[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	configuration since they're no longer applicable.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, 54 insertions, 36 deletions

diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index fe3fc76..f56f3fa 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -8,13 +8,14 @@
  * Purpose:	Hyperslab selection data space I/O functions.
  */
 #include <H5private.h>
+#include <H5Dprivate.h>
 #include <H5Eprivate.h>
 #include <H5Iprivate.h>
-#include <H5Sprivate.h>
-#include <H5Vprivate.h>
 #include <H5MMprivate.h>
+#include <H5Pprivate.h>
+#include <H5Sprivate.h>
 #include <H5TBprivate.h>
-#include <H5Dprivate.h>
+#include <H5Vprivate.h>
 
 /* Interface initialization */
 #define PABLO_MASK      H5Shyper_mask
@@ -33,7 +34,7 @@ typedef struct {
     const H5S_t *space;
     H5S_sel_iter_t *iter;
 	size_t nelmts;
-    const H5F_xfer_t *xfer_parms;
+    hid_t dxpl_id;
     const void *src;
     void *dst;
     hsize_t	mem_size[H5O_LAYOUT_NDIMS];
@@ -79,14 +80,14 @@ static size_t H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout,
 			       const struct H5O_efl_t *efl, size_t elmt_size,
 			       const H5S_t *file_space,
 			       H5S_sel_iter_t *file_iter, size_t nelmts,
-			       const H5F_xfer_t *xfer_parms, void *buf/*out*/);
+			       hid_t dxpl_id, void *buf/*out*/);
 static herr_t H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout,
 			       const struct H5O_pline_t *pline,
 			       const struct H5O_fill_t *fill,
 			       const struct H5O_efl_t *efl, size_t elmt_size,
 			       const H5S_t *file_space,
 			       H5S_sel_iter_t *file_iter, size_t nelmts,
-			       const H5F_xfer_t *xfer_parms, const void *buf);
+			       hid_t dxpl_id, const void *buf);
 static size_t H5S_hyper_mgath (const void *_buf, size_t elmt_size,
 			       const H5S_t *mem_space,
 			       H5S_sel_iter_t *mem_iter, size_t nelmts,
@@ -474,10 +475,10 @@ H5S_hyper_block_cache (H5S_hyper_node_t *node,
             hsize[i]=(node->end[i]-node->start[i])+1;
         hsize[io_info->space->extent.u.simple.rank]=io_info->elmt_size;
 
-        if (H5F_arr_read (io_info->f, io_info->xfer_parms,
-			  io_info->layout, io_info->pline,
-			  io_info->fill, io_info->efl, hsize, hsize,
-			  zero, file_offset, node->cinfo.block/*out*/)<0)
+        if (H5F_arr_read(io_info->f, io_info->dxpl_id,
+			 io_info->layout, io_info->pline,
+			 io_info->fill, io_info->efl, hsize, hsize,
+			 zero, file_offset, node->cinfo.block/*out*/)<0)
             HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, FAIL, "read error");
     } /* end if */
     else {
@@ -595,10 +596,10 @@ H5S_hyper_block_write (H5S_hyper_node_t *node,
             hsize[i]=(node->end[i]-node->start[i])+1;
         hsize[io_info->space->extent.u.simple.rank]=io_info->elmt_size;
 
-        if (H5F_arr_write (io_info->f, io_info->xfer_parms,
-			   io_info->layout, io_info->pline,
-			   io_info->fill, io_info->efl, hsize, hsize,
-			   zero, file_offset, node->cinfo.block/*out*/)<0)
+        if (H5F_arr_write(io_info->f, io_info->dxpl_id, io_info->layout,
+			  io_info->pline, io_info->fill, io_info->efl, hsize,
+			  hsize, zero, file_offset,
+			  node->cinfo.block/*out*/)<0)
             HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error");
 
         /* Release the temporary buffer */
@@ -639,10 +640,17 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
     size_t i;                   /* Counters */
     intn j;
     size_t num_read=0;          /* Number of elements read */
+    const H5F_xfer_t *xfer_parms;/* Data transfer property list */
 
     FUNC_ENTER (H5S_hyper_fread, 0);
 
     assert(io_info);
+    if (H5P_DEFAULT==io_info->dxpl_id) {
+	xfer_parms = &H5F_xfer_dflt;
+    } else {
+	xfer_parms = H5I_object(io_info->dxpl_id);
+	assert(xfer_parms);
+    }
 
 #ifdef QAK
     printf("%s: check 1.0, dim=%d\n",FUNC,dim);
@@ -680,9 +688,9 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
 
                 /* Check if this hyperslab block is cached or could be cached */
                 if(!regions[i].node->cinfo.cached &&
-		   (io_info->xfer_parms->cache_hyper &&
-		    (io_info->xfer_parms->block_limit==0 ||
-		     io_info->xfer_parms->block_limit>=(regions[i].node->cinfo.size*io_info->elmt_size)))) {
+		   (xfer_parms->cache_hyper &&
+		    (xfer_parms->block_limit==0 ||
+		     xfer_parms->block_limit>=(regions[i].node->cinfo.size*io_info->elmt_size)))) {
                     /* if we aren't cached, attempt to cache the block */
                     H5S_hyper_block_cache(regions[i].node,io_info,1);
                 } /* end if */
@@ -713,11 +721,12 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
                     /*
                      * Gather from file.
                      */
-                    if (H5F_arr_read (io_info->f, io_info->xfer_parms,
-				      io_info->layout, io_info->pline,
-				      io_info->fill, io_info->efl,
-				      io_info->hsize, io_info->hsize, zero, io_info->offset,
-				      io_info->dst/*out*/)<0) {
+                    if (H5F_arr_read(io_info->f, io_info->dxpl_id,
+				     io_info->layout, io_info->pline,
+				     io_info->fill, io_info->efl,
+				     io_info->hsize, io_info->hsize,
+				     zero, io_info->offset,
+				     io_info->dst/*out*/)<0) {
                         HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0,
 				       "read error");
                     }
@@ -807,7 +816,9 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
  *              Tuesday, June 16, 1998
  *
  * Modifications:
- *
+ *		Robb Matzke, 1999-08-03
+ *		The data transfer properties are passed by ID since that's
+ *		what the virtual file layer needs.
  *-------------------------------------------------------------------------
  */
 static size_t
@@ -816,8 +827,7 @@ H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout,
 		 const struct H5O_fill_t *fill,
 		 const struct H5O_efl_t *efl, size_t elmt_size,
 		 const H5S_t *file_space, H5S_sel_iter_t *file_iter,
-		 size_t nelmts, const H5F_xfer_t *xfer_parms,
-		 void *_buf/*out*/)
+		 size_t nelmts, hid_t dxpl_id, void *_buf/*out*/)
 {
     H5S_hyper_bound_t **lo_bounds;    /* Lower (closest to the origin) bound array for each dimension */
     H5S_hyper_bound_t **hi_bounds;    /* Upper (farthest from the origin) bound array for each dimension */
@@ -864,7 +874,7 @@ H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout,
     io_info.space=file_space;
     io_info.iter=file_iter;
     io_info.nelmts=nelmts;
-    io_info.xfer_parms=xfer_parms;
+    io_info.dxpl_id = dxpl_id;
     io_info.src=NULL;
     io_info.dst=_buf;
 
@@ -921,10 +931,17 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_io_info_t *io_info)
     size_t i;                   /* Counters */
     intn j;
     size_t num_written=0;          /* Number of elements read */
+    const H5F_xfer_t *xfer_parms;	/* Data transfer properties */
 
     FUNC_ENTER (H5S_hyper_fwrite, 0);
 
     assert(io_info);
+    if (H5P_DEFAULT==io_info->dxpl_id) {
+	xfer_parms = &H5F_xfer_dflt;
+    } else {
+	xfer_parms = H5I_object(io_info->dxpl_id);
+	assert(xfer_parms);
+    }
 
 #ifdef QAK
     printf("%s: check 1.0\n", FUNC);
@@ -958,7 +975,7 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_io_info_t *io_info)
                 region_size=MIN(io_info->nelmts, (regions[i].end-regions[i].start)+1);
 
                 /* Check if this hyperslab block is cached or could be cached */
-                if(!regions[i].node->cinfo.cached && (io_info->xfer_parms->cache_hyper && (io_info->xfer_parms->block_limit==0 || io_info->xfer_parms->block_limit>=(regions[i].node->cinfo.size*io_info->elmt_size)))) {
+                if(!regions[i].node->cinfo.cached && (xfer_parms->cache_hyper && (xfer_parms->block_limit==0 || xfer_parms->block_limit>=(regions[i].node->cinfo.size*io_info->elmt_size)))) {
                     /* if we aren't cached, attempt to cache the block */
                     H5S_hyper_block_cache(regions[i].node,io_info,0);
                 } /* end if */
@@ -985,11 +1002,11 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_io_info_t *io_info)
                     /*
                      * Scatter to file.
                      */
-                    if (H5F_arr_write (io_info->f, io_info->xfer_parms,
-				       io_info->layout, io_info->pline,
-				       io_info->fill, io_info->efl,
-				       io_info->hsize, io_info->hsize, zero, io_info->offset,
-				       io_info->src)<0) {
+                    if (H5F_arr_write(io_info->f, io_info->dxpl_id,
+				      io_info->layout, io_info->pline,
+				      io_info->fill, io_info->efl,
+				      io_info->hsize, io_info->hsize, zero,
+				      io_info->offset, io_info->src)<0) {
                         HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, 0, "write error");
                     }
                 } /* end else */
@@ -1063,7 +1080,9 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_io_info_t *io_info)
  *              Tuesday, June 16, 1998
  *
  * Modifications:
- *
+ *		Robb Matzke, 1999-08-03
+ *		The data transfer properties are passed by ID since that's
+ *		what the virtual file layer needs.
  *-------------------------------------------------------------------------
  */
 static herr_t
@@ -1072,8 +1091,7 @@ H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout,
 		 const struct H5O_fill_t *fill,
 		 const struct H5O_efl_t *efl, size_t elmt_size,
 		 const H5S_t *file_space, H5S_sel_iter_t *file_iter,
-		 size_t nelmts, const H5F_xfer_t *xfer_parms,
-		 const void *_buf)
+		 size_t nelmts, hid_t dxpl_id, const void *_buf)
 {
     H5S_hyper_bound_t **lo_bounds;    /* Lower (closest to the origin) bound array for each dimension */
     H5S_hyper_bound_t **hi_bounds;    /* Upper (farthest from the origin) bound array for each dimension */
@@ -1121,7 +1139,7 @@ H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout,
     io_info.space=file_space;
     io_info.iter=file_iter;
     io_info.nelmts=nelmts;
-    io_info.xfer_parms=xfer_parms;
+    io_info.dxpl_id = dxpl_id;
     io_info.src=_buf;
     io_info.dst=NULL;