[svn-r5894] Purpose:

    Bug fix/Code cleanup/New Feature

Description:
    Correct problems with writing fill-values to external storage and allocate
    the data storage at the correct times.

    Also, mostly straighten out the strange code which allocates and fills
    raw data storage for datasets.  Things are still a bit odd in that the
    fill-values for chunked datasets are written when the space is allocated,
    instead of in a separate routine, but there are two reasons for this:
    it's inefficient (especially in parallel) to iterate through all the chunks
    twice, and (more importantly) the space needed to store compressed chunks
    isn't known until we've got a buffer of compressed fill-values ready to
    write to the chunk.

    Additionally, add in the H5D_SPACE_ALLOC_INCR and H5D_SPACE_ALLOC_DEFAULT
    setting for the "space time", which incorporate the previous behavior of
    the space allocation for chunked datasets.

    The default settings for the different types of dataset storage are now
    as follows:
        Contiguous - Late
        Chunked    - Incremental
        Compact    - Early

    This checkin also incorporates a change to the behavior of external data
    storage in two ways - fill-values are _never_ written to external storage
    (under the assumption that writing fill-values is triggered by allocating
    space in an HDF5 file, and since space is not allocated in the file, the
    fill-values should not be written) and external data files are now created
    if they don't exist when data is written to them.  The fill-value will
    probably need to be revisited at some time in the future, this just seemed
    like the safer course currently.

    I think I cleaned up some compiler errors also, before getting bogged down
    in the fixes for the space allocation and fill-values.

Platforms tested:
    FreeBSD 4.6 (sleipnir) w/serial & parallel.  Will be testing on IRIX64
    6.5 (modi4) in serial & parallel shortly.

1 files changed, 49 insertions, 29 deletions

diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index 0bba74e..f36b6200 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -1758,7 +1758,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
         if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
                 chunk_addr!=HADDR_UNDEF)
 
-#ifdef H5_HAVE_PARALLEL
         /*
          * If MPIO or MPIPOSIX is used and file can be written to, we must bypass the
          * chunk-cache scheme because other MPI processes could be writing to
@@ -1766,7 +1765,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
          * Do a direct write-through of only the elements requested.
          */
             || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags))
-#endif /* H5_HAVE_PARALLEL */
             ) {
             H5O_layout_t	l;	/* temporary layout */
 
@@ -1942,14 +1940,12 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
         if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
                 chunk_addr!=HADDR_UNDEF)
 
-#ifdef H5_HAVE_PARALLEL
         /*
          * If MPIO or MPIPOSIX is used, must bypass the chunk-cache scheme because other
          * MPI processes could be writing to other elements in the same chunk.
          * Do a direct write-through of only the elements requested.
          */
             || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags))
-#endif /* H5_HAVE_PARALLEL */
             ) {
             H5O_layout_t	l;	/* temporary layout */
 
@@ -2334,6 +2330,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
     H5P_genplist_t *dx_plist;   /* Data xfer property list */
     double	split_ratios[3];/* B-tree node splitting ratios		*/
 #ifdef H5_HAVE_PARALLEL
+    MPI_Comm	mpi_comm=MPI_COMM_NULL;	/* MPI communicator for file */
     int         mpi_rank=(-1);  /* This process's rank  */
     int         mpi_size=(-1);  /* Total # of processes */
     int         mpi_round=0;    /* Current process responsible for I/O */
@@ -2342,6 +2339,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
     unsigned    using_mpi=0;    /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
 #endif /* H5_HAVE_PARALLEL */
     int		carry;          /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
+    unsigned	chunk_exists;   /* Flag to indicate whether a chunk exists already */
     int		i;              /* Local index variable */
     unsigned	u;              /* Local index variable */
     herr_t	ret_value=SUCCEED;	/* Return value */
@@ -2374,6 +2372,11 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
 #ifdef H5_HAVE_PARALLEL
     /* Retrieve up MPI parameters */
     if(IS_H5FD_MPIO(f)) {
+        /* Get the MPI communicator */
+        if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf)))
+            HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
+        /* Get the MPI rank & size */
         if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0)
             HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
         if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0)
@@ -2384,6 +2387,10 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
     } /* end if */
     else {
         if(IS_H5FD_MPIPOSIX(f)) {
+            /* Get the MPI communicator */
+            if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf)))
+                HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
             /* Get the MPI rank & size */
             if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0)
                 HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
@@ -2396,12 +2403,6 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
     } /* end else */
 #endif /* H5_HAVE_PARALLEL */
 
-#ifdef H5_HAVE_PARALLEL
-    /* Can't use data I/O pipeline in parallel (yet) */
-    if (using_mpi && pline.nfilters>0)
-        HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, FAIL, "can't use data pipeline in parallel");
-#endif /* H5_HAVE_PARALLEL */
-
     /*
      * Setup indice to go through all chunks. (Future improvement
      * should allocate only chunks that have no file space assigned yet.
@@ -2450,8 +2451,32 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
     /* Loop over all chunks */
     carry=0;
     while (carry==0) {
-        /* Check if the chunk exists yet */
+        /* Check if the chunk exists yet on disk */
+        chunk_exists=1;
         if(H5F_istore_get_addr(f,layout,chunk_offset)==HADDR_UNDEF) {
+            H5F_rdcc_t             *rdcc = &(f->shared->rdcc);	/*raw data chunk cache */
+            H5F_rdcc_ent_t         *ent = NULL;              	/*cache entry  */
+
+            /* Didn't find the chunk on disk */
+            chunk_exists = 0;
+
+            /* Look for chunk in cache */
+            for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
+                /* Make certain we are dealing with the correct B-tree, etc */
+                if (layout->ndims==ent->layout->ndims &&
+                        H5F_addr_eq(layout->addr, ent->layout->addr)) {
+
+                    /* Assume a match */
+                    chunk_exists = 1;
+                    for(u = 0; u < layout->ndims && chunk_exists; u++) {
+                        if(ent->offset[u] != chunk_offset[u])
+                            chunk_exists = 0;       /* Reset if no match */
+                    } /* end for */
+                } /* end if */
+            } /* end for */
+        } /* end if */
+
+        if(!chunk_exists) {
             /* Initialize the chunk information */
             udata.mesg = *layout;
             udata.key.filter_mask = 0;
@@ -2507,17 +2532,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
          * still writing out chunks and other processes race ahead to read
          * them in, getting bogus data.
          */
-        if(IS_H5FD_MPIO(f)) {
-            if (MPI_SUCCESS != (mpi_code=MPI_Barrier(H5FD_mpio_communicator(f->shared->lf))))
-                HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
-        } /* end if */
-        else {
-            /* Sanity Check */
-            assert(IS_H5FD_MPIPOSIX(f));
-
-            if (MPI_SUCCESS!=(mpi_code=MPI_Barrier(H5FD_mpiposix_communicator(f->shared->lf))))
-                HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
-        } /* end else */
+        if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm)))
+            HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
     } /* end if */
 #endif /* H5_HAVE_PARALLEL */
 
@@ -2662,13 +2678,17 @@ H5F_istore_prune_by_extent(H5F_t *f, const H5O_layout_t *layout, const H5S_t * s
     for(ent = rdcc->head; ent; ent = next) {
 	next = ent->next;
 
-	found = 0;
-	for(u = 0; u < ent->layout->ndims - 1; u++) {
-	    if((hsize_t)ent->offset[u] > curr_dims[u]) {
-		found = 1;
-		break;
-	    }
-	}
+        /* Make certain we are dealing with the correct B-tree, etc */
+        if (layout->ndims==ent->layout->ndims &&
+                H5F_addr_eq(layout->addr, ent->layout->addr)) {
+            found = 0;
+            for(u = 0; u < ent->layout->ndims - 1; u++) {
+                if((hsize_t)ent->offset[u] > curr_dims[u]) {
+                    found = 1;
+                    break;
+                }
+            }
+        } /* end if */
 
 	if(found) {
 #if defined (H5F_ISTORE_DEBUG)