[svn-r2657]

Purpose:
    Parallel Bug Fixes
Description:
    Was out of sync with header file re-arrangements I checked in last night.

Solution:
    Fixed to use new header files, etc.
Platforms tested:
	O2K (modi4)

12 files changed, 64 insertions, 322 deletions

diff --git a/src/H5Dseq.c b/src/H5Dseq.c
index 9aa3a48..db1a8c2 100644
--- a/src/H5Dseq.c
+++ b/src/H5Dseq.c
@@ -83,7 +83,7 @@ H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 #ifdef H5_HAVE_PARALLEL
     {
         /* Get the transfer mode */
-        H5F_xfer_t *dxpl;
+        H5D_xfer_t *dxpl;
         H5FD_mpio_dxpl_t *dx;
 
         if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
@@ -312,7 +312,7 @@ H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 #ifdef H5_HAVE_PARALLEL
     {
         /* Get the transfer mode */
-        H5F_xfer_t *dxpl;
+        H5D_xfer_t *dxpl;
         H5FD_mpio_dxpl_t *dx;
 
         if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index fe9fd08..f48d881 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -698,7 +698,7 @@ H5FD_mpio_open(const char *name, unsigned flags, hid_t fapl_id,
 #ifdef H5FDmpio_DEBUG
     if (H5FD_mpio_Debug[(int)'t']) {
     	fprintf(stdout, "Entering H5FD_mpio_open(name=\"%s\", flags=0x%x, "
-		"fapl_id=%lu, maxaddr=%lu)\n", name, flags, fapl_id, maxaddr);
+		"fapl_id=%d, maxaddr=%lu)\n", name, flags, (int)fapl_id, (unsigned long)maxaddr);
     }
 #endif
 
diff --git a/src/H5Farray.c b/src/H5Farray.c
index 798be54..aeb4c03 100644
--- a/src/H5Farray.c
+++ b/src/H5Farray.c
@@ -149,7 +149,7 @@ H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
     H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
 #endif
 #ifdef COALESCE_READS
-    H5F_xfer_t *xfer_parms;                     /*transfer property list*/
+    H5D_xfer_t *xfer_parms;                     /*transfer property list*/
 #endif
    
     FUNC_ENTER(H5F_arr_read, FAIL);
@@ -169,7 +169,7 @@ H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 #ifdef H5_HAVE_PARALLEL
     {
 	/* Get the transfer mode */
-	H5F_xfer_t *dxpl;
+	H5D_xfer_t *dxpl;
 	H5FD_mpio_dxpl_t *dx;
 	if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
 	    H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
@@ -281,7 +281,7 @@ H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 #ifdef COALESCE_READS
         /* Get the dataset transfer property list */
         if (H5P_DEFAULT == dxpl_id) {
-            xfer_parms = &H5F_xfer_dflt;
+            xfer_parms = &H5D_xfer_dflt;
         } else if (H5P_DATA_XFER != H5P_get_class (dxpl_id) ||
                NULL == (xfer_parms = H5I_object (dxpl_id))) {
             HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
@@ -385,7 +385,7 @@ printf("%s: feature_flags=%lx\n",FUNC,(unsigned long)f->shared->lf->feature_flag
  *
  * 		Robb Matzke, 1998-09-28
  *		Added `xfer' argument, removed `xfer_mode' argument since it
- *		is a member of H5F_xfer_t.
+ *		is a member of H5D_xfer_t.
  *
  * 		Robb Matzke, 1999-08-02
  *		Data transfer properties are passed by ID since that's how
@@ -434,7 +434,7 @@ H5F_arr_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 #ifdef H5_HAVE_PARALLEL
     {
 	/* Get the transfer mode */
-	H5F_xfer_t *dxpl;
+	H5D_xfer_t *dxpl;
 	H5FD_mpio_dxpl_t *dx;
 	if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
 	    H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
diff --git a/src/H5Fseq.c b/src/H5Fseq.c
index 9aa3a48..db1a8c2 100644
--- a/src/H5Fseq.c
+++ b/src/H5Fseq.c
@@ -83,7 +83,7 @@ H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 #ifdef H5_HAVE_PARALLEL
     {
         /* Get the transfer mode */
-        H5F_xfer_t *dxpl;
+        H5D_xfer_t *dxpl;
         H5FD_mpio_dxpl_t *dx;
 
         if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
@@ -312,7 +312,7 @@ H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 #ifdef H5_HAVE_PARALLEL
     {
         /* Get the transfer mode */
-        H5F_xfer_t *dxpl;
+        H5D_xfer_t *dxpl;
         H5FD_mpio_dxpl_t *dx;
 
         if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
diff --git a/src/H5R.c b/src/H5R.c
index ab7921a..b9240bd 100644
--- a/src/H5R.c
+++ b/src/H5R.c
@@ -454,7 +454,6 @@ H5R_dereference(H5F_t *file, H5R_type_t ref_type, void *_ref)
         default:
             HGOTO_ERROR(H5E_REFERENCE, H5E_BADTYPE, FAIL,
                   "can't identify type of object referenced");
-            break;
      } /* end switch */
 
 done:
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index 336536b..47badf8 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -95,7 +95,7 @@ static herr_t H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout,
 			       H5S_sel_iter_t *file_iter, size_t nelmts,
 			       hid_t dxpl_id, const void *buf);
 static size_t H5S_hyper_mread (intn dim, H5S_hyper_io_info_t *io_info);
-static herr_t H5S_hyper_mread_opt (const void *_buf, size_t elmt_size,
+static size_t H5S_hyper_mread_opt (const void *_buf, size_t elmt_size,
 		 const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
 		 size_t nelmts, void *_tconv_buf/*out*/);
 static size_t H5S_hyper_mgath (const void *_buf, size_t elmt_size,
@@ -103,7 +103,7 @@ static size_t H5S_hyper_mgath (const void *_buf, size_t elmt_size,
 			       H5S_sel_iter_t *mem_iter, size_t nelmts,
 			       void *_tconv_buf/*out*/);
 static size_t H5S_hyper_mwrite (intn dim, H5S_hyper_io_info_t *io_info);
-static herr_t H5S_hyper_mwrite_opt (const void *_tconv_buf, size_t elmt_size,
+static size_t H5S_hyper_mwrite_opt (const void *_tconv_buf, size_t elmt_size,
 		 const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
 		 size_t nelmts, void *_buf/*out*/);
 static herr_t H5S_hyper_mscat (const void *_tconv_buf, size_t elmt_size,
@@ -946,11 +946,11 @@ H5S_hyper_fread_opt (H5F_t *f, const struct H5O_layout_t *layout,
     intn fast_dim;  /* Rank of the fastest changing dimension for the dataspace */
     intn temp_dim;  /* Temporary rank holder */
     hsize_t	acc;	/* Accumulator */
-    size_t	buf_off;  /* Buffer offset for copying memory */
+    hssize_t	buf_off;  /* Buffer offset for copying memory */
     intn i;         /* Counters */
     intn   	ndims;      /* Number of dimensions of dataset */
-    uintn actual_read;      /* The actual number of elements to read in */
-    uintn actual_bytes;     /* The actual number of bytes to copy */
+    size_t actual_read;      /* The actual number of elements to read in */
+    size_t actual_bytes;     /* The actual number of bytes to copy */
     size_t num_read=0;      /* Number of elements read */
 
     FUNC_ENTER (H5S_hyper_fread_opt, 0);
@@ -981,7 +981,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
 
     /* Check if we stopped in the middle of a sequence of elements */
     if((file_iter->hyp.pos[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) {
-        uintn leftover;  /* The number of elements left over from the last sequence */
+        size_t leftover;  /* The number of elements left over from the last sequence */
 
 #ifdef QAK
 printf("%s: Check 1.0\n",FUNC);
@@ -1466,11 +1466,11 @@ H5S_hyper_fwrite_opt (H5F_t *f, const struct H5O_layout_t *layout,
     intn fast_dim;  /* Rank of the fastest changing dimension for the dataspace */
     intn temp_dim;  /* Temporary rank holder */
     hsize_t	acc;	/* Accumulator */
-    size_t	buf_off;  /* Buffer offset for copying memory */
+    hssize_t	buf_off;  /* Buffer offset for copying memory */
     intn i;         /* Counters */
     intn   	ndims;      /* Number of dimensions of dataset */
-    uintn actual_write;     /* The actual number of elements to read in */
-    uintn actual_bytes;     /* The actual number of bytes to copy */
+    size_t actual_write;     /* The actual number of elements to read in */
+    size_t actual_bytes;     /* The actual number of bytes to copy */
     size_t num_write=0;     /* Number of elements read */
 
     FUNC_ENTER (H5S_hyper_fwrite_opt, 0);
@@ -1501,7 +1501,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
 
     /* Check if we stopped in the middle of a sequence of elements */
     if((file_iter->hyp.pos[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) {
-        uintn leftover;  /* The number of elements left over from the last sequence */
+        size_t leftover;  /* The number of elements left over from the last sequence */
 
 #ifdef QAK
 printf("%s: Check 1.0\n",FUNC);
@@ -1944,7 +1944,7 @@ H5S_hyper_mread (intn dim, H5S_hyper_io_info_t *io_info)
  *
  *-------------------------------------------------------------------------
  */
-static herr_t
+static size_t
 H5S_hyper_mread_opt (const void *_buf, size_t elmt_size,
 		 const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
 		 size_t nelmts, void *_tconv_buf/*out*/)
@@ -1962,8 +1962,8 @@ H5S_hyper_mread_opt (const void *_buf, size_t elmt_size,
     size_t	buf_off;  /* Buffer offset for copying memory */
     intn i;         /* Counters */
     intn   	ndims;      /* Number of dimensions of dataset */
-    uintn actual_read;       /* The actual number of elements to read in */
-    uintn actual_bytes;     /* The actual number of bytes to copy */
+    size_t actual_read;       /* The actual number of elements to read in */
+    size_t actual_bytes;     /* The actual number of bytes to copy */
     size_t num_read=0;      /* Number of elements read */
 
     FUNC_ENTER (H5S_hyper_mread_opt, 0);
@@ -2002,7 +2002,7 @@ for(i=0; i<ndims; i++)
 
     /* Check if we stopped in the middle of a sequence of elements */
     if((mem_iter->hyp.pos[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) {
-        uintn leftover;  /* The number of elements left over from the last sequence */
+        size_t leftover;  /* The number of elements left over from the last sequence */
 
 #ifdef QAK
 printf("%s: Check 1.0\n",FUNC);
@@ -2419,259 +2419,6 @@ H5S_hyper_mwrite (intn dim, H5S_hyper_io_info_t *io_info)
     FUNC_LEAVE (num_read);
 }   /* H5S_hyper_mwrite() */
 
-#ifdef WORKS_QAK
-
-/*-------------------------------------------------------------------------
- * Function:	H5S_hyper_mwrite_opt
- *
- * Purpose:	Performs an optimized scatter to a memory buffer, based on a
- *      regular hyperslab (i.e. one which was generated from just one call to
- *      H5Sselect_hyperslab).
- *
- * Return:	Success:	Number of elements copied.
- *		Failure:	0
- *
- * Programmer:	Quincey Koziol
- *              Tuesday, September 12, 2000
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5S_hyper_mwrite_opt (const void *_tconv_buf, size_t elmt_size,
-		 const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
-		 size_t nelmts, void *_buf/*out*/)
-{
-    hsize_t	mem_size[H5O_LAYOUT_NDIMS];     /* Size of the source buffer */
-    hsize_t	hsize[H5O_LAYOUT_NDIMS];        /* Hyperslab size */
-    hssize_t zero[H5O_LAYOUT_NDIMS];		/*zero			*/
-    hssize_t offset[H5O_LAYOUT_NDIMS];      /* Offset on disk */
-    hsize_t	tmp_count[H5O_LAYOUT_NDIMS];    /* Temporary block count */
-    hsize_t	tmp_block[H5O_LAYOUT_NDIMS];    /* Temporary block offset */
-    const uint8_t	*src=(const uint8_t *)_tconv_buf;   /* Alias for pointer arithmetic */
-    uint8_t	*dst=(uint8_t *)_buf;   /* Alias for pointer arithmetic */
-    intn fast_dim;  /* Rank of the fastest changing dimension for the dataspace */
-    intn temp_dim;  /* Temporary rank holder */
-    intn i;         /* Counters */
-    intn   	ndims;      /* Number of dimensions of dataset */
-    uintn actual_write;       /* The actual number of elements to read in */
-    size_t num_write=0;      /* Number of elements read */
-
-    FUNC_ENTER (H5S_hyper_fwrite_opt, 0);
-
-#ifdef QAK
-printf("%s: Called!\n",FUNC);
-#endif /* QAK */
-    /* Check if this is the first element read in from the hyperslab */
-    if(mem_iter->hyp.pos[0]==(-1)) {
-        for(i=0; i<mem_space->extent.u.simple.rank; i++)
-            mem_iter->hyp.pos[i]=mem_space->select.sel_info.hslab.diminfo[i].start;
-    } /* end if */
-
-#ifdef QAK
-for(i=0; i<mem_space->extent.u.simple.rank; i++)
-    printf("%s: mem_file->hyp.pos[%d]=%d\n",FUNC,(int)i,(int)mem_iter->hyp.pos[i]);
-#endif /* QAK */
-
-    /* Set the rank of the fastest changing dimension */
-    fast_dim=mem_space->extent.u.simple.rank-1;
-
-    /* Set up the hyperslab and 'zero' arrays */
-    ndims=mem_space->extent.u.simple.rank;
-    /* initialize hyperslab size and offset in memory buffer */
-    for(i=0; i<(ndims+1); i++) {
-        hsize[i]=1;     /* hyperslab size is 1, except for last element */
-        zero[i]=0;      /* memory offset is 0 */
-    } /* end for */
-    hsize[ndims] = elmt_size;
-
-    /* Set up the size of the memory space */
-    HDmemcpy(mem_size, mem_space->extent.u.simple.size,mem_space->extent.u.simple.rank*sizeof(hsize_t));
-    mem_size[mem_space->extent.u.simple.rank]=elmt_size;
-
-    /* Check if we stopped in the middle of a sequence of elements */
-    if((mem_iter->hyp.pos[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) {
-        uintn leftover;  /* The number of elements left over from the last sequence */
-
-#ifdef QAK
-printf("%s: Check 1.0\n",FUNC);
-#endif /* QAK */
-        /* Calculate the number of elements left in the sequence */
-        leftover=mem_space->select.sel_info.hslab.diminfo[fast_dim].block-((mem_iter->hyp.pos[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride);
-
-        /* Make certain that we don't write too many */
-        actual_write=MIN(leftover,nelmts);
-
-        /* Set the hyperslab size in the fastest changing dimension to write in */
-        hsize[fast_dim]=actual_write;
-
-        /* Copy the location of the point to get */
-        HDmemcpy(offset, mem_iter->hyp.pos,ndims*sizeof(hssize_t));
-        offset[ndims] = 0;
-
-        /* Add in the selection offset */
-        for(i=0; i<ndims; i++)
-            offset[i] += mem_space->select.offset[i];
-
-        /* Scatter out the rest of the sequence, if possible */
-        if (H5V_hyper_copy (ndims+1, hsize,
-            mem_size, offset, dst,
-            hsize, zero, src)<0) {
-            HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "unable to gather data from memory");
-        }
-
-        /* Increment the offset of the buffer */
-        src+=elmt_size*actual_write;
-
-        /* Increment the count write */
-        num_write+=actual_write;
-
-        /* Decrement the number of elements left in selection */
-        mem_iter->hyp.elmt_left-=actual_write;
-
-        /* Advance the point iterator */
-        /* If we had enough buffer space to write out the rest of the sequence
-         * in the fastest changing dimension, move the iterator offset to
-         * the beginning of the next block to write.  Otherwise, just advance
-         * the iterator in the fastest changing dimension.
-         */
-        if(actual_write==leftover) {
-            /* Move iterator offset to beginning of next sequence in the fastest changing dimension */
-            H5S_hyper_iter_next(mem_space,mem_iter);
-        } /* end if */
-        else {
-            mem_iter->hyp.pos[fast_dim]+=actual_write; /* whole sequence not written out, just advance fastest dimension offset */
-        } /* end if */
-    } /* end if */
-
-    /* Now that we've cleared the "remainder" of the previous fastest dimension
-     * sequence, we must be at the beginning of a sequence, so use the fancy
-     * algorithm to compute the offsets and run through as many as possible,
-     * until the buffer fills up.
-     */
-    if(num_write<nelmts) { /* Just in case the "remainder" above filled the buffer */
-#ifdef QAK
-printf("%s: Check 2.0\n",FUNC);
-#endif /* QAK */
-        /* Compute the arrays to perform I/O on */
-        /* Copy the location of the point to get */
-        HDmemcpy(offset, mem_iter->hyp.pos,ndims*sizeof(hssize_t));
-        offset[ndims] = 0;
-
-        /* Add in the selection offset */
-        for(i=0; i<ndims; i++)
-            offset[i] += mem_space->select.offset[i];
-
-        /* Compute the current "counts" for this location */
-        for(i=0; i<ndims; i++) {
-            tmp_count[i] = (mem_iter->hyp.pos[i]-mem_space->select.sel_info.hslab.diminfo[i].start)%mem_space->select.sel_info.hslab.diminfo[i].stride;
-            tmp_block[i] = (mem_iter->hyp.pos[i]-mem_space->select.sel_info.hslab.diminfo[i].start)/mem_space->select.sel_info.hslab.diminfo[i].stride;
-        } /* end for */
-
-        /* Set the number of elements to write each time */
-        actual_write=mem_space->select.sel_info.hslab.diminfo[fast_dim].block;
-        hsize[fast_dim]=actual_write;
-#ifdef QAK
-printf("%s: actual_write=%d\n",FUNC,(int)actual_write);
-for(i=0; i<file_space->extent.u.simple.rank; i++)
-    printf("%s: diminfo: start[%d]=%d, stride[%d]=%d, block[%d]=%d, count[%d]=%d\n",FUNC,
-        (int)i,(int)mem_space->select.sel_info.hslab.diminfo[i].start,
-        (int)i,(int)mem_space->select.sel_info.hslab.diminfo[i].stride,
-        (int)i,(int)mem_space->select.sel_info.hslab.diminfo[i].block,
-        (int)i,(int)mem_space->select.sel_info.hslab.diminfo[i].count);
-#endif /* QAK */
-
-        /* Read in data until an entire sequence can't be written out any longer */
-        while(num_write<nelmts) {
-            /* Check if we are running out of room in the buffer */
-            if((actual_write+num_write)>nelmts) {
-                actual_write=nelmts-num_write;
-                hsize[fast_dim]=actual_write;
-            } /* end if */
-
-#ifdef QAK
-printf("%s: num_write=%d\n",FUNC,(int)num_write);
-for(i=0; i<mem_space->extent.u.simple.rank; i++)
-    printf("%s: tmp_count[%d]=%d, offset[%d]=%d\n",FUNC,(int)i,(int)tmp_count[i],(int)i,(int)offset[i]);
-#endif /* QAK */
-
-            /* Scatter out the rest of the sequence, if possible */
-            if (H5V_hyper_copy (ndims+1, hsize,
-                mem_size, offset, dst,
-                hsize, zero, src)<0) {
-                HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "unable to gather data from memory");
-            }
-
-            /* Increment the offset of the buffer */
-            src+=elmt_size*actual_write;
-
-            /* Increment the count write */
-            num_write+=actual_write;
-
-            /* Decrement the number of elements left in selection */
-            mem_iter->hyp.elmt_left-=actual_write;
-
-            /* Increment the offset and count */
-            temp_dim=fast_dim;
-            while(temp_dim>=0) {
-                if(temp_dim==fast_dim) {
-                    /* Move to the next block in the current dimension */
-                    /* Check for partial block write! */
-                    if(actual_write<mem_space->select.sel_info.hslab.diminfo[fast_dim].block) {
-                        offset[temp_dim]+=actual_write;
-                        break;
-                    } /* end if */
-                    else {
-                        offset[temp_dim]+=mem_space->select.sel_info.hslab.diminfo[temp_dim].stride;    /* reset the offset in the fastest dimension */
-                        tmp_count[temp_dim]++;
-                    } /* end else */
-
-                    /* If this block is still in the range of blocks to output for the dimension, break out of loop */
-                    if(tmp_count[temp_dim]<mem_space->select.sel_info.hslab.diminfo[temp_dim].count)
-                        break;
-                    else {
-                        tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
-                        offset[temp_dim]=mem_space->select.sel_info.hslab.diminfo[temp_dim].start+mem_space->select.offset[temp_dim];
-                    } /* end else */
-                } /* end if */
-                else {
-                    /* Move to the next row in the curent dimension */
-                    offset[temp_dim]++;
-                    tmp_block[temp_dim]++;
-
-                    /* If this block is still in the range of blocks to output for the dimension, break out of loop */
-                    if(tmp_block[temp_dim]<mem_space->select.sel_info.hslab.diminfo[temp_dim].block)
-                        break;
-                    else {
-                        /* Move to the next block in the current dimension */
-                        offset[temp_dim]+=(mem_space->select.sel_info.hslab.diminfo[temp_dim].stride-mem_space->select.sel_info.hslab.diminfo[temp_dim].block);
-                        tmp_block[temp_dim]=0;
-                        tmp_count[temp_dim]++;
-
-                        /* If this block is still in the range of blocks to output for the dimension, break out of loop */
-                        if(tmp_count[temp_dim]<mem_space->select.sel_info.hslab.diminfo[temp_dim].count)
-                            break;
-                        else {
-                            tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
-                            tmp_block[temp_dim]=0;
-                            offset[temp_dim]=mem_space->select.sel_info.hslab.diminfo[temp_dim].start+mem_space->select.offset[temp_dim];
-                        }
-                    } /* end else */
-                } /* end else */
-
-                /* Decrement dimension count */
-                temp_dim--;
-            } /* end while */
-        } /* end while */
-
-        /* Update the iterator with the location we stopped */
-        HDmemcpy(mem_iter->hyp.pos, offset, ndims*sizeof(hssize_t));
-    } /* end if */
-
-    FUNC_LEAVE (num_write);
-} /* end H5S_hyper_mwrite_opt() */
-#else /* WORKS_QAK */
 
 /*-------------------------------------------------------------------------
  * Function:	H5S_hyper_mwrite_opt
@@ -2690,7 +2437,7 @@ for(i=0; i<mem_space->extent.u.simple.rank; i++)
  *
  *-------------------------------------------------------------------------
  */
-static herr_t
+static size_t
 H5S_hyper_mwrite_opt (const void *_tconv_buf, size_t elmt_size,
 		 const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
 		 size_t nelmts, void *_buf/*out*/)
@@ -2708,8 +2455,8 @@ H5S_hyper_mwrite_opt (const void *_tconv_buf, size_t elmt_size,
     size_t	buf_off;  /* Buffer offset for copying memory */
     intn i;         /* Counters */
     intn   	ndims;      /* Number of dimensions of dataset */
-    uintn actual_write;       /* The actual number of elements to read in */
-    uintn actual_bytes;     /* The actual number of bytes to copy */
+    size_t actual_write;       /* The actual number of elements to read in */
+    size_t actual_bytes;     /* The actual number of bytes to copy */
     size_t num_write=0;      /* Number of elements read */
 
     FUNC_ENTER (H5S_hyper_fwrite_opt, 0);
@@ -2947,7 +2694,6 @@ printf("%s: buf_off=%u, actual_bytes=%u\n",FUNC,(unsigned)buf_off,(int)actual_by
 
     FUNC_LEAVE (num_write);
 } /* end H5S_hyper_mwrite_opt() */
-#endif /* WORKS_QAK */
 
 
 /*-------------------------------------------------------------------------
@@ -4298,7 +4044,7 @@ H5S_hyper_select_serialize (const H5S_t *space, uint8_t *buf)
     H5S_hyper_dim_t *diminfo;               /* Alias for dataspace's diminfo information */
     hsize_t tmp_count[H5O_LAYOUT_NDIMS];    /* Temporary hyperslab counts */
     hssize_t offset[H5O_LAYOUT_NDIMS];      /* Offset of element in dataspace */
-    size_t temp_off;            /* Offset in a given dimension */
+    hssize_t temp_off;            /* Offset in a given dimension */
     H5S_hyper_node_t *curr;     /* Hyperslab information nodes */
     uint8_t *lenp;          /* pointer to length location for later storage */
     uint32_t len=0;         /* number of bytes used */
@@ -4988,7 +4734,6 @@ for(i=0; i<space->extent.u.simple.rank; i++)
             case H5S_SEL_ALL:
                 /* break out now, 'or'ing with an all selection leaves the all selection */
                 HGOTO_DONE(SUCCEED);
-                break;
 
             case H5S_SEL_HYPERSLABS:
                 /* Is this the first 'or' operation? */
@@ -5273,7 +5018,7 @@ H5S_hyper_select_iterate_mem_opt(H5S_sel_iter_t UNUSED *iter, void *buf, hid_t t
     hssize_t offset[H5O_LAYOUT_NDIMS];      /* Offset of element in dataspace */
     hsize_t slab[H5O_LAYOUT_NDIMS];         /* Size of objects in buffer */
     size_t elem_size;           /* Size of data element in buffer */
-    size_t temp_off;            /* Offset in a given dimension */
+    hssize_t temp_off;            /* Offset in a given dimension */
     uint8_t *loc;               /* Current element location */
     intn i;                     /* Counter */
     intn fast_dim;      /* Rank of the fastest changing dimension for the dataspace */
diff --git a/src/H5Smpio.c b/src/H5Smpio.c
index afc6640..150f918 100644
--- a/src/H5Smpio.c
+++ b/src/H5Smpio.c
@@ -10,11 +10,12 @@
  *		I didn't make them portable.
  */
 
+#define H5F_PACKAGE		/*suppress error about including H5Fpkg	  */
 #define H5S_PACKAGE		/*suppress error about including H5Spkg	  */
 
 #include <H5private.h>
 #include <H5Eprivate.h>
-#include <H5FDprivate.h>
+#include <H5Fpkg.h>         /* Ugly, but necessary for the MPIO I/O accesses */
 #include <H5Spkg.h>
 
 #include <H5FDmpio.h>		/*the MPIO file driver			*/
diff --git a/src/H5Spkg.h b/src/H5Spkg.h
index a517378..9fadfb5 100644
--- a/src/H5Spkg.h
+++ b/src/H5Spkg.h
@@ -204,31 +204,4 @@ __DLL__ herr_t H5S_none_select_deserialize(H5S_t *space, const uint8_t *buf);
 __DLL__ herr_t H5S_none_select_iterate(void *buf, hid_t type_id, H5S_t *space,
 				       H5D_operator_t op, void *operator_data);
 
-#ifdef H5_HAVE_PARALLEL
-/* MPI-IO function to read directly from app buffer to file rky980813 */
-__DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
-				    const struct H5O_layout_t *layout,
-				    const struct H5O_pline_t *pline,
-				    const struct H5O_efl_t *efl,
-				    size_t elmt_size, const H5S_t *file_space,
-				    const H5S_t *mem_space, hid_t dxpl_id,
-				    void *buf/*out*/,
-				    hbool_t *must_convert /*out*/ );
-
-/* MPI-IO function to write directly from app buffer to file rky980813 */
-__DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f,
-				     const struct H5O_layout_t *layout,
-				     const struct H5O_pline_t *pline,
-				     const struct H5O_efl_t *efl,
-				     size_t elmt_size, const H5S_t *file_space,
-				     const H5S_t *mem_space, hid_t dxpl_id,
-				     const void *buf,
-				     hbool_t *must_convert /*out*/ );
-#ifndef _H5S_IN_H5S_C
-/* Global var whose value comes from environment variable */
-__DLLVAR__ hbool_t		H5_mpi_opt_types_g;
-#endif /* _H5S_IN_H5S_C */
-
-#endif /* H5_HAVE_PARALLEL */
-
 #endif
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index 4ae3510..3290a2b 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -236,4 +236,31 @@ __DLL__ herr_t H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space,
 __DLL__ herr_t H5S_sel_iter_release(const H5S_t *space,
 				    H5S_sel_iter_t *sel_iter);
 
+#ifdef H5_HAVE_PARALLEL
+/* MPI-IO function to read directly from app buffer to file rky980813 */
+__DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
+				    const struct H5O_layout_t *layout,
+				    const struct H5O_pline_t *pline,
+				    const struct H5O_efl_t *efl,
+				    size_t elmt_size, const H5S_t *file_space,
+				    const H5S_t *mem_space, hid_t dxpl_id,
+				    void *buf/*out*/,
+				    hbool_t *must_convert /*out*/ );
+
+/* MPI-IO function to write directly from app buffer to file rky980813 */
+__DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f,
+				     const struct H5O_layout_t *layout,
+				     const struct H5O_pline_t *pline,
+				     const struct H5O_efl_t *efl,
+				     size_t elmt_size, const H5S_t *file_space,
+				     const H5S_t *mem_space, hid_t dxpl_id,
+				     const void *buf,
+				     hbool_t *must_convert /*out*/ );
+#ifndef _H5S_IN_H5S_C
+/* Global var whose value comes from environment variable */
+__DLLVAR__ hbool_t		H5_mpi_opt_types_g;
+#endif /* _H5S_IN_H5S_C */
+
+#endif /* H5_HAVE_PARALLEL */
+
 #endif /* _H5Sprivate_H */
diff --git a/src/H5Sselect.c b/src/H5Sselect.c
index 641acaa..c2b2fd2 100644
--- a/src/H5Sselect.c
+++ b/src/H5Sselect.c
@@ -763,7 +763,7 @@ H5S_get_select_hyper_blocklist(H5S_t *space, hsize_t startblock, hsize_t numbloc
     H5S_hyper_dim_t *diminfo;               /* Alias for dataspace's diminfo information */
     hsize_t tmp_count[H5O_LAYOUT_NDIMS];    /* Temporary hyperslab counts */
     hssize_t offset[H5O_LAYOUT_NDIMS];      /* Offset of element in dataspace */
-    size_t temp_off;            /* Offset in a given dimension */
+    hssize_t temp_off;            /* Offset in a given dimension */
     H5S_hyper_node_t *node;     /* Hyperslab node */
     intn rank;                  /* Dataspace rank */
     intn i;                     /* Counter */
diff --git a/src/H5T.c b/src/H5T.c
index 1139fd1..94cca1e 100644
--- a/src/H5T.c
+++ b/src/H5T.c
@@ -4631,7 +4631,6 @@ H5T_create(H5T_class_t type, size_t size)
     case H5T_VLEN:  /* Variable length datatype */
         HRETURN_ERROR(H5E_DATATYPE, H5E_UNSUPPORTED, NULL,
 		      "base type required - use H5Tvlen_create()");
-        break;
 
     default:
 	HRETURN_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, NULL,
diff --git a/src/H5Tconv.c b/src/H5Tconv.c
index ffbcd86..66fa3e2 100644
--- a/src/H5Tconv.c
+++ b/src/H5Tconv.c
@@ -975,7 +975,7 @@ H5T_conv_struct(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
     H5T_cmemb_t	*src_memb = NULL;	/*source struct member descript.*/
     H5T_cmemb_t	*dst_memb = NULL;	/*destination struct memb desc.	*/
     size_t	offset;			/*byte offset wrt struct	*/
-    size_t	src_delta, dst_delta;	/*source & destination stride	*/
+    size_t	src_delta;	    /*source stride	*/
     uintn	elmtno;
     intn	i;			/*counters			*/
     H5T_conv_struct_t *priv = (H5T_conv_struct_t *)(cdata->priv);
@@ -1047,16 +1047,14 @@ H5T_conv_struct(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
 	 */
 	if (buf_stride) {
 	    src_delta = buf_stride;
-            dst_delta = buf_stride;
-            if (!bkg_stride) bkg_stride = dst->size;
+        if (!bkg_stride)
+            bkg_stride = dst->size;
 	} else if (dst->size <= src->size) {
 	    src_delta = src->size;
-	    dst_delta = dst->size;
-            bkg_stride = dst->size;
+        bkg_stride = dst->size;
 	} else {
 	    src_delta = -(src->size);
-	    dst_delta = -(dst->size);
-            bkg_stride = -(dst->size);
+        bkg_stride = -(dst->size);
 	    xbuf += (nelmts-1) * src->size;
 	    xbkg += (nelmts-1) * dst->size;
 	}