[svn-r6252] Purpose:

    Lots of performance improvements & a couple new internal API interfaces.

Description:
    Performance Improvements:
        - Cached file offset & length sizes in shared file struct, to avoid
            constantly looking them up in the FCPL.
        - Generic property improvements:
            - Added "revision" number to generic property classes to speed
                up comparisons.
            - Changed method of storing properties from using a hash-table
                to the TBBT routines in the library.
            - Share the propery names between classes and the lists derived
                from them.
            - Removed redundant 'def_value' buffer from each property.
            - Switching code to use a "copy on write" strategy for
                properties in each list, where the properties in each list
                are shared with the properties in the class, until a
                property's value is changed in a list.
        - Fixed error in layout code which was allocating too many buffers.
        - Redefined public macros of the form (H5open()/H5check, <variable>)
            internally to only be (<variable>), avoiding innumerable useless
            calls to H5open() and H5check_version().
        - Reuse already zeroed buffers in H5F_contig_fill instead of
            constantly re-zeroing them.
        - Don't write fill values if writing entire dataset.
        - Use gettimeofday() system call instead of time() system when
            checking the modification time of a dataset.
        - Added reference counted string API and use it for tracking the
            names of objects opening in a file (for the ID->name code).
        - Removed redundant H5P_get() calls in B-tree routines.
        - Redefine H5T datatype macros internally to the library, to avoid
            calling H5check redundantly.
        - Keep dataspace information for dataset locally instead of reading
            from disk each time.  Added new module to track open objects
            in a file, to allow this (which will be useful eventually for
            some FPH5 metadata caching issues).
        - Remove H5AC_find macro which was inlining metadata cache lookups,
            and call function instead.
        - Remove redundant memset() calls from H5G_namei() routine.
        - Remove redundant checking of object type when locating objects
            in metadata cache and rely on the address only.
        - Create default dataset object to use when default dataset creation
            property list is used to create datasets, bypassing querying
            for all the property list values.
        - Use default I/O vector size when performing raw data with the
            default dataset transfer property list, instead of querying for
            I/O vector size.
        - Remove H5P_DEFAULT internally to the library, replacing it with
            more specific default property list based on the type of
            property list needed.
        - Remove redundant memset() calls in object header message (H5O*)
            routines.
        - Remove redunant memset() calls in data I/O routines.
        - Split free-list allocation routines into malloc() and calloc()-
            like routines, instead of one combined routine.
        - Remove lots of indirection in H5O*() routines.
        - Simplify metadata cache entry comparison routine (used when
            flushing entire cache out).
        - Only enable metadata cache statistics when H5AC_DEBUG is turned
            on, instead of always tracking them.
        - Simplify address comparison macro (H5F_addr_eq).
        - Remove redundant metadata cache entry protections during dataset
            creation by protecting the object header once and making all
            the modifications necessary for the dataset creation before
            unprotecting it.
        - Reduce # of "number of element in extent" computations performed
            by computing and storing the value during dataspace creation.
        - Simplify checking for group location's file information, when file
            has not been involving in file-mounting operations.
        - Use binary encoding for modification time, instead of ASCII.
        - Hoist H5HL_peek calls (to get information in a local heap)
            out of loops in many group routine.
        - Use static variable for iterators of selections, instead of
            dynamically allocation them each time.
        - Lookup & insert new entries in one step, avoiding traversing
            group's B-tree twice.
        - Fixed memory leak in H5Gget_objname_idx() routine (tangential to
            performance improvements, but fixed along the way).
        - Use free-list for reference counted strings.
        - Don't bother copying object names into cached group entries,
            since they are re-created when an object is opened.

        The benchmark I used to measure these results created several thousand
        small (2K) datasets in a file and wrote out the data for them.  This is
        Elena's "regular.c" benchmark.

        These changes resulted in approximately ~4.3x speedup of the
        development branch when compared to the previous code in the
        development branch and ~1.4x speedup compared to the release
        branch.

        Additionally, these changes reduce the total memory used (code and
        data) by the development branch by ~800KB, bringing the development
        branch back into the same ballpark as the release branch.

        I'll send out a more detailed description of the benchmark results
        as a followup note.

    New internal API routines:
        Added "reference counted strings" API for tracking strings that get
            used by multiple owners without duplicating the strings.
        Added "ternary search tree" API for text->object mappings.

Platforms tested:
    Tested h5committest {arabica (fortran), eirene (fortran, C++)
	modi4 (parallel, fortran)}
    Other platforms/configurations tested?
        FreeBSD 4.7 (sleipnir) serial & parallel
        Solaris 2.6 (baldric) serial

1 files changed, 7 insertions, 6 deletions

diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index ea74165..f617092 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -862,7 +862,7 @@ H5F_istore_init (H5F_t *f)
     HDmemset (rdcc, 0, sizeof(H5F_rdcc_t));
     if (f->shared->rdcc_nbytes>0 && f->shared->rdcc_nelmts>0) {
 	rdcc->nslots = f->shared->rdcc_nelmts;
-	rdcc->slot = H5FL_ARR_ALLOC (H5F_rdcc_ent_ptr_t,rdcc->nslots,1);
+	rdcc->slot = H5FL_ARR_CALLOC (H5F_rdcc_ent_ptr_t,rdcc->nslots);
 	if (NULL==rdcc->slot)
 	    HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed");
     }
@@ -1440,7 +1440,7 @@ H5F_istore_lock(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
             HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk(s) from cache");
 
         /* Create a new entry */
-        ent = H5FL_ALLOC(H5F_rdcc_ent_t,0);
+        ent = H5FL_MALLOC(H5F_rdcc_ent_t);
         ent->locked = 0;
         ent->dirty = FALSE;
         ent->chunk_size = chunk_size;
@@ -1943,8 +1943,9 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
 
 #ifdef H5_HAVE_PARALLEL
             /* Additional sanity check when operating in parallel */
-            if (chunk_addr==HADDR_UNDEF || pline.nfilters>0)
+            if (chunk_addr==HADDR_UNDEF || pline.nfilters>0) {
                 HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk");
+            }
 #endif /* H5_HAVE_PARALLEL */
             
             /*
@@ -2312,7 +2313,7 @@ done:
  */
 herr_t
 H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
-		    const hsize_t *space_dim, H5P_genplist_t *dc_plist)
+        const hsize_t *space_dim, H5P_genplist_t *dc_plist, hbool_t full_overwrite)
 {
     hssize_t	chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */
     hsize_t	chunk_size;     /* Size of chunk in bytes */
@@ -2407,7 +2408,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
     } /* end for */
 
     /* Check if fill values should be written to blocks */
-    if(fill_time != H5D_FILL_TIME_NEVER) {
+    if(fill_time != H5D_FILL_TIME_NEVER && !full_overwrite) {
         /* Allocate chunk buffer for processes to use when writing fill values */
         H5_CHECK_OVERFLOW(chunk_size,hsize_t,size_t);
         if (NULL==(chunk = H5MM_malloc((size_t)chunk_size)))
@@ -2484,7 +2485,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
                 HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk");
 
             /* Check if fill values should be written to blocks */
-            if(fill_time != H5D_FILL_TIME_NEVER) {
+            if(fill_time != H5D_FILL_TIME_NEVER && !full_overwrite) {
 #ifdef H5_HAVE_PARALLEL
                 /* Check if this file is accessed with an MPI-capable file driver */
                 if(using_mpi) {