[svn-r1568] Changes since 19990730

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

This extensive change is the virtual file layer implementation. I've
ported and tested the sec2, family, and core drivers and only ported
the mpio driver (Albert will test it).  So if you need MPIO I would
recommend sticking with the previous version for a while.

You will get a few compile warnings about split and stdio drivers not
being implemented and possibly tracing information not inserted in
some of the drivers. You can safely ignore them but I plan to fix
them.

I'm still working on the split driver because I just realized that it
needs a part of the VFL that isn't written yet.

Documentation is being updated also because there were some minor
changes (mostly just name changes). It should be available on my web
site later this week.

./MANIFEST
./src/Makefile.in
./src/hdf5.h
./src/H5Flow.c			[REMOVED]
./src/H5Fstdio.c		[REMOVED]
./src/H5Fsec2.c			[REMOVED]
./src/H5Fsplit.c		[REMOVED]
./src/H5Fmpio.c			[REMOVED]
./src/H5Ffamily.c		[REMOVED]
./src/H5Fcore.c			[REMOVED]
./src/H5MFpublic.h		[REMOVED]
./src/H5FD.c			[NEW]
./src/H5FDcore.c		[NEW]
./src/H5FDcore.h		[NEW]
./src/H5FDfamily.c		[NEW]
./src/H5FDfamily.h		[NEW]
./src/H5FDmpio.c		[NEW]
./src/H5FDmpio.h		[NEW]
./src/H5FDprivate.h		[NEW]
./src/H5FDpublic.h		[NEW]
./src/H5FDsec2.c		[NEW]
./src/H5FDsec2.h		[NEW]
	Removed/added files for virtual file layer.

./bin/trace
./src/H5.c
	Removed unused public datatypes and added new VFL public
	datatypes.

	Changed an error message.

./config/BlankForm
./config/dec-flags
./config/gnu-flags
./config/hpux10.20
./config/hpux9.03
./config/irix5.x
./config/irix6.x
./config/solaris2.x
./config/unicosmk
	Removed the H5F_OPT_SEEK and H5F_LOW_DFLT constants from the
	configuration since they're no longer applicable. The default
	file driver is always the sec2 driver and it always optimizes
	calls to lseek() or lseek64().

./config/depend.in
	C preprocessor errors generated during automatic dependency
	building are sent to /dev/null to prevent them from appearing
	twice in the make output.

./src/H5AC.c
./src/H5B.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Oshared.c
./src/H5T.c
./src/H5detect.c
./test/ohdr.c
	Changed H5F_ADDR_UNDEF to HADDR_UNDEF to be more consistent
	with the `haddr_t' datatype which is now a public type.

./src/H5D.c
./src/H5P.c
./src/H5Ppublic.h
./src/H5Tconv.c
./test/cmpd_dset.c
./test/dsets.c
./test/overhead.c
./test/tselect.c
./test/tvltypes.c
	The H5P_DATASET_XFER constant was changed to H5P_DATA_XFER
	because the properties apply to all types of I/O operations,
	not just datasets.

./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5Dpublic.h
./src/H5F.c
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5R.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Spoint.c
./src/H5Sprivate.h
./test/big.c
./test/h5test.c
./test/istore.c
./testpar/t_dset.c
./testpar/t_file.c
./tools/h5debug.c
./tools/h5ls.c
	Modified to work with the virtual file layer by calling H5FD_*
	functions instead of H5F_low_* functions and by passing file
	access and data transfer properties by object ID instead of
	pointer.

	Changed H5D_transfer_t to H5FD_mpio_xfer_t since the
	COLLECTIVE vs. INDEPENDENT transfer mode is specific to the
	MPIO file driver.

	Moved MPIO-specific stuff into the MPIO driver.

./src/H5B.c
./src/H5D.c
./src/H5Fprivate.h
	The H5F_mpio_* private functions were renamed and placed in
	the H5FDmpio driver except those which appeared in H5Smpio.c.

./src/H5E.c
./src/H5Epublic.h
	Added major error number H5E_VFL for virtual file layer
	related errors.

./src/H5F.c
./src/H5Fprivate.h
	Changed the logic that controls whether the boot block is
	written. Instead of assuming that the first call to write the
	boot block is only to allocate space, I've added a function
	argument which makes this explicit.

	Changed the way files are compared so that a driver-defined
	comparison function can be called.  Files which belong to
	different drivers are always considered different.

	Removed H5F_driver_t since file drivers are now identified by
	object ID instead of a special non-user-extendible datatype.

	Removed all the hard-coded low-level file properties which
	have been replaced by the various file drivers.

./src/H5I.c
./src/H5Iprivate.h
	Added the H5I_inc_ref() which was removed a few months ago
	since we finally have a use for it.

./src/H5Ipublic.h
	Added the H5I_VFL object ID type to identify file drivers in
	the virtual file layer.

./src/H5MF.c
./src/H5MFprivate.h
	Moved all the allocation/deallocation code into the virtual
	file layer which allows file drivers to override much of it.

./src/H5P.c
./src/H5Ppublic.h
	Moved file driver-specific code into the various file driver
	files.

	The H5Pcopy() and H5Pclose() functions make calls into the
	virtual file driver to manage the memory for driver-specific
	file access and data transfer properties.

./src/H5private.h
./src/H5public.h
	The `haddr_t' type is now public.

./test/tfile.c
	Added a few more comments.

1 files changed, 491 insertions, 0 deletions

diff --git a/src/H5FDcore.c b/src/H5FDcore.c
new file mode 100644
index 0000000..4be868e
--- /dev/null
+++ b/src/H5FDcore.c
@@ -0,0 +1,491 @@
+/*
+ * Copyright © 1999 NCSA
+ *                  All rights reserved.
+ *
+ * Programmer:  Robb Matzke <matzke@llnl.gov>
+ *              Tuesday, August 10, 1999
+ *
+ * Purpose:	A driver which stores the HDF5 data in main memory  using
+ *		only the HDF5 public API. This driver is useful for fast
+ *		access to small, temporary hdf5 files.
+ */
+#include <assert.h>
+#include <hdf5.h>
+#include <stdlib.h>
+
+#undef MAX
+#define MAX(X,Y)	((X)>(Y)?(X):(Y))
+
+#undef MIN
+#define MIN(X,Y)	((X)<(Y)?(X):(Y))
+
+/* The driver identification number, initialized at runtime */
+static hid_t H5FD_CORE_g = 0;
+
+/*
+ * The description of a file belonging to this driver. The `eoa' and `eof'
+ * determine the amount of hdf5 address space in use and the high-water mark
+ * of the file (the current size of the underlying memory).
+ */
+typedef struct H5FD_core_t {
+    H5FD_t	pub;			/*public stuff, must be first	*/
+    char	*name;			/*for equivalence testing	*/
+    unsigned char *mem;			/*the underlying memory		*/
+    haddr_t	eoa;			/*end of allocated region	*/
+    haddr_t	eof;			/*current allocated size	*/
+    size_t	increment;		/*multiples for mem allocation	*/
+} H5FD_core_t;
+
+/* Driver-specific file access properties */
+typedef struct H5FD_core_fapl_t {
+    size_t	increment;		/*how much to grow memory	*/
+} H5FD_core_fapl_t;
+
+/* Allocate memory in multiples of this size by default */
+#define H5FD_CORE_INCREMENT		8192
+
+/*
+ * These macros check for overflow of various quantities.  These macros
+ * assume that file_offset_t is signed and haddr_t and size_t are unsigned.
+ * 
+ * ADDR_OVERFLOW:	Checks whether a file address of type `haddr_t'
+ *			is too large to be represented by the second argument
+ *			of the file seek function.
+ *
+ * SIZE_OVERFLOW:	Checks whether a buffer size of type `hsize_t' is too
+ *			large to be represented by the `size_t' type.
+ *
+ * REGION_OVERFLOW:	Checks whether an address and size pair describe data
+ *			which can be addressed entirely in memory.
+ */
+#define MAXADDR 		((haddr_t)~(size_t)0)
+#define ADDR_OVERFLOW(A)	(HADDR_UNDEF==(A) ||			      \
+				 ((A) & ~(haddr_t)MAXADDR))
+#define SIZE_OVERFLOW(Z)	((Z) & ~(hsize_t)MAXADDR)
+#define REGION_OVERFLOW(A,Z)	(ADDR_OVERFLOW(A) || SIZE_OVERFLOW(Z) ||      \
+                                 HADDR_UNDEF==(A)+(Z) ||		      \
+				 (size_t)((A)+(Z))<(size_t)(A))
+
+/* Prototypes */
+static H5FD_t *H5FD_core_open(const char *name, unsigned flags, hid_t fapl_id,
+			      haddr_t maxaddr);
+static herr_t H5FD_core_close(H5FD_t *_file);
+static int H5FD_core_cmp(const H5FD_t *_f1, const H5FD_t *_f2);
+static haddr_t H5FD_core_get_eoa(H5FD_t *_file);
+static herr_t H5FD_core_set_eoa(H5FD_t *_file, haddr_t addr);
+static haddr_t H5FD_core_get_eof(H5FD_t *_file);
+static herr_t H5FD_core_read(H5FD_t *_file, hid_t fapl_id, haddr_t addr,
+			     hsize_t size, void *buf);
+static herr_t H5FD_core_write(H5FD_t *_file, hid_t fapl_id, haddr_t addr,
+			      hsize_t size, const void *buf);
+
+static const H5FD_class_t H5FD_core_g = {
+    "core",					/*name			*/
+    MAXADDR,					/*maxaddr		*/
+    sizeof(H5FD_core_fapl_t),			/*fapl_size		*/
+    NULL,					/*fapl_copy		*/
+    NULL, 					/*fapl_free		*/
+    0,						/*dxpl_size		*/
+    NULL,					/*dxpl_copy		*/
+    NULL,					/*dxpl_free		*/
+    H5FD_core_open,				/*open			*/
+    H5FD_core_close,				/*close			*/
+    H5FD_core_cmp,				/*cmp			*/
+    NULL,					/*alloc			*/
+    NULL,					/*free			*/
+    H5FD_core_get_eoa,				/*get_eoa		*/
+    H5FD_core_set_eoa, 				/*set_eoa		*/
+    H5FD_core_get_eof,				/*get_eof		*/
+    H5FD_core_read,				/*read			*/
+    H5FD_core_write,				/*write			*/
+    NULL,					/*flush			*/
+    H5FD_FLMAP_SINGLE,				/*fl_map		*/
+};
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_init
+ *
+ * Purpose:	Initialize this driver by registering the driver with the
+ *		library.
+ *
+ * Return:	Success:	The driver ID for the core driver.
+ *
+ *		Failure:	Negative.
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 29, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+hid_t
+H5FD_core_init(void)
+{
+    if (!H5FD_CORE_g) {
+	H5FD_CORE_g = H5FDregister(&H5FD_core_g);
+    }
+    return H5FD_CORE_g;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5Pset_fapl_core
+ *
+ * Purpose:	Modify the file access property list to use the H5FD_CORE
+ *		driver defined in this source file.  The INCREMENT specifies
+ *		how much to grow the memory each time we need more.
+ *		
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Robb Matzke
+ *		Thursday, February 19, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Pset_fapl_core(hid_t fapl_id, size_t increment)
+{
+    H5FD_core_fapl_t	fa;
+    
+    /*NO TRACE*/
+    if (H5P_FILE_ACCESS!=H5Pget_class(fapl_id)) return -1;
+    fa.increment = increment;
+    return H5Pset_driver(fapl_id, H5FD_CORE, &fa);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5Pget_fapl_core
+ *
+ * Purpose:	Queries properties set by the H5Pset_fapl_core() function.
+ *
+ * Return:	Success:	Non-negative
+ *
+ *		Failure:	Negative
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, August 10, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/)
+{
+    H5FD_core_fapl_t	*fa;
+
+    /*NO TRACE*/
+    if (H5P_FILE_ACCESS!=H5Pget_class(fapl_id)) return -1;
+    if (H5FD_CORE!=H5Pget_driver(fapl_id)) return -1;
+    if (NULL==(fa=H5Pget_driver_info(fapl_id))) return -1;
+    if (increment) *increment = fa->increment;
+    return 0;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_open
+ *
+ * Purpose:	Create memory as an HDF5 file.
+ *
+ * Return:	Success:	A pointer to a new file data structure. The
+ *				public fields will be initialized by the
+ *				caller, which is always H5FD_open().
+ *
+ *		Failure:	NULL
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 29, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static H5FD_t *
+H5FD_core_open(const char *name, unsigned flags/*unused*/, hid_t fapl_id,
+	       haddr_t maxaddr)
+{
+    H5FD_core_t		*file=NULL;
+    H5FD_core_fapl_t	*fa=NULL;
+    
+    /* Check arguments */
+    if (0==maxaddr || HADDR_UNDEF==maxaddr) return NULL;
+    if (ADDR_OVERFLOW(maxaddr)) return NULL;
+    if (H5P_DEFAULT!=fapl_id) fa = H5Pget_driver_info(fapl_id);
+
+    /* Create the new file struct */
+    file = calloc(1, sizeof(H5FD_core_t));
+    if (name && *name) {
+	file->name = malloc(strlen(name)+1);
+	strcpy(file->name, name);
+    }
+
+    /*
+     * The increment comes from either the file access property list or the
+     * default value. But if the file access property list was zero then use
+     * the default value instead.
+     */
+    file->increment = (fa && fa->increment>0) ?
+		      fa->increment : H5FD_CORE_INCREMENT;
+
+    return (H5FD_t*)file;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_close
+ *
+ * Purpose:	Closes the file.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 29, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5FD_core_close(H5FD_t *_file)
+{
+    H5FD_core_t	*file = (H5FD_core_t*)_file;
+
+    if (file->name) free(file->name);
+    if (file->mem) free(file->mem);
+    memset(file, 0, sizeof(H5FD_core_t));
+    return 0;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_cmp
+ *
+ * Purpose:	Compares two files belonging to this driver by name. If one
+ *		file doesn't have a name then it is less than the other file.
+ *		If neither file has a name then the comparison is by file
+ *		address.
+ *
+ * Return:	Success:	A value like strcmp()
+ *
+ *		Failure:	never fails (arguments were checked by the
+ *				caller).
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 29, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5FD_core_cmp(const H5FD_t *_f1, const H5FD_t *_f2)
+{
+    const H5FD_core_t	*f1 = (const H5FD_core_t*)_f1;
+    const H5FD_core_t	*f2 = (const H5FD_core_t*)_f2;
+
+    if (NULL==f1->name && NULL==f2->name) {
+	if (f1<f2) return -1;
+	if (f1>f2) return 1;
+	return 0;
+    }
+    
+    if (NULL==f1->name) return -1;
+    if (NULL==f2->name) return 1;
+
+    return strcmp(f1->name, f2->name);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_get_eoa
+ *
+ * Purpose:	Gets the end-of-address marker for the file. The EOA marker
+ *		is the first address past the last byte allocated in the
+ *		format address space.
+ *
+ * Return:	Success:	The end-of-address marker.
+ *
+ *		Failure:	HADDR_UNDEF
+ *
+ * Programmer:	Robb Matzke
+ *              Monday, August  2, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static haddr_t
+H5FD_core_get_eoa(H5FD_t *_file)
+{
+    H5FD_core_t	*file = (H5FD_core_t*)_file;
+    return file->eoa;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_set_eoa
+ *
+ * Purpose:	Set the end-of-address marker for the file. This function is
+ *		called shortly after an existing HDF5 file is opened in order
+ *		to tell the driver where the end of the HDF5 data is located.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 29, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5FD_core_set_eoa(H5FD_t *_file, haddr_t addr)
+{
+    H5FD_core_t	*file = (H5FD_core_t*)_file;
+    if (ADDR_OVERFLOW(addr)) return -1;
+    file->eoa = addr;
+    return 0;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_get_eof
+ *
+ * Purpose:	Returns the end-of-file marker, which is the greater of
+ *		either the size of the underlying memory or the HDF5
+ *		end-of-address markers.
+ *
+ * Return:	Success:	End of file address, the first address past
+ *				the end of the "file", either the memory
+ *				or the HDF5 file.
+ *
+ *		Failure:	HADDR_UNDEF
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 29, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static haddr_t
+H5FD_core_get_eof(H5FD_t *_file)
+{
+    H5FD_core_t	*file = (H5FD_core_t*)_file;
+    return MAX(file->eof, file->eoa);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_read
+ *
+ * Purpose:	Reads SIZE bytes of data from FILE beginning at address ADDR
+ *		into buffer BUF according to data transfer properties in
+ *		DXPL_ID.
+ *
+ * Return:	Success:	Zero. Result is stored in caller-supplied
+ *				buffer BUF.
+ *
+ *		Failure:	-1, Contents of buffer BUF are undefined.
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 29, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5FD_core_read(H5FD_t *_file, hid_t dxpl_id/*unused*/, haddr_t addr,
+	       hsize_t size, void *buf/*out*/)
+{
+    H5FD_core_t		*file = (H5FD_core_t*)_file;
+    ssize_t		nbytes;
+    
+    assert(file && file->pub.cls);
+    assert(buf);
+
+    /* Check for overflow conditions */
+    if (HADDR_UNDEF==addr) return -1;
+    if (REGION_OVERFLOW(addr, size)) return -1;
+    if (addr+size>file->eoa) return -1;
+
+    /* Read the part which is before the EOF marker */
+    if (addr<file->eof) {
+	nbytes = MIN(size, file->eof-addr);
+	memcpy(buf, file->mem+addr, nbytes);
+	size -= nbytes;
+	addr += nbytes;
+	(char*)buf += nbytes;
+    }
+
+    /* Read zeros for the part which is after the EOF markers */
+    if (size>0) {
+	memset(buf, 0, size);
+    }
+    return 0;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5FD_core_write
+ *
+ * Purpose:	Writes SIZE bytes of data to FILE beginning at address ADDR
+ *		from buffer BUF according to data transfer properties in
+ *		DXPL_ID.
+ *
+ * Return:	Success:	Zero
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, July 29, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5FD_core_write(H5FD_t *_file, hid_t dxpl_id/*unused*/, haddr_t addr,
+		hsize_t size, const void *buf)
+{
+    H5FD_core_t		*file = (H5FD_core_t*)_file;
+    
+    assert(file && file->pub.cls);
+    assert(buf);
+
+    /* Check for overflow conditions */
+    if (REGION_OVERFLOW(addr, size)) return -1;
+    if (addr+size>file->eoa) return -1;
+
+    /*
+     * Allocate more memory if necessary, careful of overflow. Also, if the
+     * allocation fails then the file should remain in a usable state.  Be
+     * careful of non-Posix realloc() that doesn't understand what to do when
+     * the first argument is null.
+     */
+    if (addr+size>file->eof) {
+	unsigned char *x;
+	size_t new_eof = file->increment * ((addr+size)/file->increment);
+	if ((addr+size) % file->increment) new_eof += file->increment;
+	if (NULL==file->mem) x = malloc(new_eof);
+	else x = realloc(file->mem, new_eof);
+	if (!x) return -1;
+	file->mem = x;
+	file->eof = new_eof;
+    }
+
+    /* Write from BUF to memory */
+    memcpy(file->mem+addr, buf, size);
+    return 0;
+}