[svn-r3479] Purpose:

    Bug Fixes
Description:
    Fixed a bug in H5Shyper.c where 'contiguous' hyperslabs (i.e. ones which
    took up an entire dataset) were not being detected correctly and would
    instead be read a part at a time instead of all at once.

    Also fixed a bug in the handling of hyperslabs for chunked datasets where
    hyperslabs from chunks which weren't aligned on exact dimension bounaries
    were not reading/writing data correctly.
Solution:
    H5Shyper.c was a single line change from a 'block' size to a 'count' size.

    H5Fseq.c changes we much more significant and involved detecting when
    non-chunk aligned sequences of data were being written and constructing
    hyperslab blocks to pass down to the chunking I/O routine (which only
    understand hyperslab I/O requests, not element sequence requests).
    This was complicated by the need to align the hyperslabs requested on
    dimension boundaries...

Platforms tested:
    FreeBSD 4.2. (hawkwind)

1 files changed, 464 insertions, 51 deletions

diff --git a/src/H5Dseq.c b/src/H5Dseq.c
index 01d484d..c369074 100644
--- a/src/H5Dseq.c
+++ b/src/H5Dseq.c
@@ -62,11 +62,13 @@ H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
          hsize_t seq_len, hsize_t file_offset, void *buf/*out*/)
 {
     hsize_t	dset_dims[H5O_LAYOUT_NDIMS];	/* dataspace dimensions */
-    hssize_t coords[H5O_LAYOUT_NDIMS];	    /* offset of hyperslab in dataspace */
+    hssize_t    coords[H5O_LAYOUT_NDIMS];	/* offset of hyperslab in dataspace */
     hsize_t	hslab_size[H5O_LAYOUT_NDIMS];	/* hyperslab size in dataspace*/
+    hsize_t     down_size[H5O_LAYOUT_NDIMS];    /* Cumulative yperslab sizes (in elements) */
+    hsize_t     acc;    /* Accumulator for hyperslab sizes (in elements) */
     intn ndims;
-    haddr_t	addr;				/*address in file	*/
-    intn	i;				    /*counters		*/
+    haddr_t	addr=0;				/*address in file	*/
+    intn	i,j;				/*counters		*/
 #ifdef H5_HAVE_PARALLEL
     H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
 #endif
@@ -167,6 +169,9 @@ H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
             break;
 
         case H5D_CHUNKED:
+        {
+            uintn       leading_partials;       /* Flag set if there are leading partial hyperslabs to take care of */
+
             /*
              * This method is unable to access external raw data files 
              */
@@ -189,7 +194,7 @@ H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 {
     static int count=0;
 
-    if(count<10) {
+    if(count<1000000) {
         printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
         printf("%s: file_offset=%d\n",FUNC,(int)file_offset);
         count++;
@@ -203,41 +208,131 @@ H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
             seq_len/=elmt_size;
             addr/=elmt_size;
 
+            /* Build the array of cumulative hyperslab sizes */
+            for(acc=1, i=(ndims-1); i>=0; i--) {
+                down_size[i]=acc;
+                acc*=dset_dims[i];
+#ifdef QAK
+printf("%s: acc=%ld, down_size[%d]=%ld\n",FUNC,(long)acc,i,(long)down_size[i]);
+#endif /* QAK */
+            } /* end for */
+
             /* Compute the hyperslab offset from the address given */
+            leading_partials=0;
             for(i=ndims-1; i>=0; i--) {
                 coords[i]=addr%dset_dims[i];
                 addr/=dset_dims[i];
+                if(i>0 && coords[i]>0)
+                    leading_partials=1;
+#ifdef QAK
+printf("%s: addr=%lu, coords[%d]=%ld\n",FUNC,(unsigned long)addr,i,(long)coords[i]);
+#endif /* QAK */
             } /* end for */
             coords[ndims]=0;   /* No offset for element info */
+#ifdef QAK
+printf("%s: addr=%lu, coords[%d]=%ld\n",FUNC,(unsigned long)addr,ndims,(long)coords[ndims]);
+printf("%s: leading_partials=%u\n",FUNC,leading_partials);
+#endif /* QAK */
 
-            /* Compute the hyperslab size from the length given */
-            for(i=ndims-1; i>=0; i--) {
-                /* Check if the hyperslab is wider than the width of the dimension */
-                if(seq_len>dset_dims[i]) {
-                    if (0!=coords[i])
-                       HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
-                    hslab_size[i]=dset_dims[i];
-                } /* end if */
-                else 
-                    hslab_size[i]=seq_len;
+            /*
+             * Peel off initial partial hyperslabs until we've got a hyperslab which starts
+             *      at coord[n]==0 for dimensions 1->(ndims-1)  (i.e. starting at coordinate
+             *      zero for all dimensions except the slowest changing one
+             */
+            for(i=ndims-1; i>0 && seq_len>down_size[i]; i--) {
+                hsize_t partial_size;       /* Size of the partial hyperslab in bytes */
 
-                /* Fold the length into the length in the next highest dimension */
-                seq_len/=dset_dims[i];
+                /* Check if we have a partial hyperslab in this lower dimension */
+                if(coords[i]>0) {
+#ifdef QAK
+printf("%s: Need to get hyperslab, seq_len=%ld, coords[%d]=%ld\n",FUNC,(long)seq_len,i,(long)coords[i]);
+#endif /* QAK */
+                    /* Reset the partial hyperslab size */
+                    partial_size=1;
+
+                    /* Build the partial hyperslab information */
+                    for(j=0; j<ndims; j++) {
+                        if(i==j)
+                            hslab_size[j]=MIN(seq_len,dset_dims[i]-coords[i]);
+                        else
+                            if(j>i)
+                                hslab_size[j]=dset_dims[j];
+                            else
+                                hslab_size[j]=1;
+                        partial_size*=hslab_size[j];
+#ifdef QAK
+printf("%s: partial_size=%lu, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,j,(long)hslab_size[j]);
+#endif /* QAK */
+                    } /* end for */
+                    hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
+#ifdef QAK
+printf("%s: partial_size=%lu, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,ndims,(long)hslab_size[ndims]);
+#endif /* QAK */
+
+                    /* Read in the partial hyperslab */
+                    if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords,
+                                 hslab_size, buf)<0) {
+                        HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
+                    }
+
+                    /* Increment the buffer offset */
+                    buf=(unsigned char *)buf+partial_size;
 
-                /* Make certain the hyperslab sizes don't go less than 1 */
-                if(seq_len<1)
-                    seq_len=1;
+                    /* Decrement the length of the sequence to read */
+                    seq_len-=partial_size;
+
+                    /* Correct the coords array */
+                    coords[i]=0;
+                    coords[i-1]++;
+                } /* end if */
             } /* end for */
-            hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
+#ifdef QAK
+printf("%s: after reading initial partial hyperslabs, seq_len=%lu\n",FUNC,(unsigned long)seq_len);
+#endif /* QAK */
+
+            /* Check if there is more than just a partial hyperslab to read */
+            if(seq_len>down_size[0]) {
+                hsize_t tmp_seq_len;    /* Temp. size of the sequence in elements */
+                hsize_t full_size;      /* Size of the full hyperslab in bytes */
+
+                /* Get the sequence length for computing the hyperslab sizes */
+                tmp_seq_len=seq_len;
+
+                /* Reset the size of the hyperslab read in */
+                full_size=1;
+
+                /* Compute the hyperslab size from the length given */
+                for(i=ndims-1; i>=0; i--) {
+                    /* Check if the hyperslab is wider than the width of the dimension */
+                    if(tmp_seq_len>dset_dims[i]) {
+                        assert(0==coords[i]);
+                        hslab_size[i]=dset_dims[i];
+                    } /* end if */
+                    else 
+                        hslab_size[i]=tmp_seq_len;
+
+                    /* compute the number of elements read in */
+                    full_size*=hslab_size[i];
+
+                    /* Fold the length into the length in the next highest dimension */
+                    tmp_seq_len/=dset_dims[i];
+#ifdef QAK
+printf("%s: tmp_seq_len=%lu, hslab_size[%d]=%ld\n",FUNC,(unsigned long)tmp_seq_len,i,(long)hslab_size[i]);
+#endif /* QAK */
+
+                    /* Make certain the hyperslab sizes don't go less than 1 for dimensions less than 0*/
+                    assert(tmp_seq_len>=1 || i==0);
+                } /* end for */
+                hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
 
 #ifdef QAK
 /* Print out the file offsets & hyperslab sizes */
 {
     static int count=0;
 
-    if(count<10) {
-        printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
-        for(i=0; i<=ndims; i++)
+    if(count<1000000) {
+        printf("%s: elmt_size=%d, addr=%d, full_size=%ld, tmp_seq_len=%ld seq_len=%ld\n",FUNC,(int)elmt_size,(int)addr,(long)full_size,(long)tmp_seq_len,(long)seq_len);
+        for(i=0; i<ndims; i++)
             printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
         for(i=0; i<=ndims; i++)
             printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
@@ -246,9 +341,122 @@ H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 }
 #endif /* QAK */
 
-            if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords,
-                         hslab_size, buf)<0) {
-                HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
+                /* Read the full hyperslab in */
+                if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords,
+                             hslab_size, buf)<0) {
+                    HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
+                }
+
+                /* Increment the buffer offset */
+                buf=(unsigned char *)buf+full_size;
+
+                /* Decrement the sequence length left */
+                seq_len-=full_size;
+
+                /* Increment coordinate of slowest changing dimension */
+                coords[0]+=hslab_size[0];
+
+            } /* end if */
+#ifdef QAK
+printf("%s: after reading 'middle' full hyperslabs, seq_len=%lu\n",FUNC,(unsigned long)seq_len);
+#endif /* QAK */
+
+            /*
+             * Peel off final partial hyperslabs until we've finished reading all the data
+             */
+            if(seq_len>0) {
+                hsize_t partial_size;       /* Size of the partial hyperslab in bytes */
+
+                /*
+                 * Peel off remaining partial hyperslabs, from the next-slowest dimension
+                 *  on down to the next-to-fastest changing dimension
+                 */
+                for(i=1; i<(ndims-1); i++) {
+                    /* Check if there are enough elements to read in a row in this dimension */
+                    if(seq_len>down_size[i]) {
+#ifdef QAK
+printf("%s: seq_len=%ld, down_size[%d]=%ld\n",FUNC,(long)seq_len,i+1,(long)down_size[i+1]);
+#endif /* QAK */
+                        /* Reset the partial hyperslab size */
+                        partial_size=1;
+
+                        /* Build the partial hyperslab information */
+                        for(j=0; j<ndims; j++) {
+                            if(j<i)
+                                hslab_size[j]=1;
+                            else
+                                if(j==i)
+                                    hslab_size[j]=seq_len/down_size[j];
+                                else
+                                    hslab_size[j]=dset_dims[j];
+
+                            partial_size*=hslab_size[j];
+#ifdef QAK
+printf("%s: partial_size=%lu, coords[%d]=%ld, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,j,(long)coords[j],j,(long)hslab_size[j]);
+#endif /* QAK */
+                        } /* end for */
+                        hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
+#ifdef QAK
+printf("%s: partial_size=%lu, coords[%d]=%ld, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,ndims,(long)coords[ndims],ndims,(long)hslab_size[ndims]);
+#endif /* QAK */
+
+                        /* Read in the partial hyperslab */
+                        if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords,
+                                     hslab_size, buf)<0) {
+                            HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
+                        }
+
+                        /* Increment the buffer offset */
+                        buf=(unsigned char *)buf+partial_size;
+
+                        /* Decrement the length of the sequence to read */
+                        seq_len-=partial_size;
+
+                        /* Correct the coords array */
+                        coords[i]=hslab_size[i];
+                    } /* end if */
+                } /* end for */
+#ifdef QAK
+printf("%s: after reading trailing hyperslabs for all but the last dimension, seq_len=%ld\n",FUNC,(long)seq_len);
+#endif /* QAK */
+
+                /* Handle fastest changing dimension if there are any elements left */
+                if(seq_len>0) {
+#ifdef QAK
+printf("%s: i=%d, seq_len=%ld\n",FUNC,ndims-1,(long)seq_len);
+#endif /* QAK */
+                    assert(seq_len<dset_dims[ndims-1]);
+
+                    /* Reset the partial hyperslab size */
+                    partial_size=1;
+
+                    /* Build the partial hyperslab information */
+                    for(j=0; j<ndims; j++) {
+                        if(j==(ndims-1))
+                            hslab_size[j]=seq_len;
+                        else
+                            hslab_size[j]=1;
+
+                        partial_size*=hslab_size[j];
+#ifdef QAK
+printf("%s: partial_size=%lu, coords[%d]=%ld, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,j,(long)coords[j],j,(long)hslab_size[j]);
+#endif /* QAK */
+                    } /* end for */
+                    hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
+#ifdef QAK
+printf("%s: partial_size=%lu, coords[%d]=%ld, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,ndims,(long)coords[ndims],ndims,(long)hslab_size[ndims]);
+#endif /* QAK */
+
+                    /* Read in the partial hyperslab */
+                    if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords,
+                                 hslab_size, buf)<0) {
+                        HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
+                    }
+
+                    /* Double-check the amount read in */
+                    assert(seq_len==partial_size);
+                } /* end if */
+            } /* end if */
         }
             break;
 
@@ -288,11 +496,13 @@ H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
          hsize_t seq_len, hsize_t file_offset, const void *buf)
 {
     hsize_t	dset_dims[H5O_LAYOUT_NDIMS];	/* dataspace dimensions */
-    hssize_t coords[H5O_LAYOUT_NDIMS];	    /* offset of hyperslab in dataspace */
+    hssize_t    coords[H5O_LAYOUT_NDIMS];	/* offset of hyperslab in dataspace */
     hsize_t	hslab_size[H5O_LAYOUT_NDIMS];	/* hyperslab size in dataspace*/
+    hsize_t     down_size[H5O_LAYOUT_NDIMS];    /* Cumulative hyperslab sizes (in elements) */
+    hsize_t     acc;            /* Accumulator for hyperslab sizes (in elements) */
     intn ndims;
     haddr_t	addr;				/*address in file	*/
-    intn	i;				    /*counters		*/
+    intn	i,j;				/*counters		*/
 #ifdef H5_HAVE_PARALLEL
     H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
 #endif
@@ -393,6 +603,9 @@ H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
             break;
 
         case H5D_CHUNKED:
+        {
+            uintn       leading_partials;       /* Flag set if there are leading partial hyperslabs to take care of */
+
             /*
              * This method is unable to access external raw data files 
              */
@@ -409,7 +622,7 @@ H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 {
     static int count=0;
 
-    if(count<10) {
+    if(count<1000000) {
         printf("%s: elmt_size=%d, addr=%d, seq_len=%lu\n",FUNC,(int)elmt_size,(int)addr,(unsigned long)seq_len);
         printf("%s: file_offset=%d\n",FUNC,(int)file_offset);
         count++;
@@ -429,41 +642,131 @@ H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
             seq_len/=elmt_size;
             addr/=elmt_size;
 
+            /* Build the array of cumulative hyperslab sizes */
+            for(acc=1, i=(ndims-1); i>=0; i--) {
+                down_size[i]=acc;
+                acc*=dset_dims[i];
+#ifdef QAK
+printf("%s: acc=%ld, down_size[%d]=%ld\n",FUNC,(long)acc,i,(long)down_size[i]);
+#endif /* QAK */
+            } /* end for */
+
             /* Compute the hyperslab offset from the address given */
+            leading_partials=0;
             for(i=ndims-1; i>=0; i--) {
                 coords[i]=addr%dset_dims[i];
                 addr/=dset_dims[i];
+                if(i>0 && coords[i]>0)
+                    leading_partials=1;
+#ifdef QAK
+printf("%s: addr=%lu, dset_dims[%d]=%ld, coords[%d]=%ld\n",FUNC,(unsigned long)addr,i,(long)dset_dims[i],i,(long)coords[i]);
+#endif /* QAK */
             } /* end for */
             coords[ndims]=0;   /* No offset for element info */
+#ifdef QAK
+printf("%s: addr=%lu, coords[%d]=%ld\n",FUNC,(unsigned long)addr,ndims,(long)coords[ndims]);
+printf("%s: leading_partials=%u\n",FUNC,leading_partials);
+#endif /* QAK */
 
-            /* Compute the hyperslab size from the length given */
-            for(i=ndims-1; i>=0; i--) {
-                /* Check if the hyperslab is wider than the width of the dimension */
-                if(seq_len>dset_dims[i]) {
-                    if (0!=coords[i])
-                       HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
-                    hslab_size[i]=dset_dims[i];
-                } /* end if */
-                else 
-                    hslab_size[i]=seq_len;
+            /*
+             * Peel off initial partial hyperslabs until we've got a hyperslab which starts
+             *      at coord[n]==0 for dimensions 1->(ndims-1)  (i.e. starting at coordinate
+             *      zero for all dimensions except the slowest changing one
+             */
+            for(i=ndims-1; i>0 && seq_len>down_size[i]; i--) {
+                hsize_t partial_size;       /* Size of the partial hyperslab in bytes */
 
-                /* Fold the length into the length in the next highest dimension */
-                seq_len/=dset_dims[i];
+                /* Check if we have a partial hyperslab in this lower dimension */
+                if(coords[i]>0) {
+#ifdef QAK
+printf("%s: Need to get hyperslab, seq_len=%ld, coords[%d]=%ld\n",FUNC,(long)seq_len,i,(long)coords[i]);
+#endif /* QAK */
+                    /* Reset the partial hyperslab size */
+                    partial_size=1;
+
+                    /* Build the partial hyperslab information */
+                    for(j=0; j<ndims; j++) {
+                        if(i==j)
+                            hslab_size[j]=MIN(seq_len,dset_dims[i]-coords[i]);
+                        else
+                            if(j>i)
+                                hslab_size[j]=dset_dims[j];
+                            else
+                                hslab_size[j]=1;
+                        partial_size*=hslab_size[j];
+#ifdef QAK
+printf("%s: partial_size=%lu, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,j,(long)hslab_size[j]);
+#endif /* QAK */
+                    } /* end for */
+                    hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
+#ifdef QAK
+printf("%s: partial_size=%lu, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,ndims,(long)hslab_size[ndims]);
+#endif /* QAK */
+
+                    /* Write out the partial hyperslab */
+                    if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords,
+                                 hslab_size, buf)<0) {
+                        HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked write failed");
+                    }
+
+                    /* Increment the buffer offset */
+                    buf=(const unsigned char *)buf+partial_size;
 
-                /* Make certain the hyperslab sizes don't go less than 1 */
-                if(seq_len<1)
-                    seq_len=1;
+                    /* Decrement the length of the sequence to read */
+                    seq_len-=partial_size;
+
+                    /* Correct the coords array */
+                    coords[i]=0;
+                    coords[i-1]++;
+                } /* end if */
             } /* end for */
-            hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
+#ifdef QAK
+printf("%s: seq_len=%lu\n",FUNC,(unsigned long)seq_len);
+#endif /* QAK */
+
+            /* Check if there is more than just a partial hyperslab to read */
+            if(seq_len>down_size[0]) {
+                hsize_t tmp_seq_len;    /* Temp. size of the sequence in elements */
+                hsize_t full_size;      /* Size of the full hyperslab in bytes */
+
+                /* Get the sequence length for computing the hyperslab sizes */
+                tmp_seq_len=seq_len;
+
+                /* Reset the size of the hyperslab read in */
+                full_size=1;
+
+                /* Compute the hyperslab size from the length given */
+                for(i=ndims-1; i>=0; i--) {
+                    /* Check if the hyperslab is wider than the width of the dimension */
+                    if(tmp_seq_len>dset_dims[i]) {
+                        assert(0==coords[i]);
+                        hslab_size[i]=dset_dims[i];
+                    } /* end if */
+                    else 
+                        hslab_size[i]=tmp_seq_len;
+
+                    /* compute the number of elements read in */
+                    full_size*=hslab_size[i];
+
+                    /* Fold the length into the length in the next highest dimension */
+                    tmp_seq_len/=dset_dims[i];
+#ifdef QAK
+printf("%s: tmp_seq_len=%lu, hslab_size[%d]=%ld\n",FUNC,(unsigned long)tmp_seq_len,i,(long)hslab_size[i]);
+#endif /* QAK */
+
+                    /* Make certain the hyperslab sizes don't go less than 1 for dimensions less than 0*/
+                    assert(tmp_seq_len>=1 || i==0);
+                } /* end for */
+                hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
 
 #ifdef QAK
 /* Print out the file offsets & hyperslab sizes */
 {
     static int count=0;
 
-    if(count<10) {
-        printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
-        for(i=0; i<=ndims; i++)
+    if(count<1000000) {
+        printf("%s: elmt_size=%d, addr=%d, full_size=%ld, tmp_seq_len=%ld seq_len=%ld\n",FUNC,(int)elmt_size,(int)addr,(long)full_size,(long)tmp_seq_len,(long)seq_len);
+        for(i=0; i<ndims; i++)
             printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
         for(i=0; i<=ndims; i++)
             printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
@@ -472,9 +775,119 @@ H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
 }
 #endif /* QAK */
 
-            if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords,
-                         hslab_size, buf)<0) {
-                HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed");
+                /* Write the full hyperslab in */
+                if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords,
+                             hslab_size, buf)<0) {
+                    HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked write failed");
+                }
+
+                /* Increment the buffer offset */
+                buf=(const unsigned char *)buf+full_size;
+
+                /* Decrement the sequence length left */
+                seq_len-=full_size;
+
+                /* Increment coordinate of slowest changing dimension */
+                coords[0]+=hslab_size[0];
+
+            } /* end if */
+#ifdef QAK
+printf("%s: seq_len=%lu\n",FUNC,(unsigned long)seq_len);
+#endif /* QAK */
+
+            /*
+             * Peel off final partial hyperslabs until we've finished reading all the data
+             */
+            if(seq_len>0) {
+                hsize_t partial_size;       /* Size of the partial hyperslab in bytes */
+
+                /*
+                 * Peel off remaining partial hyperslabs, from the next-slowest dimension
+                 *  on down to the next-to-fastest changing dimension
+                 */
+                for(i=1; i<(ndims-1); i++) {
+                    /* Check if there are enough elements to read in a row in this dimension */
+                    if(seq_len>down_size[i]) {
+#ifdef QAK
+printf("%s: seq_len=%ld, down_size[%d]=%ld\n",FUNC,(long)seq_len,i+1,(long)down_size[i+1]);
+#endif /* QAK */
+                        /* Reset the partial hyperslab size */
+                        partial_size=1;
+
+                        /* Build the partial hyperslab information */
+                        for(j=0; j<ndims; j++) {
+                            if(j<i)
+                                hslab_size[j]=1;
+                            else
+                                if(j==i)
+                                    hslab_size[j]=seq_len/down_size[j];
+                                else
+                                    hslab_size[j]=dset_dims[j];
+
+                            partial_size*=hslab_size[j];
+#ifdef QAK
+printf("%s: partial_size=%lu, coords[%d]=%ld, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,j,(long)coords[j],j,(long)hslab_size[j]);
+#endif /* QAK */
+                        } /* end for */
+                        hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
+#ifdef QAK
+printf("%s: partial_size=%lu, coords[%d]=%ld, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,ndims,(long)coords[ndims],ndims,(long)hslab_size[ndims]);
+#endif /* QAK */
+
+                        /* Write out the partial hyperslab */
+                        if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords,
+                                     hslab_size, buf)<0) {
+                            HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked write failed");
+                        }
+
+                        /* Increment the buffer offset */
+                        buf=(const unsigned char *)buf+partial_size;
+
+                        /* Decrement the length of the sequence to read */
+                        seq_len-=partial_size;
+
+                        /* Correct the coords array */
+                        coords[i]=hslab_size[i];
+                    } /* end if */
+                } /* end for */
+
+                /* Handle fastest changing dimension if there are any elements left */
+                if(seq_len>0) {
+#ifdef QAK
+printf("%s: i=%d, seq_len=%ld\n",FUNC,ndims-1,(long)seq_len);
+#endif /* QAK */
+                    assert(seq_len<dset_dims[ndims-1]);
+
+                    /* Reset the partial hyperslab size */
+                    partial_size=1;
+
+                    /* Build the partial hyperslab information */
+                    for(j=0; j<ndims; j++) {
+                        if(j==(ndims-1))
+                            hslab_size[j]=seq_len;
+                        else
+                            hslab_size[j]=1;
+
+                        partial_size*=hslab_size[j];
+#ifdef QAK
+printf("%s: partial_size=%lu, coords[%d]=%ld, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,j,(long)coords[j],j,(long)hslab_size[j]);
+#endif /* QAK */
+                    } /* end for */
+                    hslab_size[ndims]=elmt_size;   /* basic hyperslab size is the element */
+#ifdef QAK
+printf("%s: partial_size=%lu, coords[%d]=%ld, hslab_size[%d]=%ld\n",FUNC,(unsigned long)partial_size,ndims,(long)coords[ndims],ndims,(long)hslab_size[ndims]);
+#endif /* QAK */
+
+                    /* Write in the final partial hyperslab */
+                    if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords,
+                                 hslab_size, buf)<0) {
+                        HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked write failed");
+                    }
+
+                    /* Double-check the amount read in */
+                    assert(seq_len==partial_size);
+                } /* end if */
+            } /* end if */
         }
             break;