[svn-r1087] Changes since 19990218

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

./src/H5F.c
./src/H5private.h
./src/H5Ipublic.h
./src/H5O.c
	Fixed a rather nasty bug with file closing that caused the
	file boot block to be updated incorrectly, effectively
	truncating the file.  The bug I fixed was triggered by:

	    1. Create a file, F
	    2. Open an object, X
	    3. Close file F
	    4. Reopen file F for read/write.
	    5. Create and close some objects
	    6. Close file F
	    7. Close library (exit).

	Step 3 pended the close because object X is still open, but
	the file ID was removed from the H5I_FILE ID group. Step 4
	created a new file because it didn't see any matching file on
	the H5I_FILE ID group.  Step 5 extends the file. Step 6 writes
	the new file boot block to disk. Step 7 closes object X and
	completes the close from step 3, writing the old boot block
	information to disk.

	The new behavior is that step 3 moves the file from the
	H5I_FILE group to the H5I_FILE_CLOSING group. Step 4 searches
	both groups and finds the file. Step 5 extends the file using
	the same H5F_file_t struct as step 3. Step 6 closes the H5F_t
	struct opened in step 3 but not the H5F_file_t struct shared
	by steps 1 and 3. Step 7 closes object X which closes the
	H5F_file_t from step 1, flushing the boot block which was
	shared by all steps.

./src/H5F.c
	Added some bulletproofing to file reference counting and
	removed comments which no longer apply.  Added H5F_flush_all()
	and H5F_close_all() which apply to all files.

./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
	Added the new H5I_free_t data type to describe the function
	type to be passed as the `free_func' argument to
	H5I_init_group().

./src/H5I.c
	Bulletproofed the object removal functions. Removed comments
	which no longer apply. Changed global variable names so they
	don't violate the naming scheme. Added H5I_debug() that prints
	the contents of an ID group.  Removed H5I_inc_ref() because it
	isn't used. Reindented a couple of functions.

./src/H5.c
./src/H5G.c
./src/H5Ipublic.h
	Changed H5I_MAXID to H5I_NGROUPS to better relect the fact
	that it's the total number of valid ID groups.

./src/H5Shyper.c
	Changed hyperslab offset arrays to signed quantities to get
	rid of warnings on DEC cluster.

./src/H5Flow.c
./src/H5Fprivate.h
	Changed the objno argument of H5F_addr_pack() to be unsigned
	to get rid of warnings on DEC cluster.

1 files changed, 40 insertions, 24 deletions

diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 2032129..71b6ca4 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -336,6 +336,12 @@ typedef struct H5F_low_class_t {
 			 haddr_t *addr/*out*/);
 } H5F_low_class_t;
 
+/*
+ * One of these H5F_low_t structs is allocated for each H5F_file_t struct.
+ * This struct describes how to access the storage for the hdf5 address space,
+ * whether that storage is file, local memory, shared memory, network
+ * distributed global memory, etc.
+ */
 typedef struct H5F_low_t {
     const H5F_low_class_t *type;/* What type of file is this?		*/
     haddr_t		eof;	/* Address of logical end-of-file	*/
@@ -427,28 +433,12 @@ typedef struct H5F_rdcc_t {
     struct H5F_rdcc_ent_t **slot; /* Chunk slots, each points to a chunk*/
 } H5F_rdcc_t;
 
-/* Mount property list */
-typedef struct H5F_mprop_t {
-    hbool_t		local;	/* Are absolute symlinks local to file?	*/
-} H5F_mprop_t;
-
-/* A record of the mount table */
-typedef struct H5F_mount_t {
-    struct H5G_t	*group;	/* Mount point group held open		*/
-    struct H5F_t	*file;	/* File mounted at that point		*/
-} H5F_mount_t;
-    
-/* The mount table */
-typedef struct H5F_mtab_t {
-    struct H5F_t	*parent;/* Parent file				*/
-    uintn		nmounts;/* Number of children which are mounted	*/
-    uintn		nalloc;	/* Number of mount slots allocated	*/
-    H5F_mount_t		*child;	/* An array of mount records		*/
-} H5F_mtab_t;
-
 /*
  * Define the structure to store the file information for HDF5 files. One of
- * these structures is allocated per file, not per H5Fopen().
+ * these structures is allocated per file, not per H5Fopen(). That is, set of
+ * H5F_t structs can all point to the same H5F_file_t struct. The `nrefs'
+ * count in this struct indicates the number of H5F_t structs which are
+ * pointing to this struct.
  */
 typedef struct H5F_file_t {
     H5F_search_t key;		/* The key for looking up files		*/
@@ -471,10 +461,35 @@ typedef struct H5F_file_t {
     H5MF_free_t fl_free[H5MF_NFREE]; /*free block array			*/
 } H5F_file_t;
 
+/* Mount property list */
+typedef struct H5F_mprop_t {
+    hbool_t		local;	/* Are absolute symlinks local to file?	*/
+} H5F_mprop_t;
+
+/* A record of the mount table */
+typedef struct H5F_mount_t {
+    struct H5G_t	*group;	/* Mount point group held open		*/
+    struct H5F_t	*file;	/* File mounted at that point		*/
+} H5F_mount_t;
+    
+/*
+ * The mount table describes what files are attached to (mounted on) the file
+ * to which this table belongs.
+ */
+typedef struct H5F_mtab_t {
+    struct H5F_t	*parent;/* Parent file				*/
+    uintn		nmounts;/* Number of children which are mounted	*/
+    uintn		nalloc;	/* Number of mount slots allocated	*/
+    H5F_mount_t		*child;	/* An array of mount records		*/
+} H5F_mtab_t;
+
 /*
  * This is the top-level file descriptor.  One of these structures is
- * allocated every time H5Fopen() is called although they may contain
- * pointers to shared H5F_file_t structs.
+ * allocated every time H5Fopen() is called although they may contain pointers
+ * to shared H5F_file_t structs. The reference count (nrefs) indicates the
+ * number of times the file has been opened (the application can only open a
+ * file once explicitly, but the library can open the file a second time to
+ * indicate that the file is mounted on some other file).
  */
 typedef struct H5F_t {
     uintn		nrefs;		/* Reference count		*/
@@ -482,7 +497,7 @@ typedef struct H5F_t {
     char		*name;		/* Name used to open file	*/
     H5F_file_t		*shared;	/* The shared file info		*/
     uintn		nopen_objs;	/* Number of open object headers*/
-    hbool_t		close_pending;	/* File close is pending	*/
+    hid_t		closing;	/* H5I_FILE_CLOSING ID or zero	*/
     H5F_mtab_t		mtab;		/* File mount table		*/
 } H5F_t;
 
@@ -545,13 +560,14 @@ __DLLVAR__  hbool_t H5_mpi_1_metawrite_g;
 
 /* Private functions, not part of the publicly documented API */
 __DLL__ herr_t H5F_init(void);
-__DLL__ herr_t H5F_close_all(void);
 __DLL__ void H5F_encode_length_unusual(const H5F_t *f, uint8_t **p,
 				       uint8_t *l);
 __DLL__ H5F_t *H5F_open(const char *name, uintn flags,
 			const H5F_create_t *create_parms,
 			const H5F_access_t *access_parms);
 __DLL__ herr_t H5F_close(H5F_t *f);
+__DLL__ herr_t H5F_close_all(void);
+__DLL__ herr_t H5F_flush_all(hbool_t invalidate);
 __DLL__ herr_t H5F_debug(H5F_t *f, const haddr_t *addr, FILE * stream,
 			 intn indent, intn fwidth);
 __DLL__ herr_t H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream,