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-rw-r--r--tools/h5repack/h5repack_copy.c326
1 files changed, 269 insertions, 57 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index d96e08b..55cf932 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -53,6 +53,7 @@
* local functions
*-------------------------------------------------------------------------
*/
+static int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
static void print_dataset_info(hid_t dcpl_id,char *objname,double per, int pr);
static int do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options);
static int copy_user_block(const char *infile, const char *outfile, hsize_t size);
@@ -491,6 +492,184 @@ out:
}
/*-------------------------------------------------------------------------
+* Function: Get_hyperslab
+*
+* Purpose: Calulate a hyperslab from a dataset for higher performance.
+* The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
+* Return the hyperslab dimentions and size in byte.
+*
+* Return: 0 - SUCCEED, -1 FAILED
+*
+* Parameters:
+* dcpl_id : [IN] dataset creation property.
+* rank_dset : [IN] dataset rank
+* dims_dset[] : [IN] dataset dimentions
+* size_datum : [IN] size of a data element in byte
+* dims_hslab[] : [OUT] calculated hyperslab dimentions
+* * hslab_nbytes_p : [OUT] total byte of the hyperslab
+*
+* Programmer: Jonathan Kim
+* Date: Feburary, 2012
+* Update:
+* The hyperslab calucation would be depend on if the dataset is chunked
+* or not.
+*
+* There care 3 conditions to cover:
+* 1. If chunked and a chunk fits in buffer, each chunk would be a unit of
+* collection and the boundary would be dataset's dims.
+* 2. If chunked but a chunk doesn't fit in buffer, each data element would
+* be a unit of collection and the boundary would be the chunk itself.
+* 3. If not chunked, each data element would be a unit of collection and
+* the boundary would be dataset's dims.
+*
+* The calulation starts from the last dimention (h5dump dims output).
+*
+* Note:
+* Added for JIRA HDFFV-7862.
+*-----------------------------------------*/
+
+int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+ size_t size_datum,
+ hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
+{
+ int status = 0;
+ int k;
+ H5D_layout_t dset_layout;
+ int rank_chunk;
+ hsize_t dims_chunk[H5S_MAX_RANK];
+ hsize_t size_chunk=1;
+ hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+ hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+ hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
+ hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
+ hsize_t hslab_nbytes; /* size of hyperslab in byte */
+
+ /* init to set as size of a data element */
+ hslab_nbytes = size_datum;
+
+ /* get layout of dataset */
+ dset_layout = H5Pget_layout(dcpl_id);
+
+ /* if dataset is chunked */
+ if ( dset_layout == H5D_CHUNKED )
+ {
+ /* get chunk dims */
+ rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
+ if (rank_chunk < 0)
+ {
+ status = -1;
+ goto out;
+ }
+
+ for (k = rank_dset; k > 0; --k)
+ size_chunk *= dims_chunk[k-1];
+
+ /* figure out how many chunks can fit in the hyperslab buffer */
+ nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
+
+
+ /* 1. if a chunk fit in hyperslab buffer */
+ if (nchunk_fit >= 1)
+ {
+ /* Calulate a hyperslab that contains as many chunks that can fit
+ * in hyperslab buffer. Hyperslab will be increased starting from
+ * the last dimention of the dataset (see h5dump's dims output).
+ * The calculation boundary is dataset dims.
+ * In the loop, used mapping from a datum to a chunk to figure out
+ * chunk based hyperslab.
+ */
+ for (k = rank_dset; k > 0; --k)
+ {
+ /* map dataset dimentions with a chunk dims */
+ chunk_dims_map[k-1]= dims_dset[k-1] / dims_chunk[k-1];
+
+ /* if reminder exist, increse by 1 to cover partial edge chunks */
+ if (dims_dset[k-1] % dims_chunk[k-1] > 0)
+ chunk_dims_map[k-1]++;
+
+ /* get mapped hyperslab dims */
+ hs_dims_map[k-1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
+
+ /* prepare next round */
+ nchunk_fit = nchunk_fit / chunk_dims_map[k-1];
+ /* if a chunk is bigger than the rest of buffer */
+ if (nchunk_fit == 0)
+ nchunk_fit=1;
+
+ /* get hyperslab dimentions as unmapping to actual size */
+ dims_hslab[k-1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k-1];
+ }
+ }
+ /* 2. if a chunk is bigger than hyperslab buffer */
+ else
+ {
+ /* Calulate a hyperslab that contains as many data elements that
+ * can fit in hyperslab buffer. Hyperslab will be increased
+ * starting from the last dimention of the chunk (see h5dump's dims
+ * output).
+ * The calculation boundary is a chunk dims.
+ */
+ for (k = rank_dset; k > 0; --k)
+ {
+ ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+ /* if a datum is bigger than rest of buffer */
+ if ( ndatum_fit == 0)
+ ndatum_fit = 1;
+ /* get hyperslab dimentions within a chunk boundary */
+ dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+
+ if (hslab_nbytes <= 0)
+ {
+ status = -1;
+ goto out;
+ }
+ }
+ }
+ }
+ /* 3. if dataset is not chunked */
+ else
+ {
+ /* Calulate a hyperslab that contains as many data elements that can
+ * fit in hyperslab buffer. Hyperslab will be increased starting from
+ * the last dimention of the dataset (see h5dump's dims output).
+ * The calculation boundary is dataset dims.
+ */
+ for (k = rank_dset; k > 0; --k)
+ {
+ ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+ /* if a datum is bigger than rest of buffer */
+ if ( ndatum_fit == 0)
+ ndatum_fit = 1;
+ /* get hyperslab dimentions within dataset boundary */
+ dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+
+ if (hslab_nbytes <= 0)
+ {
+ status = -1;
+ goto out;
+ }
+ }
+ }
+
+ /* pass out the hyperslab size*/
+ *hslab_nbytes_p = hslab_nbytes;
+
+out:
+ return status;
+}
+
+/*-------------------------------------------------------------------------
* Function: do_copy_objects
*
* Purpose: duplicate all HDF5 objects in the file
@@ -557,6 +736,30 @@ out:
*
* May, 1, 2008: Add a printing of the compression ratio of old size / new size
*
+* Feburary 2012: improve Read/Write by hyperslabs for big datasets.
+* Programmer: Jonathan Kim
+*
+* A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
+* i.e., if the memory needed to read a dataset is greater than this limit,
+* then hyperslab I/O is done instead of one operation I/O
+* For each dataset, the memory needed is calculated according to
+*
+* memory needed = number of elements * size of each element
+*
+* if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
+* are done
+*
+* H5Dread( input_dataset )
+* H5Dwrite( output_dataset )
+*
+* with all elements in the datasets selected. If the memory needed is greater than
+* H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+*
+* 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()).
+* 2. Calculate the hyperslab selections as the selection is moving forward.
+* Selection would be same as the hyperslab except for the remaining edge portion
+* of the dataset. The code take care of the remaining portion if exist.
+*
*-------------------------------------------------------------------------
*/
@@ -573,7 +776,7 @@ int do_copy_objects(hid_t fidin,
hid_t gcpl_out = -1; /* group creation property list */
hid_t type_in = -1; /* named type ID */
hid_t type_out = -1; /* named type ID */
- hid_t dcpl_id = -1; /* dataset creation property list ID */
+ hid_t dcpl_in = -1; /* dataset creation property list ID */
hid_t dcpl_out = -1; /* dataset creation property list ID */
hid_t f_space_id = -1; /* file space ID */
hid_t ftype_id = -1; /* file type ID */
@@ -589,7 +792,7 @@ int do_copy_objects(hid_t fidin,
int apply_s; /* flag for apply filter to small dataset sizes */
int apply_f; /* flag for apply filter to return error on H5Dcreate */
void *buf=NULL; /* buffer for raw data */
- void *sm_buf=NULL; /* buffer for raw data */
+ void *hslab_buf=NULL; /* hyperslab buffer for raw data */
int has_filter; /* current object has a filter */
int req_filter; /* there was a request for a filter */
unsigned crt_order_flags; /* group creation order flag */
@@ -598,6 +801,7 @@ int do_copy_objects(hid_t fidin,
int is_ref=0;
htri_t is_named;
+
/*-------------------------------------------------------------------------
* copy the suppplied object list
*-------------------------------------------------------------------------
@@ -760,9 +964,9 @@ int do_copy_objects(hid_t fidin,
goto error;
if((ftype_id = H5Dget_type(dset_in)) < 0)
goto error;
- if((dcpl_id = H5Dget_create_plist(dset_in)) < 0)
+ if((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
goto error;
- if((dcpl_out = H5Pcopy(dcpl_id)) < 0)
+ if((dcpl_out = H5Pcopy(dcpl_in)) < 0)
goto error;
if((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
goto error;
@@ -795,7 +999,7 @@ int do_copy_objects(hid_t fidin,
* 2) the internal filters might be turned off
*-------------------------------------------------------------------------
*/
- if (h5tools_canreadf((travt->objs[i].name),dcpl_id)==1)
+ if (h5tools_canreadf((travt->objs[i].name),dcpl_in)==1)
{
apply_s=1;
apply_f=1;
@@ -855,7 +1059,7 @@ int do_copy_objects(hid_t fidin,
printf(" warning: could not create dataset <%s>. Applying original settings\n",
travt->objs[i].name);
- if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
+ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
goto error;
apply_f = 0;
}
@@ -886,100 +1090,108 @@ int do_copy_objects(hid_t fidin,
else /* possibly not enough memory, read/write by hyperslabs */
{
size_t p_type_nbytes = msize; /*size of memory type */
- hsize_t p_nelmts = nelmts; /*total selected elmts */
+ hsize_t p_nelmts = nelmts; /*total elements */
hsize_t elmtno; /*counter */
int carry; /*counter carry value */
unsigned int vl_data = 0; /*contains VL datatypes */
- /* stripmine info */
- hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
- hsize_t sm_nbytes; /*bytes per stripmine */
- hsize_t sm_nelmts; /*elements per stripmine*/
- hid_t sm_space; /*stripmine data space */
-
/* hyperslab info */
- hsize_t hs_offset[H5S_MAX_RANK];/*starting offset */
- hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */
- hsize_t hs_nelmts; /*elements in request */
+ hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
+ hsize_t hslab_nbytes; /*bytes per hyperslab */
+ hsize_t hslab_nelmts; /*elements per hyperslab*/
+ hid_t hslab_space; /*hyperslab data space */
+
+ /* hyperslab selection info */
+ hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
+ hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
+ hsize_t hs_select_nelmts; /* selected elements */
hsize_t zero[8]; /*vector of zeros */
int k;
+ H5D_layout_t dset_layout;
+ hid_t dcpl_tmp = -1; /* dataset creation property list ID */
/* check if we have VL data in the dataset's datatype */
if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
vl_data = TRUE;
- /*
- * determine the strip mine size and allocate a buffer. The strip mine is
- * a hyperslab whose size is manageable.
- */
- sm_nbytes = p_type_nbytes;
- for (k = rank; k > 0; --k)
+ /* check first if writing dataset is chunked,
+ * if so use its chunk layout for better performance. */
+ dset_layout = H5Pget_layout(dcpl_out);
+ if (dset_layout == H5D_CHUNKED)
+ dcpl_tmp = dcpl_out; /* writing dataset */
+ else /* if reading dataset is chunked */
{
- hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
- if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */
- size = 1;
- sm_size[k - 1] = MIN(dims[k - 1], size);
- sm_nbytes *= sm_size[k - 1];
- HDassert(sm_nbytes > 0);
+ dset_layout = H5Pget_layout(dcpl_in);
+ if (dset_layout == H5D_CHUNKED)
+ dcpl_tmp = dcpl_in; /* reading dataset */
}
- sm_buf = HDmalloc((size_t)sm_nbytes);
- sm_nelmts = sm_nbytes / p_type_nbytes;
- sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
+ /* get hyperslab dims and size in byte */
+ if(Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
+ goto error;
+
+ hslab_buf = HDmalloc((size_t)hslab_nbytes);
+
+ hslab_nelmts = hslab_nbytes / p_type_nbytes;
+ hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);
- /* the stripmine loop */
- HDmemset(hs_offset, 0, sizeof hs_offset);
+ /* the hyperslab selection loop */
+ HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset);
HDmemset(zero, 0, sizeof zero);
- for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts)
+ for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts)
{
- /* calculate the hyperslab size */
if (rank > 0)
{
- for (k = 0, hs_nelmts = 1; k < rank; k++)
+ /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
+ */
+ for (k = 0, hs_select_nelmts = 1; k < rank; k++)
{
- hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]);
- hs_nelmts *= hs_size[k];
+ /* MIN() is used to get the remaining edge portion if exist.
+ * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
+ hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
+ hs_select_nelmts *= hs_sel_count[k];
}
- if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
+ if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
goto error;
- if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
+ if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
goto error;
}
else
{
H5Sselect_all(f_space_id);
- H5Sselect_all(sm_space);
- hs_nelmts = 1;
+ H5Sselect_all(hslab_space);
+ hs_select_nelmts = 1;
} /* rank */
/* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
- CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf);
- CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf);
+ CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
+ CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
/* reclaim any VL memory, if necessary */
if(vl_data)
- H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf);
+ H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
/* calculate the next hyperslab offset */
for (k = rank, carry = 1; k > 0 && carry; --k)
{
- hs_offset[k - 1] += hs_size[k - 1];
- if (hs_offset[k - 1] == dims[k - 1])
- hs_offset[k - 1] = 0;
+ hs_sel_offset[k - 1] += hs_sel_count[k - 1];
+ /* if reached the end of a dim */
+ if (hs_sel_offset[k - 1] == dims[k - 1])
+ hs_sel_offset[k - 1] = 0;
else
carry = 0;
} /* k */
} /* elmtno */
- H5Sclose(sm_space);
+ H5Sclose(hslab_space);
/* free */
- if (sm_buf!=NULL)
+ if (hslab_buf!=NULL)
{
- HDfree(sm_buf);
- sm_buf=NULL;
+ HDfree(hslab_buf);
+ hslab_buf=NULL;
}
} /* hyperslab read */
} /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
@@ -1005,7 +1217,7 @@ int do_copy_objects(hid_t fidin,
print_dataset_info(dcpl_out,travt->objs[i].name,ratio,1);
}
else
- print_dataset_info(dcpl_id,travt->objs[i].name,ratio,0);
+ print_dataset_info(dcpl_in,travt->objs[i].name,ratio,0);
/* print a message that the filter was not applied
(in case there was a filter)
@@ -1044,7 +1256,7 @@ int do_copy_objects(hid_t fidin,
goto error;
if (H5Tclose(wtype_id) < 0)
goto error;
- if (H5Pclose(dcpl_id) < 0)
+ if (H5Pclose(dcpl_in) < 0)
goto error;
if (H5Pclose(dcpl_out) < 0)
goto error;
@@ -1199,7 +1411,7 @@ error:
H5E_BEGIN_TRY {
H5Gclose(grp_in);
H5Gclose(grp_out);
- H5Pclose(dcpl_id);
+ H5Pclose(dcpl_in);
H5Pclose(gcpl_in);
H5Pclose(gcpl_out);
H5Sclose(f_space_id);
@@ -1214,8 +1426,8 @@ error:
/* free */
if (buf!=NULL)
HDfree(buf);
- if (sm_buf!=NULL)
- HDfree(sm_buf);
+ if (hslab_buf!=NULL)
+ HDfree(hslab_buf);
return -1;
}
generated by cgit v0.12 at 2024-11-01 14:53:14 (GMT)