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-rw-r--r--tools/src/h5repack/h5repack_copy.c233
1 files changed, 126 insertions, 107 deletions
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index e7c3bfe..946f5ad 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -31,7 +31,7 @@
*/
/* size of buffer/# of bytes to xfer at a time when copying userblock */
-#define USERBLOCK_XFER_SIZE 512
+#define USERBLOCK_XFER_SIZE 512
/* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */
#define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf) { \
@@ -52,12 +52,12 @@
*-------------------------------------------------------------------------
*/
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);
+ 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);
+ pack_opt_t *options);
static int copy_user_block(const char *infile, const char *outfile,
- hsize_t size);
+ hsize_t size);
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static void print_user_block(const char *filename, hid_t fid);
#endif
@@ -65,18 +65,19 @@ static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void
/* get the major number from the error stack. */
static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
- if (err_desc)
- *((hid_t *) udata) = err_desc->maj_num;
+ if (err_desc)
+ *((hid_t *) udata) = err_desc->maj_num;
- return 0;
+ return 0;
}
/*-------------------------------------------------------------------------
* Function: copy_objects
*
- * Purpose: duplicate all HDF5 objects in the file
+ * Purpose: duplicate all HDF5 objects in the file
*
- * Return: 0, ok, -1 no
+ * Return: 0, ok,
+ * -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
@@ -87,21 +88,22 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t
int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
{
- int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ int ret_value = 0; /* no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t fidin;
hid_t fidout = -1;
trav_table_t *travt = NULL;
- hsize_t ub_size = 0; /* size of user block */
- hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
- hid_t fapl = H5P_DEFAULT; /* file access property list ID */
- H5F_fspace_strategy_t set_strategy; /* Strategy to be set in outupt file */
- hbool_t set_persist; /* Persist free-space status to be set in output file */
- hsize_t set_threshold; /* Free-space section threshold to be set in output file */
- hsize_t set_pagesize; /* File space page size to be set in output file */
- H5F_fspace_strategy_t in_strategy; /* Strategy from input file */
- hbool_t in_persist; /* Persist free-space status from input file */
- hsize_t in_threshold; /* Free-space section threshold from input file */
- hsize_t in_pagesize; /* File space page size from input file */
+ hsize_t ub_size = 0; /* size of user block */
+ hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
+ hid_t fapl = H5P_DEFAULT; /* file access property list ID */
+ H5F_fspace_strategy_t set_strategy; /* Strategy to be set in outupt file */
+ hbool_t set_persist; /* Persist free-space status to be set in output file */
+ hsize_t set_threshold; /* Free-space section threshold to be set in output file */
+ hsize_t set_pagesize; /* File space page size to be set in output file */
+ H5F_fspace_strategy_t in_strategy; /* Strategy from input file */
+ hbool_t in_persist; /* Persist free-space status from input file */
+ hsize_t in_threshold; /* Free-space section threshold from input file */
+ hsize_t in_pagesize; /* File space page size from input file */
+ unsigned crt_order_flags; /* group creation order flag */
/*-------------------------------------------------------------------------
* open input file
@@ -115,6 +117,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
/* get user block size and file space strategy/persist/threshold */
{
hid_t fcpl_in; /* file creation property list ID for input file */
+ hid_t grp_in = -1; /* group ID */
+ hid_t gcpl_in = -1; /* group creation property list */
if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
error_msg("failed to retrieve file creation property list\n");
@@ -126,17 +130,28 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- /* If the -S option is not set, get "strategy" from the input file */
- if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) {
- error_msg("failed to retrieve file space strategy\n");
+ /* If the -S option is not set, get "strategy" from the input file */
+ if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) {
+ error_msg("failed to retrieve file space strategy\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ /* If the -G option is not set, get "pagesize" from the input file */
+ if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) {
+ error_msg("failed to retrieve file space threshold\n");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
+ /* open root group */
+ if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
- /* If the -G option is not set, get "pagesize" from the input file */
- if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) {
- error_msg("failed to retrieve file space threshold\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ /* get root group creation property list */
+ if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
+
+ /* query and set the group creation properties */
+ if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
if (H5Pclose(fcpl_in) < 0) {
error_msg("failed to close property list\n");
@@ -295,9 +310,9 @@ print_user_block(fnamein, fidin);
}
/*-------------------------------------------------------------------------
- * Set file space information
- *-------------------------------------------------------------------------
- */
+ * Set file space information
+ *-------------------------------------------------------------------------
+ */
/* either use the FCPL already created or create a new one */
if (fcpl == H5P_DEFAULT) {
@@ -308,6 +323,9 @@ print_user_block(fnamein, fidin);
}
}
+ if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
+
/* Set file space info to those from input file */
set_strategy = in_strategy;
set_persist = in_persist;
@@ -323,7 +341,7 @@ print_user_block(fnamein, fidin);
set_persist = FS_PERSIST_DEF;
else if(options->fs_persist != 0) /* Set "persist" as specified by user */
set_persist = (hbool_t)options->fs_persist;
-
+
if(options->fs_threshold == -1) /* A "0" threshold is specified by user */
set_threshold = (hsize_t)0;
else if(options->fs_threshold != 0) /* Set threshold as specified by user */
@@ -331,7 +349,7 @@ print_user_block(fnamein, fidin);
/* Set file space information as specified */
if(H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0) {
- error_msg("failed to set file space strategy\n");
+ error_msg("failed to set file space strategy\n");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
@@ -343,7 +361,7 @@ print_user_block(fnamein, fidin);
if(set_pagesize != FS_PAGESIZE_DEF) /* Set non-default file space page size as specified */
if(H5Pset_file_space_page_size(fcpl, set_pagesize) < 0) {
error_msg("failed to set file space page size\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
/*-------------------------------------------------------------------------
@@ -374,6 +392,8 @@ print_user_block(fnamein, fidin);
*-------------------------------------------------------------------------
*/
+ /* Initialize indexing options */
+ h5trav_set_index(sort_by, sort_order);
/* init table */
trav_table_init(&travt);
@@ -490,10 +510,10 @@ done:
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 ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
- int k;
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ int k;
H5D_layout_t dset_layout;
- int rank_chunk;
+ 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) */
@@ -705,36 +725,36 @@ done:
*/
int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
- pack_opt_t *options) /* repack options */
+ pack_opt_t *options) /* repack options */
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
- hid_t grp_in = -1; /* group ID */
- hid_t grp_out = -1; /* group ID */
- hid_t dset_in = -1; /* read dataset ID */
+ hid_t grp_in = -1; /* group ID */
+ hid_t grp_out = -1; /* group ID */
+ hid_t dset_in = -1; /* read dataset ID */
hid_t dset_out = -1; /* write dataset ID */
- hid_t gcpl_in = -1; /* group creation property list */
+ hid_t gcpl_in = -1; /* group creation property list */
hid_t gcpl_out = -1; /* group creation property list */
- hid_t type_in = -1; /* named type ID */
+ hid_t type_in = -1; /* named type ID */
hid_t type_out = -1; /* named type ID */
- hid_t dcpl_in = -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 */
hid_t wtype_id = -1; /* read/write type ID */
named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
- size_t msize; /* size of type */
- hsize_t nelmts; /* number of elements in dataset */
+ size_t msize; /* size of type */
+ hsize_t nelmts; /* number of elements in dataset */
H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */
- int rank; /* rank of dataset */
+ int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
- hsize_t dsize_in; /* input dataset size before filter */
- hsize_t dsize_out; /* output dataset size after filter */
- 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 */
+ hsize_t dsize_in; /* input dataset size before filter */
+ hsize_t dsize_out; /* output dataset size after filter */
+ 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 *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 */
+ int has_filter; /* current object has a filter */
+ int req_filter; /* there was a request for a filter */
int req_obj_layout = 0; /* request layout to current object */
unsigned crt_order_flags; /* group creation order flag */
unsigned i;
@@ -915,7 +935,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
/* wtype_id will have already been set if using a named dtype */
if (!is_named) {
if (options->use_native == 1)
- wtype_id = h5tools_get_native_type(ftype_id);
+ wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
else
wtype_id = H5Tcopy(ftype_id);
} /* end if */
@@ -1349,20 +1369,19 @@ done:
*
*-------------------------------------------------------------------------
*/
-static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
- int pr)
+static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
{
- char strfilter[255];
+ char strfilter[255];
#if defined (PRINT_DEBUG )
- char temp[255];
+ char temp[255];
#endif
- int nfilters; /* number of filters */
- unsigned filt_flags; /* filter flags */
- H5Z_filter_t filtn; /* filter identification number */
- unsigned cd_values[20]; /* filter client data values */
- size_t cd_nelmts; /* filter client number of values */
- char f_objname[256]; /* filter objname */
- int i;
+ int nfilters; /* number of filters */
+ unsigned filt_flags; /* filter flags */
+ H5Z_filter_t filtn; /* filter identification number */
+ unsigned cd_values[20]; /* filter client data values */
+ size_t cd_nelmts; /* filter client number of values */
+ char f_objname[256]; /* filter objname */
+ int i;
HDstrcpy(strfilter, "\0");
@@ -1461,10 +1480,9 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
*
*-------------------------------------------------------------------------
*/
-static int copy_user_block(const char *infile, const char *outfile,
- hsize_t size)
+static int copy_user_block(const char *infile, const char *outfile, hsize_t size)
{
- int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
int infid = -1, outfid = -1; /* File descriptors */
/* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
@@ -1541,67 +1559,68 @@ done:
static
void print_user_block(const char *filename, hid_t fid)
{
- int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
- int fh; /* file handle */
- hsize_t ub_size; /* user block size */
- hsize_t size; /* size read */
- hid_t fcpl; /* file creation property list ID for HDF5 file */
- int i;
-
- /* get user block size */
- if(( fcpl = H5Fget_create_plist(fid)) < 0) {
- error_msg("failed to retrieve file creation property list\n");
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ int fh; /* file handle */
+ hsize_t ub_size; /* user block size */
+ hsize_t size; /* size read */
+ hid_t fcpl; /* file creation property list ID for HDF5 file */
+ int i;
+
+ /* get user block size */
+ if(( fcpl = H5Fget_create_plist(fid)) < 0) {
+ error_msg("failed to retrieve file creation property list\n");
HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed");
}
- if(H5Pget_userblock(fcpl, &ub_size) < 0) {
- error_msg("failed to retrieve userblock size\n");
+ if(H5Pget_userblock(fcpl, &ub_size) < 0) {
+ error_msg("failed to retrieve userblock size\n");
HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed");
}
- if(H5Pclose(fcpl) < 0) {
- error_msg("failed to close property list\n");
+ if(H5Pclose(fcpl) < 0) {
+ error_msg("failed to close property list\n");
HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
}
- /* open file */
- if((fh = HDopen(filename, O_RDONLY)) < 0) {
+ /* open file */
+ if((fh = HDopen(filename, O_RDONLY)) < 0) {
+ error_msg("failed to open file\n");
HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed");
}
- size = ub_size;
+ size = ub_size;
- /* read file */
- while(size > 0) {
- ssize_t nread; /* # of bytes read */
- char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
+ /* read file */
+ while(size > 0) {
+ ssize_t nread; /* # of bytes read */
+ char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
- /* read buffer */
- if(size > USERBLOCK_XFER_SIZE)
- nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
- else
- nread = HDread(fh, rbuf, (size_t)size);
+ /* read buffer */
+ if(size > USERBLOCK_XFER_SIZE)
+ nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+ else
+ nread = HDread(fh, rbuf, (size_t)size);
- for(i = 0; i < nread; i++) {
+ for(i = 0; i < nread; i++) {
- printf("%c ", rbuf[i]);
+ printf("%c ", rbuf[i]);
- }
- printf("\n");
+ }
+ printf("\n");
- if(nread < 0) {
+ if(nread < 0) {
HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
}
- /* update size of userblock left to transfer */
- size -= nread;
- }
+ /* update size of userblock left to transfer */
+ size -= nread;
+ }
done:
- if(fh > 0)
- HDclose(fh);
+ if(fh > 0)
+ HDclose(fh);
- return;
+ return;
}
#endif