f, &istore, H5V_ZERO, whole_size, buf)<0) {
+      puts ("*FAILED*");
+      if (!isatty (1)) {
+	 AT ();
+	 printf ("   Read failed for whole array\n");
+      }
+      goto error;
+   }
+   for (i=0; i<nx; i++) {
+      for (j=0; j<ny; j++) {
+	 for (k=0; k<nz; k++) {
+	    if (whole[i*ny*nz + j*nz + k] != buf[i*ny*nz + j*nz + k]) {
+	       puts ("*FAILED*");
+	       if (!isatty (1)) {
+		  AT ();
+		  printf ("   Check failed at i=%d", i);
+		  if (ndims>1) printf (", j=%d", j);
+		  if (ndims>2) printf (", k=%d\n", k);
+		  printf ("   Check array is:\n");
+		  print_array (whole, nx, ny, nz);
+		  printf ("   Value read is:\n");
+		  print_array (buf, nx, ny, nz);
+	       }
+	       goto error;
+	    }
+	 }
+      }
+   }
+   
+   H5G_close (f, handle);
+   puts (" PASSED");
+   H5MM_xfree (buf);
+   H5MM_xfree (check);
+   H5MM_xfree (whole);
+   return SUCCEED;
+
+ error:
+   H5MM_xfree (buf);
+   H5MM_xfree (check);
+   H5MM_xfree (whole);
+   return FAIL;
+}
+      
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	Tests indexed storage stuff.
+ *
+ * Return:	Success:	exit(0)
+ *
+ *		Failure:	exit(non-zero)
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, October 15, 1997
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main (void)
+{
+   H5F_t	*f;
+   herr_t	status;
+   int		nerrors = 0;
+   
+   /* Create the test file */
+   if (NULL==(f=H5F_open (FILENAME, H5F_ACC_CREAT|H5F_ACC_WRITE|H5F_ACC_TRUNC,
+			  NULL))) {
+      printf ("Cannot create file %s; test aborted\n", FILENAME);
+      exit (1);
+   }
+
+   /*----------------------
+    * INDEXED STORAGE TESTS
+    *---------------------- 
+    */
+   status = test_create (f, "test_create_1");
+   nerrors += status<0 ? 1 : 0;
+
+   status = test_extend (f, "test_extend_1", 10, 0, 0);
+   nerrors += status<0 ? 1 : 0;
+   status = test_extend (f, "test_extend_1", 10, 10, 0);
+   nerrors += status<0 ? 1 : 0;
+   status = test_extend (f, "test_extend_1", 10, 10, 10);
+   nerrors += status<0 ? 1 : 0;
+   
+   
+   
+
+
+   /* Close the test file and exit */
+   H5F_close (f);
+   if (nerrors) {
+      printf ("***** %d I-STORE TEST%s FAILED! *****\n",
+	      nerrors, 1==nerrors?"":"S");
+      if (isatty (1)) {
+	 printf ("(Redirect output to a pager or a file to see "
+		 "debug output)\n");
+      }
+      exit (1);
+   }
+
+   printf ("All i-store tests passed.\n");
+   exit (0);
+}
diff --git a/test/tstab.c b/test/tstab.c
index 652029f..d2f6de4 100644
--- a/test/tstab.c
+++ b/test/tstab.c
@@ -84,7 +84,7 @@ test_1 (void)
     */
    HDmemset (&dir_ent, 0, sizeof(H5G_entry_t));
    HDmemset (&ent1, 0, sizeof(H5G_entry_t));
-   status = H5G_find (f, NULL, &dir_ent, "/", &ent1);
+   status = H5G_find (f, "/", &dir_ent, &ent1);
    CHECK_I (status, "H5G_find");
    VERIFY (dir_ent.header, 0, "H5G_find");
    VERIFY (ent1.header, obj1->header, "H5G_find");
@@ -107,7 +107,7 @@ test_1 (void)
 
    /* try to read the first object */
    HDmemset (&ent1, 0, sizeof(H5G_entry_t));
-   status = H5G_find (f, NULL, NULL, "/Root Object", &ent1);
+   status = H5G_find (f, "/Root Object", NULL, &ent1);
    CHECK_I (status, "H5G_find");
    VERIFY (ent1.header, obj1->header, "H5G_find");
 
@@ -151,7 +151,7 @@ test_1 (void)
     */
    HDmemset (&dir_ent, 0, sizeof(H5G_entry_t));
    HDmemset (&ent1, 0, sizeof(H5G_entry_t));
-   status = H5G_find (f, NULL, &dir_ent, "/", &ent1);
+   status = H5G_find (f, "/", &dir_ent, &ent1);
    CHECK_I (status, "H5G_find");
    VERIFY (dir_ent.header, 0, "H5G_find");
    VERIFY (ent1.header, obj1->header, "H5G_find");
@@ -163,7 +163,7 @@ test_1 (void)
    /* now as `/foo' */
    HDmemset (&dir_ent, 0, sizeof(H5G_entry_t));
    HDmemset (&ent1, 0, sizeof(H5G_entry_t));
-   status = H5G_find (f, NULL, &dir_ent, "/foo", &ent1);
+   status = H5G_find (f, "/foo", &dir_ent, &ent1);
    CHECK_I (status, "H5G_find");
    VERIFY (dir_ent.header, 0, "H5G_find");
    VERIFY (ent1.header, obj1->header, "H5G_find");
@@ -185,7 +185,7 @@ test_1 (void)
 
    /* try to read the first object */
    HDmemset (&ent1, 0, sizeof(H5G_entry_t));
-   status = H5G_find (f, NULL, NULL, "/foo", &ent1);
+   status = H5G_find (f, "/foo", NULL, &ent1);
    CHECK_I (status, "H5G_find");
    VERIFY (ent1.header, obj1->header, "H5G_find");
 
@@ -243,7 +243,7 @@ test_2 (void)
     * Create a directory that has so many entries that the root
     * of the B-tree ends up splitting.
     */
-   obj1 = H5G_mkdir (f, "/big", nsyms*12+2);
+   obj1 = H5G_new (f, "/big", nsyms*12+2);
    CHECK_PTR (obj1, "H5G_mkdir");
    H5G_close (f, obj1);
    obj1 = NULL;