[svn-r1753] Changes since 19991007

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

./configure.in
./src/H5config.h.in	[REGENERATED]
	The /usr/ncsa/{include,lib} directories are only added if they
	actually exist. This fixes a warning on some systems.

	Checks for the <pdb.h> header file and also for either the PDB or Silo
	library, and if found prepares to compile the pdb2hdf program.

./config/distdep
	Relative path names for include files are changed to base names since
	the makefile contains the logic for searching and since it's likely
	that building the .distdep files happed from a location other than
	where they would be used in the file system.

./config/conclude.in
	Fixed shell errors when `for' loops iterate over nothing for the
	`uninstall' target.

./src/H5D.c
./src/H5Oefl.c
	File names for the external files are added to the heap when the
	dataset is created instead of when the object header is written. This
	fixes a rare infinite recursion bug.

./src/H5FD.c
./src/H5FDpublic.h
	Optimization to the free list causes H5FD_alloc() usage to go from >10
	seconds to <0.4 second for one example (converting a 30MB equation of
	state file from PDB to HDF5 format). The optimization is to simply
	keep track of the largest item in the free list and not search the
	free list when the largest item is not big enough to satisfy the
	request.

./src/H5FDcore.c
./src/H5FDcore.h
./test/h5test.c
	If the `backing_store' property is true then a flush causes the entire
	contents of memory to be written to the specified file. This is  in
	preparation for the ASCI/red optimizations and is currently tested by
	the pdb2hdf `--cached' switch.

./src/H5Odtypes.c
	Wrapped three long lines.

./tools/Makefile.in
./tools/pdb2hdf.c		[NEW]
	A PDB-to-HDF5 translator. It only translates meta data -- the
	resulting HDF5 points into the PDB file for the raw data.

1 files changed, 79 insertions, 7 deletions

diff --git a/src/H5FDcore.c b/src/H5FDcore.c
index 64f93c0..51f57c4 100644
--- a/src/H5FDcore.c
+++ b/src/H5FDcore.c
@@ -35,11 +35,14 @@ typedef struct H5FD_core_t {
     haddr_t	eoa;			/*end of allocated region	*/
     haddr_t	eof;			/*current allocated size	*/
     size_t	increment;		/*multiples for mem allocation	*/
+    int		fd;			/*backing store file descriptor	*/
+    hbool_t	dirty;			/*changes not saved?		*/
 } H5FD_core_t;
 
 /* Driver-specific file access properties */
 typedef struct H5FD_core_fapl_t {
     size_t	increment;		/*how much to grow memory	*/
+    hbool_t	backing_store;		/*write to file name on flush	*/
 } H5FD_core_fapl_t;
 
 /* Allocate memory in multiples of this size by default */
@@ -71,6 +74,7 @@ typedef struct H5FD_core_fapl_t {
 static void *H5FD_core_fapl_get(H5FD_t *_file);
 static H5FD_t *H5FD_core_open(const char *name, unsigned flags, hid_t fapl_id,
 			      haddr_t maxaddr);
+static herr_t H5FD_core_flush(H5FD_t *_file);
 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);
@@ -104,7 +108,7 @@ static const H5FD_class_t H5FD_core_g = {
     H5FD_core_get_eof,				/*get_eof		*/
     H5FD_core_read,				/*read			*/
     H5FD_core_write,				/*write			*/
-    NULL,					/*flush			*/
+    H5FD_core_flush,				/*flush			*/
     H5FD_FLMAP_SINGLE,				/*fl_map		*/
 };
 
@@ -149,17 +153,21 @@ H5FD_core_init(void)
  *		Thursday, February 19, 1998
  *
  * Modifications:
- *
+ * 		Robb Matzke, 1999-10-19
+ *		Added the BACKING_STORE argument. If set then the entire file
+ *		contents are flushed to a file with the same name as this
+ *		core file.
  *-------------------------------------------------------------------------
  */
 herr_t
-H5Pset_fapl_core(hid_t fapl_id, size_t increment)
+H5Pset_fapl_core(hid_t fapl_id, size_t increment, hbool_t backing_store)
 {
     H5FD_core_fapl_t	fa;
 
     /* NO TRACE */
     if (H5P_FILE_ACCESS!=H5Pget_class(fapl_id)) return -1;
     fa.increment = increment;
+    fa.backing_store = backing_store;
     return H5Pset_driver(fapl_id, H5FD_CORE, &fa);
 }
 
@@ -177,11 +185,13 @@ H5Pset_fapl_core(hid_t fapl_id, size_t increment)
  *              Tuesday, August 10, 1999
  *
  * Modifications:
- *
+ *		Robb Matzke, 1999-10-19
+ *		Added the BACKING_STORE argument.
  *-------------------------------------------------------------------------
  */
 herr_t
-H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/)
+H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/,
+		 hbool_t *backing_store/*out*/)
 {
     H5FD_core_fapl_t	*fa;
 
@@ -189,7 +199,10 @@ H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/)
     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;
+    if (backing_store) *backing_store = fa->backing_store;
+    
     return 0;
 }
 
@@ -217,6 +230,7 @@ H5FD_core_fapl_get(H5FD_t *_file)
     H5FD_core_fapl_t	*fa = calloc(1, sizeof(H5FD_core_fapl_t));
 
     fa->increment = file->increment;
+    fa->backing_store = (file->fd>=0);
     return fa;
 }
 
@@ -236,7 +250,8 @@ H5FD_core_fapl_get(H5FD_t *_file)
  *              Thursday, July 29, 1999
  *
  * Modifications:
- *
+ *		Robb Matzke, 1999-10-19
+ *		The backing store file is created and opened if specified.
  *-------------------------------------------------------------------------
  */
 static H5FD_t *
@@ -245,14 +260,22 @@ H5FD_core_open(const char *name, unsigned UNUSED flags, hid_t fapl_id,
 {
     H5FD_core_t		*file=NULL;
     H5FD_core_fapl_t	*fa=NULL;
+    int			fd=-1;
     
     /* 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);
 
+    /* Open backing store */
+    if (fa && fa->backing_store && name &&
+	(fd=open(name, O_CREAT|O_TRUNC|O_RDWR, 0666))<0) {
+	return NULL;
+    }
+
     /* Create the new file struct */
     file = calloc(1, sizeof(H5FD_core_t));
+    file->fd = fd;
     if (name && *name) {
 	file->name = malloc(strlen(name)+1);
 	strcpy(file->name, name);
@@ -271,6 +294,47 @@ H5FD_core_open(const char *name, unsigned UNUSED flags, hid_t fapl_id,
 
 
 /*-------------------------------------------------------------------------
+ * Function:	H5FD_core_flush
+ *
+ * Purpose:	Flushes the file to backing store if there is any and if the
+ *		dirty flag is set.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Robb Matzke
+ *              Friday, October 15, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5FD_core_flush(H5FD_t *_file)
+{
+    H5FD_core_t	*file = (H5FD_core_t*)_file;
+    
+    /* Write to backing store */
+    if (file->dirty && file->fd>=0) {
+	haddr_t size = file->eof;
+	unsigned char *ptr = file->mem;
+	if (0!=lseek(file->fd, 0, SEEK_SET)) return -1;
+
+	while (size) {
+	    ssize_t n = write(file->fd, ptr, size);
+	    if (n<0 && EINTR==errno) continue;
+	    if (n<0) return -1;
+	    ptr += (size_t)n;
+	    size -= (size_t)n;
+	}
+	file->dirty = FALSE;
+    }
+    return 0;
+}
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5FD_core_close
  *
  * Purpose:	Closes the file.
@@ -283,7 +347,9 @@ H5FD_core_open(const char *name, unsigned UNUSED flags, hid_t fapl_id,
  *              Thursday, July 29, 1999
  *
  * Modifications:
- *
+ * 		Robb Matzke, 1999-10-19
+ *		The contents of memory are written to the backing store if
+ *		one is open.
  *-------------------------------------------------------------------------
  */
 static herr_t
@@ -291,6 +357,11 @@ H5FD_core_close(H5FD_t *_file)
 {
     H5FD_core_t	*file = (H5FD_core_t*)_file;
 
+    /* Flush */
+    if (H5FD_core_flush(_file)<0) return -1;
+
+    /* Release resources */
+    if (file->fd>=0) close(file->fd);
     if (file->name) free(file->name);
     if (file->mem) free(file->mem);
     memset(file, 0, sizeof(H5FD_core_t));
@@ -520,5 +591,6 @@ H5FD_core_write(H5FD_t *_file, hid_t UNUSED dxpl_id, haddr_t addr,
 
     /* Write from BUF to memory */
     memcpy(file->mem+addr, buf, size);
+    file->dirty = TRUE;
     return 0;
 }