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a6b6b75a79
hdf5/tools/h5repack/h5repack_copy.c
Jonathan Kim a6b6b75a79 [svn-r19389] Purpose: 
Fix for Bug1896 h5repack - changing layout to COMPACT does not work

Description:
Make h5repack be able to convert a layout to COMPACT for small size dataset as default.  Also add verifying layout changes in our test script.

Tested:
 jam, amani, heiwa
2010-09-15 13:32:07 -05:00

1473 lines
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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 <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "h5repack.h"
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------
* typedefs
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* globals
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* macros
*-------------------------------------------------------------------------
*/
#define USERBLOCK_XFER_SIZE 512 /* size of buffer/# of bytes to xfer at a time when copying userblock */
/*-------------------------------------------------------------------------
* local functions
*-------------------------------------------------------------------------
*/
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
/*-------------------------------------------------------------------------
* 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)
{
/* set user block size */
if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
{
error_msg("failed to set userblock size\n");
goto out;
}
}
else
{
/* 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)
{
if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
{
error_msg("failed to set alignment\n");
goto out;
}
}
else
{
/* 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;
}
}
}
/* either use the FCPL already created or create a new one */
if(fcpl != H5P_DEFAULT)
{
/* 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;
}
}
else
{
/* 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: 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
*
*-------------------------------------------------------------------------
*/
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_id=-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 */
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 *sm_buf=NULL; /* buffer for raw data */
int has_filter; /* current object has a filter */
int req_filter; /* there was a request for a filter */
unsigned crt_order_flags; /* group creation order flag */
unsigned i;
unsigned u;
int is_ref=0;
htri_t is_named;
/*-------------------------------------------------------------------------
* 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++)
{
buf = NULL;
switch ( travt->objs[i].type )
{
case H5TRAV_TYPE_UNKNOWN:
assert(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++) {
int k;
if (strcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
for (k = 0; k < options->op_tbl->objs[u].nfilters; k++) {
if (options->op_tbl->objs[u].filter->filtn > 0) {
req_filter = 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_id = H5Dget_create_plist(dset_in)) < 0)
goto error;
if((dcpl_out = H5Pcopy(dcpl_id)) < 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;
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;
/*-------------------------------------------------------------------------
* 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_id)==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 ( nelmts*msize < 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;
}
/*-------------------------------------------------------------------------
* 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_id, H5P_DEFAULT)) < 0)
goto error;
apply_f = 0;
}
/*-------------------------------------------------------------------------
* read/write
*-------------------------------------------------------------------------
*/
if (nelmts)
{
size_t need = (size_t)(nelmts*msize); /* bytes needed */
if ( need < H5TOOLS_MALLOCSIZE )
buf = HDmalloc(need);
if (buf != NULL )
{
if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0)
goto error;
if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,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 selected elmts */
hsize_t elmtno; /*counter */
int carry; /*counter carry value */
unsigned int vl_data = 0; /*contains VL datatypes */
/* stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
hsize_t sm_nbytes; /*bytes per stripmine */
hsize_t sm_nelmts; /*elements per stripmine*/
hid_t sm_space; /*stripmine data space */
/* hyperslab info */
hsize_t hs_offset[H5S_MAX_RANK];/*starting offset */
hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */
hsize_t hs_nelmts; /*elements in request */
hsize_t zero[8]; /*vector of zeros */
int k;
/* check if we have VL data in the dataset's datatype */
if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
vl_data = TRUE;
/*
* determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
sm_nbytes = p_type_nbytes;
for (k = rank; k > 0; --k)
{
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[k - 1] = MIN(dims[k - 1], size);
sm_nbytes *= sm_size[k - 1];
assert(sm_nbytes > 0);
}
sm_buf = HDmalloc((size_t)sm_nbytes);
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
/* the stripmine loop */
memset(hs_offset, 0, sizeof hs_offset);
memset(zero, 0, sizeof zero);
for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts)
{
/* calculate the hyperslab size */
if (rank > 0)
{
for (k = 0, hs_nelmts = 1; k < rank; k++)
{
hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]);
hs_nelmts *= hs_size[k];
}
if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
goto error;
if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
goto error;
}
else
{
H5Sselect_all(f_space_id);
H5Sselect_all(sm_space);
hs_nelmts = 1;
} /* rank */
/* read/write */
if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0)
goto error;
if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0)
goto error;
/* reclaim any VL memory, if necessary */
if(vl_data)
H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf);
/* calculate the next hyperslab offset */
for (k = rank, carry = 1; k > 0 && carry; --k)
{
hs_offset[k - 1] += hs_size[k - 1];
if (hs_offset[k - 1] == dims[k - 1])
hs_offset[k - 1] = 0;
else
carry = 0;
} /* k */
} /* elmtno */
H5Sclose(sm_space);
/* free */
if (sm_buf!=NULL)
{
HDfree(sm_buf);
sm_buf=NULL;
}
} /* hyperslab read */
}/*nelmts*/
/*-------------------------------------------------------------------------
* 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_id,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_id) < 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_id);
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 (sm_buf!=NULL)
HDfree(sm_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;
strcpy(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) {
default:
break;
case H5Z_FILTER_DEFLATE:
strcat(strfilter,"GZIP ");
#if defined (PRINT_DEBUG)
{
unsigned level=cd_values[0];
sprintf(temp,"(%d)",level);
strcat(strfilter,temp);
}
#endif
break;
case H5Z_FILTER_SZIP:
strcat(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);
strcat(strfilter,temp);
if (options_mask & H5_SZIP_EC_OPTION_MASK)
strcpy(temp,"EC) ");
else if (options_mask & H5_SZIP_NN_OPTION_MASK)
strcpy(temp,"NN) ");
}
strcat(strfilter,temp);
#endif
break;
case H5Z_FILTER_SHUFFLE:
strcat(strfilter,"SHUF ");
break;
case H5Z_FILTER_FLETCHER32:
strcat(strfilter,"FLET ");
break;
case H5Z_FILTER_NBIT:
strcat(strfilter,"NBIT ");
break;
case H5Z_FILTER_SCALEOFFSET:
strcat(strfilter,"SCALEOFFSET ");
break;
} /* switch */
}/*i*/
if(!pr)
printf(FORMAT_OBJ,"dset",objname );
else
{
char str[255], temp[20];
strcpy(str,"dset ");
strcat(str,strfilter);
sprintf(temp," (%.3f:1)",ratio);
strcat(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.) */
assert(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 */
assert(nwritten > 0);
assert(nwritten <= nbytes);
/* Update # of bytes left & offset in buffer */
nbytes -= nwritten;
wbuf += nwritten;
assert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
} /* end while */
/* Update size of userblock left to transfer */
size -= 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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