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-rw-r--r--tools/h5repack/h5repack_copy.c482
1 files changed, 183 insertions, 299 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index b41f7be..63233b8 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -78,49 +78,37 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t
*
* Return: 0, ok,
* -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 23, 2003
- *
*-------------------------------------------------------------------------
*/
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) */
- hid_t fidin;
+ int ret_value = 0;
+ hid_t fidin = -1;
hid_t fidout = -1;
- trav_table_t *travt = NULL;
- hsize_t ub_size = 0; /* size of user block */
+ hid_t fcpl_in = -1; /* file creation property list ID for input file */
+ hid_t grp_in = -1; /* group ID */
+ hid_t gcpl_in = -1; /* group creation property list */
hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
hid_t fapl = H5P_DEFAULT; /* file access property list ID */
+ trav_table_t *travt = NULL;
+ hsize_t ub_size = 0; /* size of user block */
unsigned crt_order_flags; /* group creation order flag */
/*-------------------------------------------------------------------------
* open input file
*-------------------------------------------------------------------------
*/
- if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) {
- error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fnamein, H5FOPENERROR);
/* get user block size and file space strategy/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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list");
- if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
- error_msg("failed to retrieve file creation property list\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
-
- if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
- error_msg("failed to retrieve userblock size\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ if (H5Pget_userblock(fcpl_in, &ub_size) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size");
/* open root group */
if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
@@ -134,26 +122,19 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
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");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ if (H5Pclose(fcpl_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed to close property list");
}
/* Check if we need to create a non-default file creation property list */
if (options->latest || ub_size > 0) {
/* Create file creation property list */
- if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
- error_msg("fail to create a file creation property list\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
- if (ub_size > 0) {
- if (H5Pset_userblock(fcpl, ub_size) < 0) {
- error_msg("failed to set non-default userblock size\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
- }
+ if (ub_size > 0)
+ if (H5Pset_userblock(fcpl, ub_size) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set non-default userblock size");
if (options->latest) {
unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
@@ -161,10 +142,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
/* Adjust group creation parameters for root group */
/* (So that it is created in "dense storage" form) */
if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
- (unsigned) options->grp_indexed) < 0) {
- error_msg("fail to adjust group creation parameters for root group\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ (unsigned) options->grp_indexed) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed to adjust group creation parameters for root group");
for (i = 0; i < 5; i++) {
if (options->msg_size[i] > 0) {
@@ -199,30 +178,21 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
} /* end for */
if (nindex > 0) {
- if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
- error_msg("fail to set the number of shared object header message indexes\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_nindexes failed to set the number of shared object header message indexes");
/* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
- for (i = 0; i < (nindex - 1); i++) {
- if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
- error_msg("fail to configure the specified shared object header message index\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- } /* end if */
- } /* end for */
+ for (i = 0; i < (nindex - 1); i++)
+ if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_index failed to configure the specified shared object header message index");
} /* if (nindex>0) */
/* Create file access property list */
- if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
- error_msg("Could not create file access property list\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- } /* end if */
-
- if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
- error_msg("Could not set property for using latest version of the format\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- } /* end if */
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
+
+ if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_libver_bounds failed to set property for using latest version of the format");
} /* end if */
} /* end if */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
@@ -235,19 +205,14 @@ print_user_block(fnamein, fidin);
*/
if (options->ublock_size > 0) {
/* either use the FCPL already created or create a new one */
- if (fcpl == H5P_DEFAULT) {
+ if (fcpl == H5P_DEFAULT)
/* create a file creation property list */
- if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
- error_msg("fail to create a file creation property list\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
- }
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
/* set user block size */
- if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
- error_msg("failed to set userblock size\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ if (H5Pset_userblock(fcpl, options->ublock_size) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set userblock size");
}
/*-------------------------------------------------------------------------
@@ -256,18 +221,13 @@ print_user_block(fnamein, fidin);
*/
if (options->alignment > 0) {
/* either use the FAPL already created or create a new one */
- if (fapl == H5P_DEFAULT) {
+ if (fapl == H5P_DEFAULT)
/* create a file access property list */
- if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
- error_msg("Could not create file access property list\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
- }
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
- if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
- error_msg("failed to set alignment\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_alignment failed to set alignment");
}
/*-------------------------------------------------------------------------
@@ -276,18 +236,13 @@ print_user_block(fnamein, fidin);
*/
if (options->meta_block_size > 0) {
/* either use the FAPL already created or create a new one */
- if (fapl == H5P_DEFAULT) {
+ if (fapl == H5P_DEFAULT)
/* create a file access property list */
- if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
- error_msg("Could not create file access property list\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
- }
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
- if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
- error_msg("failed to set metadata block size\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_meta_block_size failed to set metadata block size");
}
/*-------------------------------------------------------------------------
@@ -296,13 +251,10 @@ print_user_block(fnamein, fidin);
*/
/* either use the FCPL already created or create a new one */
- if (fcpl == H5P_DEFAULT) {
+ if (fcpl == H5P_DEFAULT)
/* create a file creation property list */
- if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
- error_msg("fail to create a file creation property list\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
- }
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
@@ -312,23 +264,18 @@ print_user_block(fnamein, fidin);
*-------------------------------------------------------------------------
*/
if (options->verbose)
- printf("Making file <%s>...\n", fnameout);
+ printf("Making new file ...\n");
- if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
- error_msg("<%s>: Could not create file\n", fnameout);
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
+ if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fcreate could not create file <%s>:", fnameout);
/*-------------------------------------------------------------------------
* write a new user block if requested
*-------------------------------------------------------------------------
*/
- if (options->ublock_size > 0) {
- if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) {
- error_msg("Could not copy user block. Exiting...\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
- }
+ if (options->ublock_size > 0)
+ if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting...");
/*-------------------------------------------------------------------------
* get list of objects
@@ -340,70 +287,45 @@ print_user_block(fnamein, fidin);
/* init table */
trav_table_init(&travt);
- /* get the list of objects in the file */
- if (h5trav_gettable(fidin, travt) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-
- /*-------------------------------------------------------------------------
- * do the copy
- *-------------------------------------------------------------------------
- */
- if (do_copy_objects(fidin, fidout, travt, options) < 0) {
- error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- } /* end if */
-
- /*-------------------------------------------------------------------------
- * do the copy of referenced objects
- * and create hard links
- *-------------------------------------------------------------------------
- */
- if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
- printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (travt) {
+ /* get the list of objects in the file */
+ if (h5trav_gettable(fidin, travt) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
+
+ /*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+ if (do_copy_objects(fidin, fidout, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_objects from <%s> could not copy data to <%s>", fnamein, fnameout);
+
+ /*-------------------------------------------------------------------------
+ * do the copy of referenced objects
+ * and create hard links
+ *-------------------------------------------------------------------------
+ */
+ if (do_copy_refobjs(fidin, fidout, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, fnameout);
}
/*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
- if (fapl > 0)
- H5Pclose(fapl);
-
- if (fcpl > 0)
- H5Pclose(fcpl);
-
- H5Fclose(fidin);
- H5Fclose(fidout);
-
- /* free table */
- trav_table_free(travt);
- travt = NULL;
-
- /*-------------------------------------------------------------------------
* write only the input file user block if there is no user block file input
*-------------------------------------------------------------------------
*/
- if (ub_size > 0 && options->ublock_size == 0) {
- if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
- error_msg("Could not copy user block. Exiting...\n");
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- }
- }
-
- return 0;
-
- /*-------------------------------------------------------------------------
- * out
- *-------------------------------------------------------------------------
- */
+ if (ub_size > 0 && options->ublock_size == 0)
+ if (copy_user_block(fnamein, fnameout, ub_size) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting...");
done:
H5E_BEGIN_TRY {
+ H5Pclose(fcpl_in);
+ H5Pclose(gcpl_in);
H5Pclose(fapl);
H5Pclose(fcpl);
+ H5Gclose(grp_in);
+ H5Fclose(fidin);
+ H5Fclose(fidout);
H5Fclose(fidin);
H5Fclose(fidout);
} H5E_END_TRY;
@@ -420,7 +342,7 @@ done:
* The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
* Return the hyperslab dimentions and size in byte.
*
- * Return: 0 - SUCCEED, -1 FAILED
+ * Return: 0 - SUCCEED, -1 FAILED
*
* Parameters:
* dcpl_id : [IN] dataset creation property.
@@ -430,8 +352,6 @@ done:
* 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.
@@ -445,25 +365,23 @@ done:
* 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[],
+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 ret_value = 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 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 */
+ 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;
@@ -476,7 +394,7 @@ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
/* get chunk dims */
rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
if (rank_chunk < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed");
for (k = rank_dset; k > 0; --k)
size_chunk *= dims_chunk[k - 1];
@@ -538,7 +456,7 @@ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
hslab_nbytes *= dims_hslab[k - 1];
if (hslab_nbytes <= 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "calculate total size for the hyperslab failed");
}
}
}
@@ -562,7 +480,7 @@ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
hslab_nbytes *= dims_hslab[k - 1];
if (hslab_nbytes <= 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "calculate total size for the hyperslab failed");
}
}
@@ -576,24 +494,9 @@ done:
/*-------------------------------------------------------------------------
* Function: do_copy_objects
*
- * Purpose: duplicate all HDF5 objects in the file
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 23, 2003
- *
- * Modifications:
- *
- * July 2004: Introduced the extra EC or NN option for SZIP
- *
- * December 2004: Added a check for H5Dcreate; if the dataset cannot be created
- * with the requested filter, use the input one
- *
- * October 2006: Read/write using the file type by default.
+ * Purpose: duplicate all HDF5 objects in the file
*
- * October 2006: Read by hyperslabs for big datasets.
+ * Return: 0, ok, -1 no
*
* A threshold of H5TOOLS_MALLOCSIZE (128 MB) 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,
@@ -634,31 +537,6 @@ done:
* in (2) is that, when using the strip mine size, it assures that the "remaining" part
* of the dataset that does not fill an entire strip mine is processed.
*
- * November 2006: Use H5Ocopy in the copy of objects. The logic for using
- * H5Ocopy or not is if a change of filters or layout is requested by the user
- * then use read/write else use H5Ocopy.
- *
- * 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
@@ -670,7 +548,7 @@ done:
int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
- int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ int ret_value = 0;
hid_t grp_in = -1; /* group ID */
hid_t grp_out = -1; /* group ID */
hid_t dset_in = -1; /* read dataset ID */
@@ -702,13 +580,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
unsigned crt_order_flags; /* group creation order flag */
unsigned i;
unsigned u;
+ unsigned uf;
int is_ref = 0;
htri_t is_named;
hbool_t limit_maxdims;
hsize_t size_dset;
/*-------------------------------------------------------------------------
- * copy the suppplied object list
+ * copy the supplied object list
*-------------------------------------------------------------------------
*/
@@ -718,14 +597,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
printf("-----------------------------------------\n");
}
- for (i = 0; i < travt->nobjs; i++) {
- /* init variables per obj */
- buf = NULL;
- limit_maxdims = FALSE;
+ if (travt->objs) {
+ for (i = 0; i < travt->nobjs; i++) {
+ /* init variables per obj */
+ buf = NULL;
+ limit_maxdims = FALSE;
- switch (travt->objs[i].type) {
+ switch (travt->objs[i].type) {
case H5TRAV_TYPE_UNKNOWN:
- HDassert(0);
break;
/*-------------------------------------------------------------------------
@@ -804,10 +683,15 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
req_filter = 1;
/* check if filters were requested for individual objects */
- for (u = 0; u < options->op_tbl->nelems; u++)
- if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
- if (options->op_tbl->objs[u].filter->filtn > 0)
- req_filter = 1;
+ if (options->op_tbl->objs) {
+ for (u = 0; u < options->op_tbl->nelems; u++) {
+ if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
+ for (uf = 0; uf < options->op_tbl->objs[uf].nfilters; uf++) {
+ if (options->op_tbl->objs[u].filter[uf].filtn > 0)
+ req_filter = 1;
+ }
+ }
+ }
/* check if layout change requested individual object */
if (options->layout_g != H5D_LAYOUT_ERROR) {
@@ -983,16 +867,22 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
buf = HDmalloc(need);
if (buf != NULL) {
- /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
- CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
- CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+ if(H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
+ if(H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
/* Check if we have VL data in the dataset's
* datatype that must be reclaimed */
if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
- }
+ /* free */
+ if (buf != NULL) {
+ HDfree(buf);
+ buf = NULL;
+ }
+ }
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 elements */
@@ -1068,9 +958,10 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
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, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
- CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
+ if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
+ if(H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
/* reclaim any VL memory, if necessary */
if (vl_data)
@@ -1161,7 +1052,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*-------------------------------------------------------------------------
*/
else {
- hid_t pid;
+ hid_t pid = -1;
/* create property to pass copy options */
if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
@@ -1239,6 +1130,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
if (H5Tclose(type_out) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ type_out = -1; /* named datatypes stack, named_dt_head, manages allocation */
break;
@@ -1264,21 +1156,23 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
default:
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found");
- } /* switch */
-
- /* free */
- if (buf != NULL) {
- HDfree(buf);
- buf = NULL;
- }
- } /* i */
+ } /* switch */
+ } /* end for */
+ } /* end if */
- /* Finalize (link) the stack of named datatypes (if any) */
- named_datatype_free(&named_dt_head, 0);
+done:
- return ret_value;
+ /* Finalize (link) the stack of named datatypes (if any) first
+ * because of reference counting */
+ if (0 == ret_value && named_dt_head != NULL) {
+ if (named_datatype_free(&named_dt_head, 0) < 0)
+ H5TOOLS_INFO(H5E_tools_min_id_g, "named_datatype_free failed");
+ }
+ else
+ H5E_BEGIN_TRY {
+ named_datatype_free(&named_dt_head, 1);
+ } H5E_END_TRY;
-done:
H5E_BEGIN_TRY
{
H5Gclose(grp_in);
@@ -1293,8 +1187,7 @@ done:
H5Tclose(wtype_id);
H5Tclose(type_in);
H5Tclose(type_out);
- named_datatype_free(&named_dt_head, 1);
- }H5E_END_TRY;
+ } H5E_END_TRY;
/* free */
if (buf != NULL)
@@ -1309,10 +1202,10 @@ done:
* Function: print_dataset_info
*
* Purpose: print name, filters, percentage compression of a dataset
- *
*-------------------------------------------------------------------------
*/
-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];
#if defined (PRINT_DEBUG )
@@ -1324,7 +1217,7 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p
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 i;
HDstrcpy(strfilter, "\0");
@@ -1335,8 +1228,11 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p
for (i = 0; i < nfilters; i++) {
cd_nelmts = NELMTS(cd_values);
- filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
- cd_values, sizeof(f_objname), f_objname, NULL);
+ if ((filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
+ cd_values, sizeof(f_objname), f_objname, NULL)) < 0) {
+ HDstrcat(strfilter, "ERROR ");
+ continue;
+ }
switch (filtn) {
case H5Z_FILTER_NONE:
@@ -1413,29 +1309,24 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p
/*-------------------------------------------------------------------------
* Function: copy_user_block
*
- * Purpose: copy user block from one file to another
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Peter Cao
- *
- * Date: October, 25, 2007
+ * Purpose: copy user block from one file to another
*
+ * Return: 0, ok, -1 no
*-------------------------------------------------------------------------
*/
-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;
int infid = -1, outfid = -1; /* File descriptors */
/* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
- HDassert(size > 0);
/* Open files */
if ((infid = HDopen(infile, O_RDONLY, 0)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed input file <%s>", infile);
if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed output file <%s>", outfile);
/* Copy the userblock from the input file to the output file */
while (size > 0) {
@@ -1449,7 +1340,7 @@ static int copy_user_block(const char *infile, const char *outfile, hsize_t size
else
nread = HDread(infid, rbuf, (size_t)size);
if (nread < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed to read userblock");
/* Write buffer to destination file */
/* (compensating for interrupted writes & checking for errors, etc.) */
@@ -1488,69 +1379,62 @@ done:
/*-------------------------------------------------------------------------
* Function: print_user_block
*
- * Purpose: print user block
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente
- *
- * Date: August, 20, 2008
+ * Purpose: print user block
*
+ * Return: 0, ok, -1 no
*-------------------------------------------------------------------------
*/
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static
-void print_user_block(const char *filename, hid_t fid)
+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 ret_value = 0;
+ int fh = -1; /* file handle */
+ hsize_t ub_size; /* user block size */
+ hsize_t size; /* size read */
+ hid_t fcpl = -1; /* 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 ((fcpl = H5Fget_create_plist(fid)) < 0) {
+ HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list");
}
- 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 (H5Pget_userblock(fcpl, &ub_size) < 0) {
+ HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size");
}
- if(H5Pclose(fcpl) < 0) {
- error_msg("failed to close property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Pclose(fcpl) < 0) {
+ HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed to close property list");
}
/* open file */
- if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed");
+ if ((fh = HDopen(filename, O_RDONLY)) < 0) {
+ HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed to open file <%s>", filename);
}
size = ub_size;
/* read file */
- while(size > 0) {
+ while (size > 0) {
ssize_t nread; /* # of bytes read */
char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
/* read buffer */
- if(size > USERBLOCK_XFER_SIZE)
+ 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("\n");
- if(nread < 0) {
+ if (nread < 0) {
HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
}
@@ -1559,7 +1443,7 @@ void print_user_block(const char *filename, hid_t fid)
}
done:
- if(fh > 0)
+ if (fh > 0)
HDclose(fh);
return;