[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.

8 files changed, 132 insertions, 29 deletions

diff --git a/src/H5D.c b/src/H5D.c
index ab3823a..2ed2565 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -865,6 +865,10 @@ done:
  * 	Robb Matzke, 27 Jul 1998
  *	Added the MTIME message to the dataset object header.
  *
+ * 	Robb Matzke, 1999-10-14
+ *	The names for the external file list are entered into the heap hear
+ *	instead of when the efl message is encoded, preventing a possible
+ *	infinite recursion situation.
  *-------------------------------------------------------------------------
  */
 H5D_t *
@@ -1066,6 +1070,17 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
 	    HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
 			 "unable to create external file list name heap");
 	}
+	for (i=0; i<efl->nused; i++) {
+	    size_t offset = H5HL_insert(f, efl->heap_addr,
+					HDstrlen(efl->slot[i].name)+1,
+					efl->slot[i].name);
+	    assert(0==efl->slot[i].name_offset);
+	    if ((size_t)(-1)==offset) {
+		HGOTO_ERROR(H5E_EFL, H5E_CANTINIT, NULL,
+			    "unable to insert URL into name heap");
+	    }
+	    efl->slot[i].name_offset = offset;
+	}
 	if (H5O_modify (&(new_dset->ent), H5O_EFL, 0, H5O_FLAG_CONSTANT,
 			efl)<0) {
 	    HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
diff --git a/src/H5FD.c b/src/H5FD.c
index 64dace3..d4a8d91 100644
--- a/src/H5FD.c
+++ b/src/H5FD.c
@@ -1083,17 +1083,21 @@ H5FD_alloc(H5FD_t *file, H5FD_mem_t type, hsize_t size)
 
     /*
      * Try to satisfy the request from the free list. First try to find an
-     * exact match, otherwise use the best match.
+     * exact match, otherwise use the best match. Only perform the search if
+     * the free list has the potential of satisfying the request.
      */
-    if (mapped_type>=0) {
+    if (mapped_type>=0 &&
+	(0==file->maxsize || size<=file->maxsize)) {
 	H5FD_free_t *prev=NULL, *best=NULL;
 	H5FD_free_t *cur = file->fl[mapped_type];
 	while (cur) {
+	    file->maxsize = MAX(file->maxsize, cur->size);
 	    if (cur->size==size) {
 		ret_value = cur->addr;
 		if (prev) prev->next = cur->next;
 		else file->fl[mapped_type] = cur->next;
 		H5MM_xfree(cur);
+		if (size==file->maxsize) file->maxsize=0; /*unknown*/
 		HRETURN(ret_value);
 	    } else if (cur->size>size &&
 		       (!best || cur->size<best->size)) {
@@ -1103,6 +1107,7 @@ H5FD_alloc(H5FD_t *file, H5FD_mem_t type, hsize_t size)
 	    cur = cur->next;
 	}
 	if (best) {
+	    if (best->size==file->maxsize) file->maxsize=0; /*unknown*/
 	    ret_value = best->addr;
 	    best->addr += size;
 	    best->size -= size;
@@ -1232,6 +1237,9 @@ H5FD_free(H5FD_t *file, H5FD_mem_t type, haddr_t addr, hsize_t size)
 	cur->size = size;
 	cur->next = file->fl[mapped_type];
 	file->fl[mapped_type] = cur;
+	if (file->maxsize && size>file->maxsize) {
+	    file->maxsize = size;
+	}
     } else if (file->cls->free) {
 	if ((file->cls->free)(file, type, addr, size)<0) {
 	    HRETURN_ERROR(H5E_VFL, H5E_CANTINIT, FAIL,
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;
 }
diff --git a/src/H5FDcore.h b/src/H5FDcore.h
index 223bb0a..f0d338a 100644
--- a/src/H5FDcore.h
+++ b/src/H5FDcore.h
@@ -15,7 +15,9 @@
 #define H5FD_CORE	(H5FD_core_init())
 
 __DLL__ hid_t H5FD_core_init(void);
-__DLL__ herr_t H5Pset_fapl_core(hid_t fapl_id, size_t increment);
-__DLL__ herr_t H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/);
+__DLL__ herr_t H5Pset_fapl_core(hid_t fapl_id, size_t increment,
+				hbool_t backing_store);
+__DLL__ herr_t H5Pget_fapl_core(hid_t fapl_id, size_t *increment/*out*/,
+				hbool_t *backing_store/*out*/);
 
 #endif
diff --git a/src/H5FDpublic.h b/src/H5FDpublic.h
index fdd07f5..40e4afc 100644
--- a/src/H5FDpublic.h
+++ b/src/H5FDpublic.h
@@ -125,6 +125,7 @@ struct H5FD_t {
     const H5FD_class_t	*cls;		/*constant class info		*/
     haddr_t		maxaddr;	/*for this file, overrides class*/
     H5FD_free_t		*fl[H5FD_MEM_NTYPES];/*freelist per allocation type*/
+    hsize_t		maxsize;	/*largest object on FL, or zero	*/
 };
 
 #ifdef __cplusplus
diff --git a/src/H5Odtype.c b/src/H5Odtype.c
index 039d6c2..4d4322b 100644
--- a/src/H5Odtype.c
+++ b/src/H5Odtype.c
@@ -301,15 +301,18 @@ H5O_dtype_decode_helper(H5F_t *f, const uint8_t **pp, H5T_t *dt)
 
             /* Decode base type of VL information */
             if (NULL==(dt->parent = H5MM_calloc(sizeof(H5T_t))))
-                HRETURN_ERROR (H5E_DATATYPE, H5E_NOSPACE, FAIL, "memory allocation failed");
+                HRETURN_ERROR (H5E_DATATYPE, H5E_NOSPACE, FAIL,
+			       "memory allocation failed");
             dt->parent->ent.header = HADDR_UNDEF;
             if (H5O_dtype_decode_helper(f, pp, dt->parent)<0)
-                HRETURN_ERROR(H5E_DATATYPE, H5E_CANTDECODE, FAIL, "unable to decode VL parent type");
+                HRETURN_ERROR(H5E_DATATYPE, H5E_CANTDECODE, FAIL,
+			      "unable to decode VL parent type");
 
             dt->force_conv=TRUE;
             /* Mark this type as on disk */
             if (H5T_vlen_mark(dt, f, H5T_VLEN_DISK)<0)
-                HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid VL location");
+                HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL,
+			      "invalid VL location");
             break;
 
         default:
diff --git a/src/H5Oefl.c b/src/H5Oefl.c
index c14203b..8030005 100644
--- a/src/H5Oefl.c
+++ b/src/H5Oefl.c
@@ -144,6 +144,11 @@ H5O_efl_decode(H5F_t *f, const uint8_t *p, H5O_shared_t UNUSED *sh)
  * Modifications:
  *	Robb Matzke, 1998-07-20
  *	Rearranged the message to add a version number near the beginning.
+ *
+ * 	Robb Matzke, 1999-10-14
+ *	Entering the name into the local heap happens when the dataset is
+ *	created. Otherwise we could end up in infinite recursion if the heap
+ *	happens to hash to the same cache slot as the object header.
  *	
  *-------------------------------------------------------------------------
  */
@@ -152,8 +157,6 @@ H5O_efl_encode(H5F_t *f, uint8_t *p, const void *_mesg)
 {
     const H5O_efl_t	*mesg = (const H5O_efl_t *)_mesg;
     int			i;
-    size_t		offset;
-    
 
     FUNC_ENTER(H5O_efl_encode, FAIL);
 
@@ -183,20 +186,10 @@ H5O_efl_encode(H5F_t *f, uint8_t *p, const void *_mesg)
     /* Encode file list */
     for (i=0; i<mesg->nused; i++) {
 	/*
-	 * If the name has not been added to the heap yet then do so now.
+	 * The name should have been added to the heap when the dataset was
+	 * created.
 	 */
-	if (0==mesg->slot[i].name_offset) {
-	    offset = H5HL_insert (f, mesg->heap_addr,
-				  HDstrlen (mesg->slot[i].name)+1,
-				  mesg->slot[i].name);
-	    if ((size_t)(-1)==offset) {
-		HRETURN_ERROR (H5E_EFL, H5E_CANTINIT, FAIL,
-			       "unable to insert URL into name heap");
-	    }
-	    mesg->slot[i].name_offset = offset;
-	}
-
-	/* Encode the file info */
+	assert(mesg->slot[i].name_offset);
 	H5F_encode_length (f, p, mesg->slot[i].name_offset);
 	H5F_encode_length (f, p, mesg->slot[i].offset);
 	H5F_encode_length (f, p, mesg->slot[i].size);
diff --git a/src/H5config.h.in b/src/H5config.h.in
index 0ae9639..d94856a 100644
--- a/src/H5config.h.in
+++ b/src/H5config.h.in
@@ -260,6 +260,9 @@
 /* Define if you have the <mfhdf.h> header file.  */
 #undef HAVE_MFHDF_H
 
+/* Define if you have the <pdb.h> header file.  */
+#undef HAVE_PDB_H
+
 /* Define if you have the <setjmp.h> header file.  */
 #undef HAVE_SETJMP_H
 
@@ -335,6 +338,12 @@
 /* Define if you have the nsl library (-lnsl).  */
 #undef HAVE_LIBNSL
 
+/* Define if you have the pdb library (-lpdb).  */
+#undef HAVE_LIBPDB
+
+/* Define if you have the silo library (-lsilo).  */
+#undef HAVE_LIBSILO
+
 /* Define if you have the xnet library (-lxnet).  */
 #undef HAVE_LIBXNET