[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	configuration since they're no longer applicable.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, 0 insertions, 398 deletions

diff --git a/src/H5Fstdio.c b/src/H5Fstdio.c
deleted file mode 100644
index 94ab0d1..0000000
--- a/src/H5Fstdio.c
+++ /dev/null
@@ -1,398 +0,0 @@
-/*
- * Copyright (C) 1997 NCSA
- *		      All rights reserved.
- *
- * Programmer: Robb Matzke <matzke@llnl.gov>
- *	       Wednesday, October 22, 1997
- *
- * Purpose:    This is the Posix stdio.h I/O subclass of H5Flow.
- */
-#include <H5private.h>
-#include <H5private.h>
-#include <H5Eprivate.h>
-#include <H5Fprivate.h>
-#include <H5MMprivate.h>
-
-#define PABLO_MASK	H5Fstdio_mask
-static intn		interface_initialize_g = 0;
-#define INTERFACE_INIT	NULL
-
-static H5F_low_t *H5F_stdio_open(const char *name,
-				 const H5F_access_t *access_parms, uintn flags,
-				 H5F_search_t *key/*out*/);
-static herr_t H5F_stdio_close(H5F_low_t *lf, const H5F_access_t *access_parms);
-static herr_t H5F_stdio_read(H5F_low_t *lf, const H5F_access_t *access_parms,
-			     const H5F_xfer_t *xfer_parms, haddr_t addr,
-			     size_t size, uint8_t *buf/*out*/);
-static herr_t H5F_stdio_write(H5F_low_t *lf, const H5F_access_t *access_parms,
-			      const H5F_xfer_t *xfer_parms, haddr_t addr,
-			      size_t size, const uint8_t *buf);
-static herr_t H5F_stdio_flush(H5F_low_t *lf, const H5F_access_t *access_parms);
-
-const H5F_low_class_t H5F_LOW_STDIO_g[1] = {{
-    NULL,			/* use default access(2) func		*/
-    H5F_stdio_open,		/* open method				*/
-    H5F_stdio_close,		/* close method				*/
-    H5F_stdio_read,		/* read method				*/
-    H5F_stdio_write,		/* write method				*/
-    H5F_stdio_flush,		/* flush method				*/
-    NULL,			/* extend method			*/
-    NULL,			/* alloc method				*/
-}};
-
-
-/*-------------------------------------------------------------------------
- * Function:	H5F_stdio_open
- *
- * Purpose:	Opens a file with name NAME.  The FLAGS are a bit field with
- *		the possible values defined in H5F_low_open().
- *
- * Bugs:	H5F_ACC_EXCL has a race condition.
- *
- * Errors:
- *		IO	  CANTOPENFILE	File doesn't exist and CREAT wasn't
- *					specified. 
- *		IO	  CANTOPENFILE	Fopen failed. 
- *		IO	  FILEEXISTS	File exists but CREAT and EXCL were
- *					specified. 
- *
- * Return:	Success:	Low-level file pointer
- *
- *		Failure:	NULL
- *
- * Programmer:	Robb Matzke
- *		Wednesday, October 22, 1997
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-static H5F_low_t *
-H5F_stdio_open(const char *name, const H5F_access_t UNUSED *access_parms,
-	       uintn flags, H5F_search_t *key/*out*/)
-{
-    H5F_low_t		   *lf = NULL;
-    FILE		   *f = NULL;
-    struct stat		    sb;
-
-    FUNC_ENTER(H5F_stdio_open, NULL);
-
-    if (HDaccess(name, F_OK) < 0) {
-	if ((flags & H5F_ACC_CREAT) && (flags & H5F_ACC_RDWR)) {
-	    f = HDfopen(name, "wb+");
-	} else {
-	    HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL,
-			  "file doesn't exist and CREAT wasn't specified");
-	}
-
-    } else if ((flags & H5F_ACC_CREAT) && (flags & H5F_ACC_EXCL)) {
-	HRETURN_ERROR(H5E_IO, H5E_FILEEXISTS, NULL,
-		      "file exists but CREAT and EXCL were specified");
-
-    } else if (flags & H5F_ACC_RDWR) {
-	if (flags & H5F_ACC_TRUNC)
-	    f = HDfopen(name, "wb+");
-	else
-	    f = HDfopen(name, "rb+");
-
-    } else {
-	f = HDfopen(name, "rb");
-    }
-    if (!f)
-	HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL, "fopen failed");
-
-    /* Build the return value */
-    if (NULL==(lf = H5MM_calloc(sizeof(H5F_low_t)))) {
-	HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
-		       "memory allocation failed");
-    }
-    lf->u.stdio.f = f;
-    lf->u.stdio.op = H5F_OP_SEEK;
-    lf->u.stdio.cur = 0;
-    lf->eof = 0;
-    if (HDfseek(lf->u.stdio.f, 0, SEEK_END) < 0) {
-	lf->u.stdio.op = H5F_OP_UNKNOWN;
-    } else {
-	hssize_t x = HDftell (lf->u.stdio.f);
-	assert (x>=0);
-	lf->eof += (hsize_t)x;
-    }
-
-    /* The unique key */
-    if (key) {
-	HDfstat(fileno(f), &sb);
-	key->dev = sb.st_dev;
-	key->ino = sb.st_ino;
-    }
-    FUNC_LEAVE(lf);
-}
-
-/*-------------------------------------------------------------------------
- * Function:	H5F_stdio_close
- *
- * Purpose:	Closes a file.
- *
- * Errors:
- *		IO	  CLOSEERROR	Fclose failed. 
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:	Robb Matzke
- *		Wednesday, October 22, 1997
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5F_stdio_close(H5F_low_t *lf, const H5F_access_t UNUSED *access_parms)
-{
-    FUNC_ENTER(H5F_stdio_close, FAIL);
-
-    if (HDfclose(lf->u.stdio.f) < 0) {
-	HRETURN_ERROR(H5E_IO, H5E_CLOSEERROR, FAIL, "fclose failed");
-    }
-    lf->u.stdio.f = NULL;
-
-    FUNC_LEAVE(SUCCEED);
-}
-
-/*-------------------------------------------------------------------------
- * Function:	H5F_stdio_read
- *
- * Purpose:	Reads SIZE bytes beginning at address ADDR in file LF and
- *		places them in buffer BUF.  Reading past the logical or
- *		physical end of file returns zeros instead of failing.
- *
- * Errors:
- *		IO	  READERROR	Fread failed. 
- *		IO	  SEEKERROR	Fseek failed. 
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:	Robb Matzke
- *		Wednesday, October 22, 1997
- *
- * Modifications:
- *		Albert Cheng, 1998-06-02
- *		Added XFER_MODE argument.
- *
- * 		Robb Matzke, 1999-07-28
- *		The ADDR argument is passed by value.
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5F_stdio_read(H5F_low_t *lf, const H5F_access_t UNUSED *access_parms,
-	       const H5F_xfer_t UNUSED *xfer_parms, haddr_t addr,
-	       size_t size, uint8_t *buf/*out*/)
-{
-    size_t		n;
-    uint64_t		mask;
-#ifdef HAVE_FSEEK64
-    int64_t		offset;
-#else
-    long		offset;
-#endif
-
-    FUNC_ENTER(H5F_stdio_read, FAIL);
-
-    /* Check for overflow */
-    mask = (uint64_t)1 << (8*sizeof(offset)-1);
-    if (addr >= mask ||
-	addr + size < addr ||
-	addr+size >= mask) {
-	HRETURN_ERROR (H5E_IO, H5E_OVERFLOW, FAIL, "file address overflowed");
-    }
-#ifdef HAVE_FSEEK64
-    offset = (int64_t)(addr); /*checked for overflow*/
-#else
-    offset = (long)(addr); /*checked for overflow*/
-#endif
-
-    /* Check easy cases */
-    if (0 == size) HRETURN(SUCCEED);
-    if ((uint64_t)offset >= lf->eof) {
-	HDmemset(buf, 0, size);
-	HRETURN(SUCCEED);
-    }
-
-    /*
-     * Seek to the correct file position.
-     */
-    if (!H5F_OPT_SEEK ||
-	lf->u.stdio.op != H5F_OP_READ ||
-	lf->u.stdio.cur != offset) {
-#ifdef HAVE_FSEEK64
-	if (fseek64 (lf->u.stdio.f, offset, SEEK_SET)<0) {
-	    HRETURN_ERROR (H5E_IO, H5E_SEEKERROR, FAIL, "fseek64 failed");
-	}
-#else
-	if (HDfseek(lf->u.stdio.f, offset, SEEK_SET) < 0) {
-	    HRETURN_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "fseek failed");
-	}
-#endif
-	lf->u.stdio.cur = offset;
-    }
-
-    /*
-     * Read zeros past the logical end of file (physical is handled below)
-     */
-    if ((size_t) offset + size > lf->eof) {
-	size_t nbytes = (size_t) offset + size - lf->eof;
-	HDmemset(buf + size - nbytes, 0, nbytes);
-	size -= nbytes;
-    }
-    
-    /*
-     * Read the data.  Since we're reading single-byte values, a partial read
-     * will advance the file position by N.  If N is negative or an error
-     * occurs then the file position is undefined.
-     */
-    n = HDfread(buf, 1, size, lf->u.stdio.f);
-    if (n <= 0 && HDferror(lf->u.stdio.f)) {
-	lf->u.stdio.op = H5F_OP_UNKNOWN;
-	HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "fread failed");
-    } else if (n < size) {
-	HDmemset(buf + n, 0, size - n);
-    }
-    
-    /*
-     * Update the file position data.
-     */
-    lf->u.stdio.op = H5F_OP_READ;
-#ifdef HAVE_FSEEK64
-    lf->u.stdio.cur = (int64_t)(offset+n); /*checked for overflow above*/
-#else
-    lf->u.stdio.cur = (off_t)(offset+n); /*checked for overflow above*/
-#endif
-    FUNC_LEAVE(SUCCEED);
-}
-
-
-/*-------------------------------------------------------------------------
- * Function:	H5F_stdio_write
- *
- * Purpose:	Writes SIZE bytes from the beginning of BUF into file LF at
- *		file address ADDR.
- *
- * Errors:
- *		IO	  SEEKERROR	Fseek failed. 
- *		IO	  WRITEERROR	Fwrite failed. 
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:	Robb Matzke
- *		Wednesday, October 22, 1997
- *
- * Modifications:
- *		Albert Cheng, 1998-06-02
- *		Added XFER_MODE argument.
- *
- * 		Robb Matzke, 1999-07-28
- *		The ADDR argument is passed by value.
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5F_stdio_write(H5F_low_t *lf, const H5F_access_t UNUSED *access_parms,
-	        const H5F_xfer_t UNUSED *xfer_parms, haddr_t addr,
-		size_t size, const uint8_t *buf)
-{
-    uint64_t		mask;
-#ifdef HAVE_FSEEK64
-    int64_t		offset;
-    uint64_t		n;
-#else
-    long		offset;
-    size_t		n;
-#endif
-
-    FUNC_ENTER(H5F_stdio_write, FAIL);
-
-    /* Check for overflow */
-    mask = (uint64_t)1 << (8*sizeof(offset)-1);
-    if (addr >= mask ||
-	addr+size < addr ||
-	addr+size >= mask) {
-	HRETURN_ERROR (H5E_IO, H5E_OVERFLOW, FAIL, "file address overflowed");
-    }
-#ifdef HAVE_FSEEK64
-    offset = (int64_t)(addr); /*checked for overflow*/
-    n = size; /*checked for overflow*/
-#else
-    offset = (long)(addr); /*checked for overflow*/
-    n = size; /*checked for overflow*/
-#endif
-
-    /*
-     * Seek to the correct file position.
-     */
-    if (!H5F_OPT_SEEK ||
-	lf->u.stdio.op != H5F_OP_WRITE ||
-	lf->u.stdio.cur != offset) {
-#ifdef HAVE_FSEEK64
-	if (fseek64 (lf->u.stdio.f, offset, SEEK_SET)<0) {
-	    HRETURN_ERROR (H5E_IO, H5E_SEEKERROR, FAIL, "fseek64 failed");
-	}
-#else
-	if (HDfseek(lf->u.stdio.f, offset, SEEK_SET) < 0) {
-	    HRETURN_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "fseek failed");
-	}
-#endif
-	lf->u.stdio.cur = offset;
-    }
-    
-    /*
-     * Write the buffer.  On successful return, the file position will be
-     * advanced by the number of bytes read.  Otherwise nobody knows where it
-     * is.
-     */
-    if (n != HDfwrite(buf, 1, size, lf->u.stdio.f)) {
-	lf->u.stdio.op = H5F_OP_UNKNOWN;
-	HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "fwrite failed");
-    }
-    
-    /*
-     * Update seek optimizing data.
-     */
-    lf->u.stdio.op = H5F_OP_WRITE;
-    lf->u.stdio.cur = offset + (int64_t)n;
-    FUNC_LEAVE(SUCCEED);
-}
-
-
-/*-------------------------------------------------------------------------
- * Function:	H5F_stdio_flush
- *
- * Purpose:	Makes sure that all data is on disk.
- *
- * Errors:
- *		IO	  WRITEERROR	Fflush failed. 
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:	Robb Matzke
- *		Wednesday, October 22, 1997
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5F_stdio_flush(H5F_low_t *lf, const H5F_access_t UNUSED *access_parms)
-{
-    FUNC_ENTER(H5F_stdio_flush, FAIL);
-
-    /*
-     * What happens to the file position?  Is it guaranteed to be the same
-     * after the fflush() as it was before?
-     */
-    lf->u.stdio.op = H5F_OP_UNKNOWN;
-
-    /*
-     * Flush
-     */
-    if (HDfflush(lf->u.stdio.f) < 0) {
-	HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "fflush failed");
-    }
-    FUNC_LEAVE(SUCCEED);
-}