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-rw-r--r--src/H5Dseq.c515
-rw-r--r--src/H5Fseq.c515
-rw-r--r--src/H5Shyper.c2
3 files changed, 929 insertions, 103 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;
diff --git a/src/H5Fseq.c b/src/H5Fseq.c
index 01d484d..c369074 100644
--- a/src/H5Fseq.c
+++ b/src/H5Fseq.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;
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index e446157..b34c79d 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -4610,7 +4610,7 @@ H5S_hyper_select_contiguous(const H5S_t *space)
*/
ret_value=TRUE; /* assume true and reset if the dimensions don't match */
for(u=1; u<space->extent.u.simple.rank; u++) {
- if(space->select.sel_info.hslab.diminfo[u].block>1 || space->select.sel_info.hslab.diminfo[u].block!=space->extent.u.simple.size[u]) {
+ if(space->select.sel_info.hslab.diminfo[u].count>1 || space->select.sel_info.hslab.diminfo[u].block!=space->extent.u.simple.size[u]) {
ret_value=FALSE;
break;
} /* end if */