[svn-r15674] Description:

	Add base support for extensible array "data blocks" to code, tests and
h5debug.

Tested on:
        Mac OS X/32 10.5.4 (amazon) in debug mode
        Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
                                in production mode
        FreeBSD/32 6.3 (duty) in debug mode
        FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
                                in debug mode
        Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
                                w/C++ & FORTRAN, in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                                w/szip filter, in production mode
        Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
                                in production mode
        Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
        Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode

1 files changed, 269 insertions, 6 deletions

diff --git a/src/H5EAhdr.c b/src/H5EAhdr.c
index 9ccec62..a49116f 100644
--- a/src/H5EAhdr.c
+++ b/src/H5EAhdr.c
@@ -43,6 +43,7 @@
 #include "H5Eprivate.h"		/* Error handling		  	*/
 #include "H5EApkg.h"		/* Extensible Arrays			*/
 #include "H5MFprivate.h"	/* File memory management		*/
+#include "H5Vprivate.h"		/* Vectors and arrays 			*/
 
 
 /****************/
@@ -77,13 +78,22 @@
 /* Library Private Variables */
 /*****************************/
 
+/* Alias for pointer to factory, for use when allocating sequences of them */
+typedef H5FL_fac_head_t *H5FL_fac_head_ptr_t;
+
 
 /*******************/
 /* Local Variables */
 /*******************/
 
 /* Declare a free list to manage the H5EA_hdr_t struct */
-H5FL_DEFINE(H5EA_hdr_t);
+H5FL_DEFINE_STATIC(H5EA_hdr_t);
+
+/* Declare a free list to manage the H5FL_fac_head_ptr_t sequence information */
+H5FL_SEQ_DEFINE_STATIC(H5FL_fac_head_ptr_t);
+
+/* Declare a free list to manage the H5EA_sblk_info_t sequence information */
+H5FL_SEQ_DEFINE_STATIC(H5EA_sblk_info_t);
 
 
 
@@ -128,13 +138,209 @@ H5EA__hdr_alloc(H5F_t *f, const H5EA_class_t *cls))
 
 CATCH
     if(!ret_value)
-        if(hdr && H5EA__cache_hdr_dest(f, hdr) < 0)
+        if(hdr && H5EA__hdr_dest(hdr) < 0)
             H5E_THROW(H5E_CANTFREE, "unable to destroy extensible array header")
 
 END_FUNC(PKG)   /* end H5EA__hdr_alloc() */
 
 
 /*-------------------------------------------------------------------------
+ * Function:	H5EA__hdr_init
+ *
+ * Purpose:	Compute useful information for extensible array, based on
+ *              "creation" information.
+ *
+ * Notes:	The equations for variables below are based on this information:
+ *
+ *	<sblk idx>  <# of dblks>  <size of dblks>       Range of elements in sblk
+ *	==========  ============  ===============       =========================
+ *	      0          1         1 * <dblk min elmts>   0 * <dblk min elmts> <->   1 * <dblk min elmts> - 1
+ *	      1          1         2 * <dblk min elmts>   1 * <dblk min elmts> <->   3 * <dblk min elmts> - 1
+ *	      2          2         2 * <dblk min elmts>   3 * <dblk min elmts> <->   7 * <dblk min elmts> - 1
+ *	      3          2         4 * <dblk min elmts>   7 * <dblk min elmts> <->  15 * <dblk min elmts> - 1
+ *	      4          4         4 * <dblk min elmts>  15 * <dblk min elmts> <->  31 * <dblk min elmts> - 1
+ *	      5          4         8 * <dblk min elmts>  31 * <dblk min elmts> <->  63 * <dblk min elmts> - 1
+ *	      6          8         8 * <dblk min elmts>  63 * <dblk min elmts> <-> 127 * <dblk min elmts> - 1
+ *	      7          8        16 * <dblk min elmts> 127 * <dblk min elmts> <-> 255 * <dblk min elmts> - 1
+ *	      .          .         . * <dblk min elmts>   . * <dblk min elmts> <->   . * <dblk min elmts> - 1
+ *	      .          .         . * <dblk min elmts>   . * <dblk min elmts> <->   . * <dblk min elmts> - 1
+ *	      .          .         . * <dblk min elmts>   . * <dblk min elmts> <->   . * <dblk min elmts> - 1
+ *
+ *	Therefore:
+ *		<sblk idx>(<elmt idx>) = lg2((<elmt idx> / <dblk min elmts>) + 1)
+ *		<# of dblks>(<sblk idx>) = 2 ^ (<sblk idx> / 2)
+ *		<size of dblk>(<sblk idx>) = 2 ^ ((<sblk idx> + 1) / 2)
+ *		<total # of sblks>(<max. # of elmts>) = 1 + (lg2(<max. # of elmts>) - lg2(<dblk min_elmts>))
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Quincey Koziol
+ *		koziol@hdfgroup.org
+ *		Sep 18 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PKG, ERR,
+herr_t, SUCCEED, FAIL,
+H5EA__hdr_init(H5EA_hdr_t *hdr))
+
+    /* Local variables */
+    hsize_t start_idx;          /* First element index for each super block */
+    hsize_t start_dblk;         /* First data block index for each super block */
+    size_t u;                   /* Local index variable */
+
+    /* Sanity check */
+    HDassert(hdr);
+    HDassert(hdr->max_nelmts_bits);
+    HDassert(hdr->data_blk_min_elmts);
+    HDassert(hdr->sup_blk_min_data_ptrs);
+
+    /* Compute general information */
+    hdr->nsblks = 1 + (hdr->max_nelmts_bits - H5V_log2_of2(hdr->data_blk_min_elmts));
+#ifdef QAK
+HDfprintf(stderr, "%s: hdr->nsblks = %Zu\n", FUNC, hdr->nsblks);
+#endif /* QAK */
+
+    /* Allocate information for each super block */
+    if(NULL == (hdr->sblk_info = H5FL_SEQ_MALLOC(H5EA_sblk_info_t, hdr->nsblks)))
+        H5E_THROW(H5E_CANTALLOC, "memory allocation failed for super block info array")
+
+    /* Compute information about each super block */
+    start_idx = 0;
+    start_dblk = 0;
+    for(u = 0; u < hdr->nsblks; u++) {
+        hdr->sblk_info[u].ndblks = (hsize_t)H5_EXP2(u / 2);
+        hdr->sblk_info[u].dblk_nelmts = (size_t)H5_EXP2((u + 1) / 2) * hdr->data_blk_min_elmts;
+        hdr->sblk_info[u].start_idx = start_idx;
+        hdr->sblk_info[u].start_dblk = start_dblk;
+#ifdef QAK
+HDfprintf(stderr, "%s: hdr->sblk_info[%Zu] = {%Hu, %Zu, %Hu, %Hu}\n", FUNC, u, hdr->sblk_info[u].ndblks, hdr->sblk_info[u].dblk_nelmts, hdr->sblk_info[u].start_idx, hdr->sblk_info[u].start_dblk);
+#endif /* QAK */
+
+        /* Advance starting indices for next super block */
+        start_idx += hdr->sblk_info[u].ndblks * hdr->sblk_info[u].dblk_nelmts;
+        start_dblk += hdr->sblk_info[u].ndblks;
+    } /* end for */
+
+    /* Set size of header on disk */
+    hdr->size = H5EA_HEADER_SIZE(hdr);
+
+CATCH
+
+END_FUNC(PKG)   /* end H5EA__hdr_init() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5EA__hdr_alloc_elmts
+ *
+ * Purpose:	Allocate extensible array data block elements
+ *
+ * Return:	Non-NULL pointer to buffer for elements on success/NULL on failure
+ *
+ * Programmer:	Quincey Koziol
+ *		koziol@hdfgroup.org
+ *		Sep 16 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PKG, ERR,
+void *, NULL, NULL,
+H5EA__hdr_alloc_elmts(H5EA_hdr_t *hdr, size_t nelmts))
+
+    /* Local variables */
+    void *elmts = NULL;         /* Element buffer allocated */
+    unsigned idx;               /* Index of element buffer factory in header */
+
+    /* Check arguments */
+    HDassert(hdr);
+    HDassert(nelmts > 0);
+
+    /* Compute the index of the element buffer factory */
+    H5_CHECK_OVERFLOW(nelmts, /*From:*/size_t, /*To:*/uint32_t);
+    idx = H5V_log2_of2((uint32_t)nelmts) - H5V_log2_of2((uint32_t)hdr->data_blk_min_elmts);
+#ifdef QAK
+HDfprintf(stderr, "%s: nelmts = %Zu, hdr->data_blk_min_elmts = %u, idx = %u\n", FUNC, nelmts, (unsigned)hdr->data_blk_min_elmts, idx);
+#endif /* QAK */
+
+    /* Check for needing to increase size of array of factories */
+    if(idx >= hdr->elmt_fac.nalloc) {
+        H5FL_fac_head_t **new_fac;      /* New array of element factories */
+        size_t new_nalloc = MAX(1, (2 * hdr->elmt_fac.nalloc));   /* New number of factories allocated */
+
+        /* Re-allocate array of element factories */
+        if(NULL == (new_fac = H5FL_SEQ_REALLOC(H5FL_fac_head_ptr_t, hdr->elmt_fac.fac, new_nalloc)))
+            H5E_THROW(H5E_CANTALLOC, "memory allocation failed for data block data element buffer factory array")
+
+        /* Zero out new elements allocated */
+        HDmemset(new_fac + hdr->elmt_fac.nalloc, 0, (new_nalloc - hdr->elmt_fac.nalloc) * sizeof(H5FL_fac_head_ptr_t));
+
+        /* Update information about element factories in header */
+        hdr->elmt_fac.nalloc = new_nalloc;
+        hdr->elmt_fac.fac = new_fac;
+    } /* end if */
+
+    /* Check for un-initialized factory at index */
+    if(NULL == hdr->elmt_fac.fac[idx]) {
+        if(NULL == (hdr->elmt_fac.fac[idx] = H5FL_fac_init(nelmts * (size_t)hdr->cls->nat_elmt_size)))
+            H5E_THROW(H5E_CANTINIT, "can't create data block data element buffer factory")
+    } /* end if */
+
+    /* Allocate buffer for elements in index block */
+    if(NULL == (elmts = H5FL_FAC_MALLOC(hdr->elmt_fac.fac[idx])))
+        H5E_THROW(H5E_CANTALLOC, "memory allocation failed for data block data element buffer")
+
+    /* Set the return value */
+    ret_value = elmts;
+
+CATCH
+    if(!ret_value)
+        if(elmts)
+            (void)H5FL_fac_free(hdr->elmt_fac.fac[idx], elmts);
+
+END_FUNC(PKG)   /* end H5EA__hdr_alloc_elmts() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5EA__hdr_free_elmts
+ *
+ * Purpose:	Free extensible array data block elements
+ *
+ * Return:	SUCCEED/FAIL
+ *
+ * Programmer:	Quincey Koziol
+ *		koziol@hdfgroup.org
+ *		Sep 18 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PKG, NOERR,
+herr_t, SUCCEED, -,
+H5EA__hdr_free_elmts(H5EA_hdr_t *hdr, size_t nelmts, void *elmts))
+
+    /* Local variables */
+    unsigned idx;               /* Index of element buffer factory in header */
+
+    /* Check arguments */
+    HDassert(hdr);
+    HDassert(nelmts > 0);
+    HDassert(elmts);
+
+    /* Compute the index of the element buffer factory */
+    H5_CHECK_OVERFLOW(nelmts, /*From:*/size_t, /*To:*/uint32_t);
+    idx = H5V_log2_of2((uint32_t)nelmts) - H5V_log2_of2((uint32_t)hdr->data_blk_min_elmts);
+#ifdef QAK
+HDfprintf(stderr, "%s: nelmts = %Zu, hdr->data_blk_min_elmts = %u, idx = %u\n", FUNC, nelmts, (unsigned)hdr->data_blk_min_elmts, idx);
+#endif /* QAK */
+
+    /* Free buffer for elements in index block */
+    HDassert(idx < hdr->elmt_fac.nalloc);
+    HDassert(hdr->elmt_fac.fac[idx]);
+    (void)H5FL_FAC_FREE(hdr->elmt_fac.fac[idx], elmts);
+
+END_FUNC(PKG)   /* end H5EA__hdr_free_elmts() */
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5EA__hdr_create
  *
  * Purpose:	Creates a new extensible array header in the file
@@ -155,7 +361,7 @@ H5EA__hdr_create(H5F_t *f, hid_t dxpl_id, const H5EA_create_t *cparam))
     H5EA_hdr_t *hdr;            /* Extensible array header */
 
 #ifdef QAK
-HDfprintf(stderr, "%s: Called\n", __func__);
+HDfprintf(stderr, "%s: Called\n", FUNC);
 #endif /* QAK */
 
     /* Check arguments */
@@ -170,6 +376,8 @@ HDfprintf(stderr, "%s: Called\n", __func__);
 	H5E_THROW(H5E_BADVALUE, "max. # of nelmts bitsmust be greater than zero")
     if(cparam->max_nelmts_bits > H5EA_MAX_NELMTS_IDX_MAX)
 	H5E_THROW(H5E_BADVALUE, "element size must be <= %u", (unsigned)H5EA_MAX_NELMTS_IDX_MAX)
+    if(cparam->sup_blk_min_data_ptrs < 2)
+	H5E_THROW(H5E_BADVALUE, "min # of data block pointers in super block must be >= two")
     if(!POWER_OF_TWO(cparam->sup_blk_min_data_ptrs))
 	H5E_THROW(H5E_BADVALUE, "min # of data block pointers in super block not power of two")
     if(!POWER_OF_TWO(cparam->data_blk_min_elmts))
@@ -190,8 +398,9 @@ HDfprintf(stderr, "%s: Called\n", __func__);
     hdr->sup_blk_min_data_ptrs = cparam->sup_blk_min_data_ptrs;
     hdr->data_blk_min_elmts = cparam->data_blk_min_elmts;
 
-    /* Set size of header on disk */
-    hdr->size = H5EA_HEADER_SIZE(hdr);
+    /* Finish initializing extensible array header */
+    if(H5EA__hdr_init(hdr) < 0)
+	H5E_THROW(H5E_CANTINIT, "initialization failed for extensible array header")
 
     /* Allocate space for the header on disk */
     if(HADDR_UNDEF == (hdr->addr = H5MF_alloc(f, H5FD_MEM_EARRAY_HDR, dxpl_id, hdr->size)))
@@ -402,7 +611,7 @@ H5EA__hdr_delete(H5EA_hdr_t *hdr, hid_t dxpl_id))
     /* Check for index block */
     if(H5F_addr_defined(hdr->idx_blk_addr)) {
 #ifdef QAK
-HDfprintf(stderr, "%s: hdr->idx_blk_addr = %a\n", __func__, hdr->idx_blk_addr);
+HDfprintf(stderr, "%s: hdr->idx_blk_addr = %a\n", FUNC, hdr->idx_blk_addr);
 #endif /* QAK */
         /* Delete index block */
         if(H5EA__iblock_delete(hdr, dxpl_id) < 0)
@@ -426,3 +635,57 @@ CATCH
 
 END_FUNC(PKG)   /* end H5EA__hdr_delete() */
 
+
+/*-------------------------------------------------------------------------
+ * Function:	H5EA__hdr_dest
+ *
+ * Purpose:	Destroys an extensible array header in memory.
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Quincey Koziol
+ *		koziol@hdfgroup.org
+ *		Sep 11 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PKG, ERR,
+herr_t, SUCCEED, FAIL,
+H5EA__hdr_dest(H5EA_hdr_t *hdr))
+
+    /* Check arguments */
+    HDassert(hdr);
+    HDassert(hdr->rc == 0);
+
+    /* Check for data block element buffer factory info to free */
+    if(hdr->elmt_fac.fac) {
+        unsigned u;         /* Local index variable */
+
+        /* Sanity check */
+        HDassert(hdr->elmt_fac.nalloc > 0);
+
+        /* Iterate over factories, shutting them down */
+        for(u = 0; u < hdr->elmt_fac.nalloc; u++) {
+            /* Check if this factory has been initialized */
+            if(hdr->elmt_fac.fac[u]) {
+                if(H5FL_fac_term(hdr->elmt_fac.fac[u]) < 0)
+                    H5E_THROW(H5E_CANTRELEASE, "unable to destroy extensible array header factory")
+                hdr->elmt_fac.fac[u] = NULL;
+            } /* end if */
+        } /* end for */
+
+        /* Free factory array */
+        hdr->elmt_fac.fac = (H5FL_fac_head_t **)H5FL_SEQ_FREE(H5FL_fac_head_ptr_t, hdr->elmt_fac.fac);
+    } /* end if */
+
+    /* Free the super block info array */
+    if(hdr->sblk_info)
+        hdr->sblk_info = (H5EA_sblk_info_t *)H5FL_SEQ_FREE(H5EA_sblk_info_t, hdr->sblk_info);
+
+    /* Free the shared info itself */
+    (void)H5FL_FREE(H5EA_hdr_t, hdr);
+
+CATCH
+
+END_FUNC(PKG)   /* end H5EA__hdr_dest() */
+