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hdf5/tools/h5repack/h5repack_copy.c
Mohamad Chaarawi fc45d5fcb0 [svn-r27133] - Add a new attribute function characterstic for format: 
* H5_ATTR_FORMAT(X,Y,Z)  __attribute__((format(X, Y, Z)))
- Rename UNUSED attribute characterstic to H5_ATTR_UNUSED.
- Rename NORETURN attribute characterstic to H5_ATTR_NORETURN

tested with h5committest.
2015-06-01 14:38:09 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------
* typedefs
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* globals
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* macros
*-------------------------------------------------------------------------
*/
/* size of buffer/# of bytes to xfer at a time when copying userblock */
#define USERBLOCK_XFER_SIZE 512
/* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */
#define CHECK_H5DRW_ERROR(_fun, _did, _mtid, _msid, _fsid, _pid, _buf) { \
H5E_BEGIN_TRY { \
if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) { \
hid_t _err_num = 0; \
char _msg[80]; \
H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \
H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \
error_msg("%s %s -- %s\n", #_fun, "failed", _msg); \
goto error; \
} \
} H5E_END_TRY; \
}
/*-------------------------------------------------------------------------
* 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);
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static void print_user_block(const char *filename, hid_t fid);
#endif
static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata);
/* 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;
return 0;
}
/*-------------------------------------------------------------------------
* Function: 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
*
* Modification:
* Peter Cao, June 13, 2007
* Add "-L, --latest" and other options to pack a file with the latest file format
*
* Peter Cao, September 25, 2007
* Copy user block when repacking a file
*
* Pedro Vicente, August 20, 2008
* Add a user block to file if requested
*
*-------------------------------------------------------------------------
*/
int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) {
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 */
/*-------------------------------------------------------------------------
* 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);
goto out;
}
/* get user block size and file space strategy/threshold */
{
hid_t fcpl_in; /* file creation property list ID for input file */
if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
error_msg("failed to retrieve file creation property list\n");
goto out;
}
if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
error_msg("failed to retrieve userblock size\n");
goto out;
}
if (!options->fs_strategy) {
if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) {
error_msg("failed to retrieve file space strategy\n");
goto out;
}
}
if (!options->fs_threshold) {
if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) {
error_msg("failed to retrieve file space threshold\n");
goto out;
}
}
if (H5Pclose(fcpl_in) < 0) {
error_msg("failed to close property list\n");
goto out;
}
}
/* 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");
goto out;
}
if (ub_size > 0) {
if (H5Pset_userblock(fcpl, ub_size) < 0) {
error_msg("failed to set non-default userblock size\n");
goto out;
}
}
if (options->latest) {
unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
/* 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");
goto out;
}
for (i = 0; i < 5; i++) {
if (options->msg_size[i] > 0) {
switch (i) {
case 0:
mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
break;
case 1:
mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
break;
case 2:
mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
break;
case 3:
mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
break;
case 4:
mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
break;
default:
break;
} /* end switch */
min_mesg_sizes[nindex] = (unsigned) options->msg_size[i];
nindex++;
} /* end if */
} /* 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");
goto out;
}
/* 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");
goto out;
} /* end if */
} /* end for */
} /* 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");
goto out;
} /* 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");
goto out;
} /* end if */
} /* end if */
} /* end if */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
print_user_block(fnamein, fidin);
#endif
/*-------------------------------------------------------------------------
* set the new user userblock options in the FCPL (before H5Fcreate )
*-------------------------------------------------------------------------
*/
if (options->ublock_size > 0) {
/* either use the FCPL already created or create a new one */
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");
goto out;
}
}
/* set user block size */
if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
error_msg("failed to set userblock size\n");
goto out;
}
}
/*-------------------------------------------------------------------------
* set alignment options
*-------------------------------------------------------------------------
*/
if (options->alignment > 0) {
/* either use the FAPL already created or create a new one */
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");
goto out;
}
}
if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
error_msg("failed to set alignment\n");
goto out;
}
}
/*-------------------------------------------------------------------------
* set metadata block size option
*-------------------------------------------------------------------------
*/
if (options->meta_block_size > 0) {
/* either use the FAPL already created or create a new one */
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");
goto out;
}
}
if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
error_msg("failed to set metadata block size\n");
goto out;
}
}
/*-------------------------------------------------------------------------
* set free-space strategy options
*-------------------------------------------------------------------------
*/
/* either use the FCPL already created or create a new one */
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");
goto out;
}
}
/* set file space strategy and free space threshold */
if (H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) {
error_msg("failed to set file space strategy & threshold \n");
goto out;
}
/*-------------------------------------------------------------------------
* create the output file
*-------------------------------------------------------------------------
*/
if (options->verbose)
printf("Making file <%s>...\n", fnameout);
if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
error_msg("<%s>: Could not create file\n", fnameout);
goto out;
}
/*-------------------------------------------------------------------------
* 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");
goto out;
}
}
/*-------------------------------------------------------------------------
* get list of objects
*-------------------------------------------------------------------------
*/
/* init table */
trav_table_init(&travt);
/* get the list of objects in the file */
if (h5trav_gettable(fidin, travt) < 0)
goto out;
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------
*/
if (do_copy_objects(fidin, fidout, travt, options) < 0) {
error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
goto out;
} /* 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);
goto out;
}
/*-------------------------------------------------------------------------
* 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");
goto out;
}
}
return 0;
/*-------------------------------------------------------------------------
* out
*-------------------------------------------------------------------------
*/
out:
H5E_BEGIN_TRY
{
H5Pclose(fapl);
H5Pclose(fcpl);
H5Fclose(fidin);
H5Fclose(fidout);
}H5E_END_TRY;
if (travt)
trav_table_free(travt);
return -1;
}
/*-------------------------------------------------------------------------
* 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
*
* 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.
*
* October 2006: Read by hyperslabs for big datasets.
*
* 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,
* 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_dataset1 )
* H5Dread( input_dataset2 )
*
* with all elements in the datasets selected. If the memory needed is greater than
* H5TOOLS_MALLOCSIZE, then the following operations are done instead:
*
* a strip mine is defined for each dimension k (a strip mine is defined as a
* hyperslab whose size is memory manageable) according to the formula
*
* (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
*
* where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
* that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
* mine size k is simply defined as its dimension k, but for larger datasets the
* hyperslab size is still memory manageable.
* a cycle is done until the number of elements in the dataset is reached. In each
* iteration, two parameters are defined for the function H5Sselect_hyperslab,
* the start and size of each hyperslab, according to
*
* (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
*
* where hyperslab_offset [k] is initially set to zero, and later incremented in
* hyperslab_size[k] offsets. The reason for the operation
*
* dimension[k] - hyperslab_offset[k]
*
* 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
* of the dataset. The code take care of the remaining portion if exist.
*
*-------------------------------------------------------------------------
*/
int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
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_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_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 */
H5D_space_status_t space_status; /* determines whether space has been allocated for the 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 */
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 req_obj_layout = 0; /* request layout to current object */
unsigned crt_order_flags; /* group creation order flag */
unsigned i;
unsigned u;
int is_ref = 0;
htri_t is_named;
hbool_t limit_maxdims;
hsize_t size_dset;
/*-------------------------------------------------------------------------
* copy the suppplied object list
*-------------------------------------------------------------------------
*/
if (options->verbose) {
printf("-----------------------------------------\n");
printf(" Type Filter (Compression) Name\n");
printf("-----------------------------------------\n");
}
for (i = 0; i < travt->nobjs; i++) {
/* init variables per obj */
buf = NULL;
limit_maxdims = FALSE;
switch (travt->objs[i].type) {
case H5TRAV_TYPE_UNKNOWN:
HDassert(0);
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_GROUP
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_GROUP:
if (options->verbose) {
printf(FORMAT_OBJ, "group", travt->objs[i].name);
}
/* open input group */
if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
< 0)
goto error;
/* get input group creation property list */
if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
goto error;
/* query and set the group creation properties */
if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
goto error;
/* set up group creation property list */
if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
goto error;
if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
goto error;
/*-------------------------------------------------------------------------
* the root is a special case, we get an ID for the root group
* and copy its attributes using that ID
*-------------------------------------------------------------------------
*/
if (HDstrcmp(travt->objs[i].name, "/") == 0) {
if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
goto error;
}
else {
if (options->grp_compact > 0 || options->grp_indexed > 0) {
if (H5Pset_link_phase_change(gcpl_out,
(unsigned) options->grp_compact,
(unsigned) options->grp_indexed) < 0)
goto error;
}
if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name,
H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
goto error;
}
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
goto error;
if (H5Pclose(gcpl_out) < 0)
goto error;
if (H5Pclose(gcpl_in) < 0)
goto error;
if (H5Gclose(grp_out) < 0)
goto error;
if (H5Gclose(grp_in) < 0)
goto error;
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_DATASET
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_DATASET:
has_filter = 0;
req_filter = 0;
/* check if global filters were requested */
if (options->n_filter_g)
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;
}
}
}
/* check if layout change requested individual object */
if (options->layout_g != H5D_LAYOUT_ERROR) {
pack_info_t *pckinfo;
/* any dataset is specified */
if (options->op_tbl->nelems > 0) {
/* check if object exist */
pckinfo = options_get_object(travt->objs[i].name,
options->op_tbl);
if (pckinfo) {
req_obj_layout = 1;
}
}
}
/* early detection of references */
if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
< 0)
goto error;
if ((ftype_id = H5Dget_type(dset_in)) < 0)
goto error;
if (H5T_REFERENCE == H5Tget_class(ftype_id))
is_ref = 1;
/* Check if the datatype is committed */
if ((is_named = H5Tcommitted(ftype_id)) < 0)
goto error;
if (is_named)
if ((wtype_id = copy_named_datatype(ftype_id, fidout,
&named_dt_head, travt, options)) < 0)
goto error;
if (H5Tclose(ftype_id) < 0)
goto error;
if (H5Dclose(dset_in) < 0)
goto error;
/*-------------------------------------------------------------------------
* check if we should use H5Ocopy or not
* if there is a request for filters/layout, we read/write the object
* otherwise we do a copy using H5Ocopy
*-------------------------------------------------------------------------
*/
if (options->op_tbl->nelems || options->all_filter == 1
|| options->all_layout == 1 || is_ref || is_named) {
int j;
if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if ((f_space_id = H5Dget_space(dset_in)) < 0)
goto error;
if ((ftype_id = H5Dget_type(dset_in)) < 0)
goto error;
if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
goto error;
if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
goto error;
if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
goto error;
HDmemset(dims, 0, sizeof dims);
if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
goto error;
if (H5Dget_space_status(dset_in, &space_status) < 0)
goto error;
nelmts = 1;
for (j = 0; j < rank; j++)
nelmts *= dims[j];
/* 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);
else
wtype_id = H5Tcopy(ftype_id);
} /* end if */
if ((msize = H5Tget_size(wtype_id)) == 0)
goto error;
/* size of current dset */
size_dset = nelmts * msize;
/*-------------------------------------------------------------------------
* check if the dataset creation property list has filters that
* are not registered in the current configuration
* 1) the external filters GZIP and SZIP might not be available
* 2) the internal filters might be turned off
*-------------------------------------------------------------------------
*/
if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) {
apply_s = 1;
apply_f = 1;
/*-------------------------------------------------------------------------
* references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
* in a second traversal of the output file
*-------------------------------------------------------------------------
*/
if (H5T_REFERENCE != H5Tget_class(wtype_id)) {
/* get the storage size of the input dataset */
dsize_in = H5Dget_storage_size(dset_in);
/* check for small size datasets (less than 1k) except
* changing to COMPACT. For the reference, COMPACT is limited
* by size 64K by library.
*/
if (options->layout_g != H5D_COMPACT) {
if (size_dset < options->min_comp)
apply_s = 0;
}
/* apply the filter */
if (apply_s) {
if (apply_filters(travt->objs[i].name, rank, dims,
msize, dcpl_out, options, &has_filter) < 0)
goto error;
}
/* only if layout change requested for entire file or
* individual obj */
if (options->all_layout > 0 || req_obj_layout == 1)
/*-------------------------------------------------
* Unset the unlimited max dims if convert to other
* than chunk layouts, because unlimited max dims
* only can be applied to chunk layout.
* Also perform only for targeted dataset
* Also check for size limit to convert to compact
*-------------------------------------------------*/
if (options->layout_g != H5D_CHUNKED) {
/* any dataset is specified */
if (options->op_tbl->nelems > 0) {
/* if current obj match specified obj */
if (options_get_object(travt->objs[i].name,
options->op_tbl))
limit_maxdims = TRUE;
}
else { /* no dataset is specified */
limit_maxdims = TRUE;
}
/* if convert to COMPACT */
if (options->layout_g == H5D_COMPACT) {
/* should be smaller than 64K */
if (size_dset > MAX_COMPACT_DSIZE)
limit_maxdims = FALSE;
}
/* unset unlimited max dims */
if (limit_maxdims)
H5Sset_extent_simple(f_space_id, rank, dims,
NULL);
}
/*-------------------------------------------------------------------------
* create the output dataset;
* disable error checking in case the dataset cannot be created with the
* modified dcpl; in that case use the original instead
*-------------------------------------------------------------------------
*/
H5E_BEGIN_TRY
{
dset_out = H5Dcreate2(fidout,
travt->objs[i].name, wtype_id,
f_space_id, H5P_DEFAULT, dcpl_out,
H5P_DEFAULT);
}H5E_END_TRY;
if (dset_out == FAIL) {
if (options->verbose)
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_in, H5P_DEFAULT)) < 0)
goto error;
apply_f = 0;
}
/*-------------------------------------------------------------------------
* read/write
*-------------------------------------------------------------------------
*/
if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) {
size_t need = (size_t)(nelmts * msize); /* bytes needed */
/* have to read the whole dataset if there is only one element in the dataset */
if (need < H5TOOLS_MALLOCSIZE)
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, dset_in, wtype_id,
H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id,
H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
/* 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)
goto error;
}
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 */
hsize_t elmtno; /*counter */
int carry; /*counter carry value */
unsigned int vl_data = 0; /*contains VL datatypes */
/* hyperslab info */
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;
/* 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 */
dset_layout = H5Pget_layout(dcpl_in);
if (dset_layout == H5D_CHUNKED)
dcpl_tmp = dcpl_in; /* reading dataset */
}
/* 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 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_select_nelmts) {
if (rank > 0) {
/* 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++) {
/* 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_sel_offset,
NULL, hs_sel_count, NULL) < 0)
goto error;
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(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, 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, hslab_space,
H5P_DEFAULT, hslab_buf);
/* calculate the next hyperslab offset */
for (k = rank, carry = 1; k > 0 && carry;
--k) {
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(hslab_space);
/* free */
if (hslab_buf != NULL) {
HDfree(hslab_buf);
hslab_buf = NULL;
}
} /* hyperslab read */
} /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
/*-------------------------------------------------------------------------
* amount of compression used
*-------------------------------------------------------------------------
*/
if (options->verbose) {
double ratio = 0;
/* only print the compression ration if there was a filter request */
if (apply_s && apply_f && req_filter) {
/* get the storage size of the output dataset */
dsize_out = H5Dget_storage_size(dset_out);
/* compression ratio = uncompressed size / compressed size */
if (dsize_out != 0)
ratio = (double) dsize_in
/ (double) dsize_out;
print_dataset_info(dcpl_out,
travt->objs[i].name, ratio, 1);
}
else
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)
*/
if (has_filter && apply_s == 0)
printf(
" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
travt->objs[i].name,
(int) options->min_comp);
if (has_filter && apply_f == 0)
printf(
" <warning: could not apply the filter to %s>\n",
travt->objs[i].name);
} /* verbose */
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
if (copy_attr(dset_in, dset_out, &named_dt_head, travt,
options) < 0)
goto error;
/*close */
if (H5Dclose(dset_out) < 0)
goto error;
}/*!H5T_REFERENCE*/
}/*h5tools_canreadf*/
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id) < 0)
goto error;
if (H5Tclose(wtype_id) < 0)
goto error;
if (H5Pclose(dcpl_in) < 0)
goto error;
if (H5Pclose(dcpl_out) < 0)
goto error;
if (H5Sclose(f_space_id) < 0)
goto error;
if (H5Dclose(dset_in) < 0)
goto error;
}
/*-------------------------------------------------------------------------
* we do not have request for filter/chunking use H5Ocopy instead
*-------------------------------------------------------------------------
*/
else {
hid_t pid;
/* create property to pass copy options */
if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
goto error;
/* set options for object copy */
if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
goto error;
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------
*/
if (H5Ocopy(fidin, /* Source file or group identifier */
travt->objs[i].name, /* Name of the source object to be copied */
fidout, /* Destination file or group identifier */
travt->objs[i].name, /* Name of the destination object */
pid, /* Properties which apply to the copy */
H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
goto error;
/* close property */
if (H5Pclose(pid) < 0)
goto error;
/*-------------------------------------------------------------------------
* copy attrs manually
*-------------------------------------------------------------------------
*/
if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
< 0)
goto error;
if ((dset_out = H5Dopen2(fidout, travt->objs[i].name,
H5P_DEFAULT)) < 0)
goto error;
if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options)
< 0)
goto error;
if (H5Dclose(dset_in) < 0)
goto error;
if (H5Dclose(dset_out) < 0)
goto error;
if (options->verbose)
printf(FORMAT_OBJ, "dset", travt->objs[i].name);
} /* end do we have request for filter/chunking */
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_NAMED_DATATYPE
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_NAMED_DATATYPE:
if (options->verbose)
printf(FORMAT_OBJ, "type", travt->objs[i].name);
if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT))
< 0)
goto error;
/* Copy the datatype anonymously */
if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
travt, options)) < 0)
goto error;
/* Link in to group structure */
if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
if (copy_attr(type_in, type_out, &named_dt_head, travt, options)
< 0)
goto error;
if (H5Tclose(type_in) < 0)
goto error;
if (H5Tclose(type_out) < 0)
goto error;
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_LINK
* H5TRAV_TYPE_UDLINK
*
* Only handles external links; H5Lcopy will fail for other UD link types
* since we don't have creation or copy callbacks for them.
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_LINK:
case H5TRAV_TYPE_UDLINK: {
if (options->verbose)
printf(FORMAT_OBJ, "link", travt->objs[i].name);
if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name,
H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
if (options->verbose)
printf(FORMAT_OBJ, "link", travt->objs[i].name);
}
break;
default:
goto error;
} /* switch */
/* free */
if (buf != NULL) {
HDfree(buf);
buf = NULL;
}
} /* i */
/* Finalize (link) the stack of named datatypes (if any) */
named_datatype_free(&named_dt_head, 0);
return 0;
error:
H5E_BEGIN_TRY
{
H5Gclose(grp_in);
H5Gclose(grp_out);
H5Pclose(dcpl_in);
H5Pclose(gcpl_in);
H5Pclose(gcpl_out);
H5Sclose(f_space_id);
H5Dclose(dset_in);
H5Dclose(dset_out);
H5Tclose(ftype_id);
H5Tclose(wtype_id);
H5Tclose(type_in);
H5Tclose(type_out);
named_datatype_free(&named_dt_head, 1);
}H5E_END_TRY;
/* free */
if (buf != NULL)
HDfree(buf);
if (hslab_buf != NULL)
HDfree(hslab_buf);
return -1;
}
/*-------------------------------------------------------------------------
* 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) {
char strfilter[255];
#if defined (PRINT_DEBUG )
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;
HDstrcpy(strfilter, "\0");
/* get information about input filters */
if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
return;
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);
switch (filtn) {
case H5Z_FILTER_NONE:
HDstrcat(strfilter, "NONE ");
break;
case H5Z_FILTER_DEFLATE:
HDstrcat(strfilter, "GZIP ");
#if defined (PRINT_DEBUG)
{
unsigned level=cd_values[0];
sprintf(temp,"(%d)",level);
HDstrcat(strfilter,temp);
}
#endif
break;
case H5Z_FILTER_SZIP:
HDstrcat(strfilter, "SZIP ");
#if defined (PRINT_DEBUG)
{
unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
unsigned ppb=cd_values[1];
sprintf(temp,"(%d,",ppb);
HDstrcat(strfilter,temp);
if (options_mask & H5_SZIP_EC_OPTION_MASK)
HDstrcpy(temp,"EC) ");
else if (options_mask & H5_SZIP_NN_OPTION_MASK)
HDstrcpy(temp,"NN) ");
}
HDstrcat(strfilter,temp);
#endif
break;
case H5Z_FILTER_SHUFFLE:
HDstrcat(strfilter, "SHUF ");
break;
case H5Z_FILTER_FLETCHER32:
HDstrcat(strfilter, "FLET ");
break;
case H5Z_FILTER_NBIT:
HDstrcat(strfilter, "NBIT ");
break;
case H5Z_FILTER_SCALEOFFSET:
HDstrcat(strfilter, "SCALEOFFSET ");
break;
default:
HDstrcat(strfilter, "UD ");
break;
} /* switch */
}/*i*/
if (!pr)
printf(FORMAT_OBJ, "dset", objname);
else {
char str[255], temp[28];
HDstrcpy(str, "dset ");
HDstrcat(str, strfilter);
sprintf(temp, " (%.3f:1)", ratio);
HDstrcat(str, temp);
printf(FORMAT_OBJ, str, objname);
}
}
/*-------------------------------------------------------------------------
* 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
*
*-------------------------------------------------------------------------
*/
static int copy_user_block(const char *infile, const char *outfile,
hsize_t size) {
int infid = -1, outfid = -1; /* File descriptors */
int status = 0; /* Return value */
/* 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) {
status = -1;
goto done;
}
if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
status = -1;
goto done;
}
/* Copy the userblock from the input file to the output file */
while (size > 0) {
ssize_t nread, nbytes; /* # of bytes transfered, etc. */
char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
const char *wbuf; /* Pointer into buffer, for writing */
/* Read buffer from source file */
if (size > USERBLOCK_XFER_SIZE)
nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
else
nread = HDread(infid, rbuf, (size_t)size);
if (nread < 0) {
status = -1;
goto done;
} /* end if */
/* Write buffer to destination file */
/* (compensating for interrupted writes & checking for errors, etc.) */
nbytes = nread;
wbuf = rbuf;
while (nbytes > 0) {
ssize_t nwritten; /* # of bytes written */
do {
nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
} while (-1 == nwritten && EINTR == errno);
if (-1 == nwritten) { /* error */
status = -1;
goto done;
} /* end if */
HDassert(nwritten > 0);
HDassert(nwritten <= nbytes);
/* Update # of bytes left & offset in buffer */
nbytes -= nwritten;
wbuf += nwritten;
HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
} /* end while */
/* Update size of userblock left to transfer */
size = size - (hsize_t) nread;
} /* end while */
done:
if (infid > 0)
HDclose(infid);
if (outfid > 0)
HDclose(outfid);
return status;
}
/*-------------------------------------------------------------------------
* Function: print_user_block
*
* Purpose: print user block
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente
*
* Date: August, 20, 2008
*
*-------------------------------------------------------------------------
*/
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static
void print_user_block(const char *filename, hid_t fid)
{
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");
goto done;
}
if(H5Pget_userblock(fcpl, &ub_size) < 0) {
error_msg("failed to retrieve userblock size\n");
goto done;
}
if(H5Pclose(fcpl) < 0) {
error_msg("failed to close property list\n");
goto done;
}
/* open file */
if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
goto done;
}
size = ub_size;
/* 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);
for(i = 0; i < nread; i++) {
printf("%c ", rbuf[i]);
}
printf("\n");
if(nread < 0) {
goto done;
}
/* update size of userblock left to transfer */
size -= nread;
}
done:
if(fh > 0)
HDclose(fh);
return;
}
#endif
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