[svn-r1065] Changes since 19990121

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

./configure.in
./acconfig.h
./configure		[REGENERATED]
./src/H5config.h.in	[REGENERATED]
./src/H5public.h
./src/H5Omtime.c
	Check for <stddef.h>

	Checks for `__tm_gmtoff' in `struct tm' because old versions
	of GNU libc are different than recent versions. This fixes the
	failing mtime test.

./bin/config.guess
./config/freebsd2.2.7	[REMOVED]
./config/freebsd	[ADDED]
	Changed the name so it works with all versions of FreeBSD.

./src/H5.c
	Moved H5F after H5T and H5G in H5_term_library() to satisfy
	dependencies.

./src/H5G.c
	Fixed a bug that caused H5Gcreate() to fail if the group name
	had trailing slashes.

./src/H5Gpublic.h
	Changed `group_name' to `name' in a prototype.

./src/Makefile.in
	Dynamic library on Linux, but needs for work to be generally
	useful.

./src/H5HG.c
./src/H5HGprivate.h
	Fixed alignment problems when using old GCC compilers (like
	the one shipped with RedHad Linux).

./tools/h5ls.c
	Fixed a bug where the contents of the root group could be
	listed twice if there was a link back to the root
	group. Similarly for groups that are mentioned on the command
	line.

	Fixed a bug where unknown types were printed with a random
	type class number.

./src/H5T.c
./src/H5Tconv.c
./src/H5Tprivate.h
	Fixed O(log N) conversion bugs.

12 files changed, 127 insertions, 42 deletions

diff --git a/src/H5.c b/src/H5.c
index 78d151f..b9bda39 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -143,6 +143,17 @@ H5_term_library(void)
      * interface later.
      */
 
+    /*
+     * Cycles: The H5F layer participates in quite a few dependency cycles
+     *	       because it's cache depends on almost all other meta object
+     *	       packages and those packages depend on H5O which depends on H5F
+     *	       (because H5F_close() can delay until all object headers are
+     *	       closed). We handle this cycle by closing the H5F interface,
+     *	       which flushes the cache of all files, breaking any cycles.
+     */
+    H5F_term_interface(-1);
+    H5F_term_interface(0);
+
     /* Function			   What depends on it?			*/
     /*-------------------------   -------------------------------	*/
     H5D_term_interface(-1);	/*					*/
@@ -150,12 +161,12 @@ H5_term_library(void)
     H5Z_term_interface(-1);	/*					*/
     H5A_term_interface(-1);	/*					*/
     H5RA_term_interface(-1);	/*					*/
-    H5F_term_interface(-1); 	/* T					*/
     H5G_term_interface(-1);	/*					*/
     H5R_term_interface(-1);	/*					*/
     H5S_term_interface(-1);	/*					*/
     H5T_native_close(-1);	/* D RA					*/
     H5T_term_interface(-1);	/* D RA					*/
+    H5F_term_interface(-1); 	/* G T					*/
     H5P_term_interface(-1);	/* D					*/
     H5I_term_interface(-1);	/* A D F G P RA S T TB Z		*/
     /*------------------------- ---------------------------------	*/
diff --git a/src/H5G.c b/src/H5G.c
index 9af5fb5..e8fd6b1 100644
--- a/src/H5G.c
+++ b/src/H5G.c
@@ -1263,9 +1263,10 @@ H5G_create(H5G_entry_t *loc, const char *name, size_t size_hint)
     rest = H5G_component(rest, &nchars);
     assert(rest && *rest);
     if (rest[nchars]) {
-	if (H5G_component(rest + nchars, NULL)) {
+	const char *t = H5G_component(rest+nchars, NULL);
+	if (t && *t) {
 	    HRETURN_ERROR(H5E_SYM, H5E_NOTFOUND, NULL, "missing component");
-	} else if (nchars + 1 > sizeof _comp) {
+	} else if (nchars+1 > sizeof _comp) {
 	    HRETURN_ERROR(H5E_SYM, H5E_COMPLEN, NULL, "component is too long");
 	} else {
 	    /* null terminate */
diff --git a/src/H5Gpublic.h b/src/H5Gpublic.h
index 8c01bae..f2b9fbf 100644
--- a/src/H5Gpublic.h
+++ b/src/H5Gpublic.h
@@ -67,7 +67,7 @@ typedef struct H5G_stat_t {
 } H5G_stat_t;
     
 
-typedef herr_t (*H5G_iterate_t)(hid_t group, const char *group_name,
+typedef herr_t (*H5G_iterate_t)(hid_t group, const char *name,
 				void *op_data);
 
 __DLL__ hid_t H5Gcreate (hid_t loc_id, const char *name, size_t size_hint);
diff --git a/src/H5HG.c b/src/H5HG.c
index e046fe6..e6cdf66 100644
--- a/src/H5HG.c
+++ b/src/H5HG.c
@@ -96,6 +96,7 @@ H5HG_create (H5F_t *f, size_t size)
     H5HG_heap_t	*ret_value = NULL;
     uint8_t	*p = NULL;
     haddr_t	addr;
+    size_t	n;
     
     FUNC_ENTER (H5HG_create, NULL);
 
@@ -135,8 +136,18 @@ H5HG_create (H5F_t *f, size_t size)
     *p++ = 0; /*reserved*/
     H5F_encode_length (f, p, size);
 
+    /*
+     * Padding so free space object is aligned. If malloc returned memory
+     * which was always at least H5HG_ALIGNMENT aligned then we could just
+     * align the pointer, but this might not be the case.
+     */
+    n = H5HG_ALIGN(p-heap->chunk) - (p-heap->chunk);
+    memset(p, 0, n);
+    p += n;
+
     /* The freespace object */
     heap->obj[0].size = size - H5HG_SIZEOF_HDR(f);
+    assert(H5HG_ISALIGNED(heap->obj[0].size));
     heap->obj[0].begin = p;
     UINT16ENCODE(p, 0);	/*object ID*/
     UINT16ENCODE(p, 0);	/*reference count*/
@@ -301,7 +312,7 @@ H5HG_load (H5F_t *f, const haddr_t *addr, const void __unused__ *udata1,
 	     * size is never padded and already includes the object header.
 	     */
 	    if (idx>0) {
-		need = H5HG_ALIGN(H5HG_SIZEOF_OBJHDR(f) + heap->obj[idx].size);
+		need = H5HG_SIZEOF_OBJHDR(f) + H5HG_ALIGN(heap->obj[idx].size);
 	    } else {
 		need = heap->obj[idx].size;
 	    }
@@ -309,7 +320,7 @@ H5HG_load (H5F_t *f, const haddr_t *addr, const void __unused__ *udata1,
 	}
     }
     assert(p==heap->chunk+heap->size);
-    assert(heap->obj[0].size==H5HG_ALIGN(heap->obj[0].size));
+    assert(H5HG_ISALIGNED(heap->obj[0].size));
 
     /*
      * Add the new heap to the CWFS list, removing some other entry if
@@ -434,7 +445,7 @@ H5HG_alloc (H5F_t *f, H5HG_heap_t *heap, int cwfsno, size_t size)
 {
     int		idx;
     uint8_t	*p = NULL;
-    size_t	need = H5HG_ALIGN(H5HG_SIZEOF_OBJHDR(f) + size);
+    size_t	need = H5HG_SIZEOF_OBJHDR(f) + H5HG_ALIGN(size);
 
     FUNC_ENTER (H5HG_alloc, FAIL);
 
@@ -487,6 +498,7 @@ H5HG_alloc (H5F_t *f, H5HG_heap_t *heap, int cwfsno, size_t size)
 	UINT16ENCODE(p, 0);	/*nrefs*/
 	UINT32ENCODE(p, 0);	/*reserved*/
 	H5F_encode_length (f, p, heap->obj[0].size);
+	assert(H5HG_ISALIGNED(heap->obj[0].size));
 		
     } else {
 	/*
@@ -495,6 +507,7 @@ H5HG_alloc (H5F_t *f, H5HG_heap_t *heap, int cwfsno, size_t size)
 	 */
 	heap->obj[0].size -= need;
 	heap->obj[0].begin += need;
+	assert(H5HG_ISALIGNED(heap->obj[0].size));
     }
 
     heap->dirty = 1;
@@ -546,7 +559,7 @@ H5HG_insert (H5F_t *f, size_t size, void *obj, H5HG_t *hobj/*out*/)
     }
 
     /* Find a large enough collection on the CWFS list */
-    need = H5HG_ALIGN(size + H5HG_SIZEOF_OBJHDR(f));
+    need = H5HG_SIZEOF_OBJHDR(f) + H5HG_ALIGN(size);
     for (cwfsno=0; cwfsno<f->shared->ncwfs; cwfsno++) {
 	if (f->shared->cwfs[cwfsno]->obj[0].size>=need) {
 	    /*
@@ -819,8 +832,11 @@ H5HG_remove (H5F_t *f, H5HG_t *hobj)
     assert (hobj->idx>0 && hobj->idx<heap->nalloc);
     assert (heap->obj[hobj->idx].begin);
     obj_start = heap->obj[hobj->idx].begin;
-    need = H5HG_ALIGN(heap->obj[hobj->idx].size);
-
+    need = H5HG_ALIGN(heap->obj[hobj->idx].size); /*
+						   * should this include the
+						   * object header size? -rpm
+						   */
+    
     /* Move the new free space to the end of the heap */
     for (i=0; i<heap->nalloc; i++) {
 	if (heap->obj[i].begin > heap->obj[hobj->idx].begin) {
diff --git a/src/H5HGprivate.h b/src/H5HGprivate.h
index 6b64e8d..c4e0f1f 100644
--- a/src/H5HGprivate.h
+++ b/src/H5HGprivate.h
@@ -32,6 +32,7 @@
 #define H5HG_ALIGNMENT	8
 #define H5HG_ALIGN(X)	(H5HG_ALIGNMENT*(((X)+H5HG_ALIGNMENT-1)/	      \
 					 H5HG_ALIGNMENT))
+#define H5HG_ISALIGNED(X) ((X)==H5HG_ALIGN(X))
 
 /*
  * All global heap collections are at least this big.  This allows us to read
@@ -53,20 +54,24 @@
 #define H5HG_MAXLINK	65535
 
 /*
- * The size of the collection header.
+ * The size of the collection header, always a multiple of the alignment so
+ * that the stuff that follows the header is aligned.
  */
-#define H5HG_SIZEOF_HDR(f) (4 +			/*magic number		*/    \
-			    1 +			/*version number	*/    \
-			    3 +			/*reserved		*/    \
-			    H5F_SIZEOF_SIZE(f)) /*collection size	*/
+#define H5HG_SIZEOF_HDR(f)						      \
+    H5HG_ALIGN(4 +			/*magic number		*/	      \
+	       1 +			/*version number	*/	      \
+	       3 +			/*reserved		*/	      \
+	       H5F_SIZEOF_SIZE(f))	/*collection size	*/
 
 /*
- * The overhead associated with each object in the heap.
+ * The overhead associated with each object in the heap, always a multiple of
+ * the alignment so that the stuff that follows the header is aligned.
  */
-#define H5HG_SIZEOF_OBJHDR(f) (2 +		/*object id number	*/    \
-			       2 +		/*reference count	*/    \
-			       4 +		/*reserved		*/    \
-			       H5F_SIZEOF_SIZE(f)) /*object data size	*/
+#define H5HG_SIZEOF_OBJHDR(f)						      \
+    H5HG_ALIGN(2 +			/*object id number	*/	      \
+	       2 +			/*reference count	*/	      \
+	       4 +			/*reserved		*/	      \
+	       H5F_SIZEOF_SIZE(f))	/*object data size	*/
 
 /*
  * The initial guess for the number of messages in a collection.  We assume
diff --git a/src/H5Omtime.c b/src/H5Omtime.c
index 3e4acb0..36157be 100644
--- a/src/H5Omtime.c
+++ b/src/H5Omtime.c
@@ -109,8 +109,11 @@ H5O_mtime_decode(H5F_t __unused__ *f, const uint8_t *p,
 #if defined(HAVE_TM_GMTOFF)
     /* FreeBSD, OSF 4.0 */
     the_time += tm.tm_gmtoff;
+#elif defined(HAVE___TM_GMTOFF)
+    /* Linux libc-4 */
+    the_time += tm.__tm_gmtoff;
 #elif defined(HAVE_TIMEZONE)
-    /* Linux */
+    /* Linux libc-5 */
     the_time -= timezone - (tm.tm_isdst?3600:0);
 #elif defined(HAVE_BSDGETTIMEOFDAY) && defined(HAVE_STRUCT_TIMEZONE)
     /* Irix5.3 */
diff --git a/src/H5T.c b/src/H5T.c
index c1d518a..097e33c 100644
--- a/src/H5T.c
+++ b/src/H5T.c
@@ -5075,7 +5075,7 @@ H5T_pack(H5T_t *dt)
 	}
 
 	/* Remove padding between members */
-	H5T_sort_value(dt);
+	H5T_sort_value(dt, NULL);
 	for (i=0, offset=0; i<dt->u.compnd.nmembs; i++) {
 	    dt->u.compnd.memb[i].offset = offset;
 	    offset += dt->u.compnd.memb[i].size;
@@ -5095,7 +5095,8 @@ H5T_pack(H5T_t *dt)
  * Purpose:	Sorts the members of a compound data type by their offsets;
  *		sorts the members of an enum type by their values. This even
  *		works for locked data types since it doesn't change the value
- *		of the type.
+ *		of the type.  MAP is an optional parallel integer array which
+ *		is also swapped along with members of DT.
  *
  * Return:	Non-negative on success/Negative on failure
  *
@@ -5107,7 +5108,7 @@ H5T_pack(H5T_t *dt)
  *-------------------------------------------------------------------------
  */
 herr_t
-H5T_sort_value(H5T_t *dt)
+H5T_sort_value(H5T_t *dt, int *map)
 {
     int		i, j, nmembs;
     size_t	size;
@@ -5132,6 +5133,11 @@ H5T_sort_value(H5T_t *dt)
 			H5T_cmemb_t tmp = dt->u.compnd.memb[j];
 			dt->u.compnd.memb[j] = dt->u.compnd.memb[j+1];
 			dt->u.compnd.memb[j+1] = tmp;
+			if (map) {
+			    int x = map[j];
+			    map[j] = map[j+1];
+			    map[j+1] = x;
+			}
 			swapped = TRUE;
 		    }
 		}
@@ -5166,6 +5172,13 @@ H5T_sort_value(H5T_t *dt)
 				 dt->u.enumer.value+(j+1)*size, size);
 			HDmemcpy(dt->u.enumer.value+(j+1)*size, tbuf, size);
 			
+			/* Swap map */
+			if (map) {
+			    int x = map[j];
+			    map[j] = map[j+1];
+			    map[j+1] = x;
+			}
+
 			swapped = TRUE;
 		    }
 		}
@@ -5204,7 +5217,7 @@ H5T_sort_value(H5T_t *dt)
  *-------------------------------------------------------------------------
  */
 herr_t
-H5T_sort_name(H5T_t *dt)
+H5T_sort_name(H5T_t *dt, int *map)
 {
     int		i, j, nmembs;
     size_t	size;
@@ -5230,6 +5243,11 @@ H5T_sort_name(H5T_t *dt)
 			dt->u.compnd.memb[j] = dt->u.compnd.memb[j+1];
 			dt->u.compnd.memb[j+1] = tmp;
 			swapped = TRUE;
+			if (map) {
+			    int x = map[j];
+			    map[j] = map[j+1];
+			    map[j+1] = x;
+			}
 		    }
 		}
 	    }
@@ -5261,7 +5279,14 @@ H5T_sort_name(H5T_t *dt)
 			HDmemcpy(dt->u.enumer.value+j*size,
 				 dt->u.enumer.value+(j+1)*size, size);
 			HDmemcpy(dt->u.enumer.value+(j+1)*size, tbuf, size);
-			
+
+			/* Swap map */
+			if (map) {
+			    int x = map[j];
+			    map[j] = map[j+1];
+			    map[j+1] = x;
+			}
+
 			swapped = TRUE;
 		    }
 		}
@@ -5390,7 +5415,7 @@ H5T_enum_nameof(H5T_t *dt, void *value, char *name/*out*/, size_t size)
     if (name && size>0) *name = '\0';
 
     /* Do a binary search over the values to find the correct one */
-    H5T_sort_value(dt);
+    H5T_sort_value(dt, NULL);
     lt = 0;
     rt = dt->u.enumer.nmembs;
     md = -1;
@@ -5458,7 +5483,7 @@ H5T_enum_valueof(H5T_t *dt, const char *name, void *value/*out*/)
     assert(value);
 
     /* Do a binary search over the names to find the correct one */
-    H5T_sort_name(dt);
+    H5T_sort_name(dt, NULL);
     lt = 0;
     rt = dt->u.enumer.nmembs;
     md = -1;
diff --git a/src/H5Tconv.c b/src/H5Tconv.c
index 86ccea3..8816894 100644
--- a/src/H5Tconv.c
+++ b/src/H5Tconv.c
@@ -550,8 +550,8 @@ H5T_conv_struct_init (H5T_t *src, H5T_t *dst, H5T_cdata_t *cdata)
 	/*
 	 * Insure that members are sorted.
 	 */
-	H5T_sort_value(src);
-	H5T_sort_value(dst);
+	H5T_sort_value(src, NULL);
+	H5T_sort_value(dst, NULL);
 
 	/*
 	 * Build a mapping from source member number to destination member
@@ -761,8 +761,8 @@ H5T_conv_struct(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
 	/*
 	 * Insure that members are sorted.
 	 */
-	H5T_sort_value(src);
-	H5T_sort_value(dst);
+	H5T_sort_value(src, NULL);
+	H5T_sort_value(dst, NULL);
 	src2dst = priv->src2dst;
 
 	/*
@@ -910,8 +910,8 @@ H5T_conv_enum_init(H5T_t *src, H5T_t *dst, H5T_cdata_t *cdata)
      * symbol names and build a map from source member index to destination
      * member index.
      */
-    H5T_sort_name(src);
-    H5T_sort_name(dst);
+    H5T_sort_name(src, NULL);
+    H5T_sort_name(dst, NULL);
     if (NULL==(priv->src2dst=H5MM_malloc(src->u.enumer.nmembs*sizeof(int)))) {
 	HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL,
 		      "memory allocation failed");;
@@ -994,6 +994,9 @@ H5T_conv_enum_init(H5T_t *src, H5T_t *dst, H5T_cdata_t *cdata)
 	    H5MM_xfree(priv->src2dst);
 	    priv->src2dst = map;
 	    HGOTO_DONE(SUCCEED);
+	} else {
+	    /* Sort source type by value and adjust src2dst[] appropriately */
+	    H5T_sort_value(src, priv->src2dst);
 	}
     }
     ret_value = SUCCEED;
@@ -1082,9 +1085,17 @@ H5T_conv_enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
 	}
 	assert (H5T_ENUM==src->type);
 	assert (H5T_ENUM==dst->type);
-	H5T_sort_name(src);
-	H5T_sort_name(dst);
 
+	if (priv->length) {
+	    /* Use O(1) lookup */
+	    H5T_sort_name(src, NULL);
+	    H5T_sort_name(dst, NULL);
+	} else {
+	    /* Use O(log N) lookup */
+	    H5T_sort_value(src, NULL); /*yes, by value*/
+	    H5T_sort_name(dst, NULL); /*yes, by name*/
+	}
+	
 	/*
 	 * Direction of conversion.
 	 */
@@ -1109,6 +1120,7 @@ H5T_conv_enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
 		} else {
 		    n = *((int*)s);
 		}
+		n -= priv->base;
 		if (n<0 || n>=priv->length || priv->src2dst[n]<0) {
 		    if (!H5T_overflow_g ||
 			(H5T_overflow_g)(src_id, dst_id, s, d)<0) {
diff --git a/src/H5Tprivate.h b/src/H5Tprivate.h
index 460f0db..34fbf52 100644
--- a/src/H5Tprivate.h
+++ b/src/H5Tprivate.h
@@ -77,14 +77,13 @@ __DLL__ herr_t H5T_struct_insert(H5T_t *parent, const char *name, size_t offset,
 			 intn ndims, const size_t *dim, const intn *perm,
 			 const H5T_t *member);
 __DLL__ herr_t H5T_enum_insert(H5T_t *dt, const char *name, void *value);
-__DLL__ herr_t H5T_sort_value(H5T_t *dt);
 __DLL__ herr_t H5T_pack(H5T_t *dt);
 __DLL__ herr_t H5T_debug(H5T_t *dt, FILE * stream);
 __DLL__ H5G_entry_t *H5T_entof(H5T_t *dt);
 __DLL__ H5T_path_t *H5T_path_find(const H5T_t *src, const H5T_t *dst,
 			  const char *name, H5T_conv_t func);
-__DLL__ herr_t H5T_sort_vaue(H5T_t *dt);
-__DLL__ herr_t H5T_sort_name(H5T_t *dt);
+__DLL__ herr_t H5T_sort_value(H5T_t *dt, int *map);
+__DLL__ herr_t H5T_sort_name(H5T_t *dt, int *map);
 __DLL__ herr_t H5T_convert(H5T_path_t *tpath, hid_t src_id, hid_t dst_id,
 		   size_t nelmts, void *buf, void *bkg);
 __DLL__ herr_t H5T_set_size(H5T_t *dt, size_t size);
diff --git a/src/H5config.h.in b/src/H5config.h.in
index 12b7523..fd69a2c 100644
--- a/src/H5config.h.in
+++ b/src/H5config.h.in
@@ -50,6 +50,9 @@
 /* Define if `tm_gmtoff' is a member of `struct tm' */
 #undef HAVE_TM_GMTOFF
 
+/* Define if `__tm_gmtoff' is a member of `struct tm' */
+#undef HAVE___TM_GMTOFF
+
 /* Define if `timezone' is a global variable */
 #undef HAVE_TIMEZONE
 
@@ -191,6 +194,9 @@
 /* Define if you have the <mfhdf.h> header file.  */
 #undef HAVE_MFHDF_H
 
+/* Define if you have the <stddef.h> header file.  */
+#undef HAVE_STDDEF_H
+
 /* Define if you have the <sys/ioctl.h> header file.  */
 #undef HAVE_SYS_IOCTL_H
 
diff --git a/src/H5public.h b/src/H5public.h
index 57c88ef..a895834 100644
--- a/src/H5public.h
+++ b/src/H5public.h
@@ -29,10 +29,12 @@ static char             RcsId[] = "@(#)$Revision$";
 #   include <limits.h>		/*for H5T_NATIVE_CHAR defn in H5Tpublic.h    */
 #endif
 
-#include <stddef.h>
+#ifdef HAVE_STDDEF_H
+#   include <stddef.h>
+#endif
 #ifdef HAVE_PARALLEL
-#  include <mpi.h>
-#  include <mpio.h>
+#   include <mpi.h>
+#   include <mpio.h>
 #endif
 #include <H5api_adpt.h>
 
diff --git a/src/Makefile.in b/src/Makefile.in
index ca2a302..7f4f84c 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -50,4 +50,9 @@ H5Tinit.c: H5detect
 H5detect: H5detect.o
 	$(CC) $(CFLAGS) -o $@ H5detect.o $(LDFLAGS) $(LIBS)
 
+# dynamic library with gcc. This needs more work to support other systems.
+shared: libhdf5.so.1.2.0
+libhdf5.so.1.2.0: $(LIB_OBJ)
+	$(CC) $(CFLAGS) -o $@ -shared -fPIC $^
+
 @CONCLUDE@