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[svn-r29924] Description:

Browse Source 
Bring h5format_convert tool from revise_chunks branch to trunk.

Tested on:
    MacoSX/64 10.11.4 (amazon) w/serial, parallel & production
    (h5committest forthcoming)
This commit is contained in:
Quincey Koziol 2016-05-12 15:47:03 -05:00
parent 92806fb5e6
commit 18ad868b23
63 changed files with 5022 additions and 52 deletions
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52
MANIFEST
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@ -1240,6 +1240,57 @@
./tools/h5diff/testh5diff.sh.in
./tools/h5diff/testph5diff.sh.in
# h5format_convert sources
./tools/h5format_convert/Makefile.am
./tools/h5format_convert/h5fc_chk_idx.c
./tools/h5format_convert/h5fc_gentest.c
./tools/h5format_convert/h5format_convert.c
./tools/h5format_convert/testfiles/h5fc_v_n_all.ddl
./tools/h5format_convert/testfiles/h5fc_v_bt1.ddl
./tools/h5format_convert/testfiles/h5fc_v_non_chunked.ddl
./tools/h5format_convert/testfiles/h5fc_d_file.ddl
./tools/h5format_convert/testfiles/h5fc_v_ndata_bt1.ddl
./tools/h5format_convert/testfiles/h5fc_dname.ddl
./tools/h5format_convert/testfiles/h5fc_nonexistdset_file.ddl
./tools/h5format_convert/testfiles/h5fc_help.ddl
./tools/h5format_convert/testfiles/h5fc_v_all.ddl
./tools/h5format_convert/testfiles/h5fc_nooption.ddl
./tools/h5format_convert/testfiles/h5fc_v_n_1d.ddl
./tools/h5format_convert/testfiles/h5fc_nonexistfile.ddl
./tools/h5format_convert/testfiles/h5fc_non_v3.h5
./tools/h5format_convert/testfiles/h5fc_edge_v3.h5
./tools/h5format_convert/testfiles/h5fc_ext1_f.h5
./tools/h5format_convert/testfiles/h5fc_ext1_i.h5
./tools/h5format_convert/testfiles/h5fc_ext1_s.h5
./tools/h5format_convert/testfiles/h5fc_ext2_if.h5
./tools/h5format_convert/testfiles/h5fc_ext2_is.h5
./tools/h5format_convert/testfiles/h5fc_ext2_sf.h5
./tools/h5format_convert/testfiles/h5fc_ext3_isf.h5
./tools/h5format_convert/testfiles/h5fc_ext_none.h5
./tools/h5format_convert/testfiles/old_h5fc_ext1_f.h5
./tools/h5format_convert/testfiles/old_h5fc_ext1_i.h5
./tools/h5format_convert/testfiles/old_h5fc_ext1_s.h5
./tools/h5format_convert/testfiles/old_h5fc_ext2_if.h5
./tools/h5format_convert/testfiles/old_h5fc_ext2_is.h5
./tools/h5format_convert/testfiles/old_h5fc_ext2_sf.h5
./tools/h5format_convert/testfiles/old_h5fc_ext3_isf.h5
./tools/h5format_convert/testfiles/old_h5fc_ext_none.h5
./tools/h5format_convert/testfiles/h5fc_ext1_f.ddl
./tools/h5format_convert/testfiles/h5fc_ext1_i.ddl
./tools/h5format_convert/testfiles/h5fc_ext1_s.ddl
./tools/h5format_convert/testfiles/h5fc_ext2_if.ddl
./tools/h5format_convert/testfiles/h5fc_ext2_is.ddl
./tools/h5format_convert/testfiles/h5fc_ext2_sf.ddl
./tools/h5format_convert/testfiles/h5fc_ext3_isf.ddl
./tools/h5format_convert/testfiles/old_h5fc_ext1_f.ddl
./tools/h5format_convert/testfiles/old_h5fc_ext1_i.ddl
./tools/h5format_convert/testfiles/old_h5fc_ext1_s.ddl
./tools/h5format_convert/testfiles/old_h5fc_ext2_if.ddl
./tools/h5format_convert/testfiles/old_h5fc_ext2_is.ddl
./tools/h5format_convert/testfiles/old_h5fc_ext2_sf.ddl
./tools/h5format_convert/testfiles/old_h5fc_ext3_isf.ddl
./tools/h5format_convert/testh5fc.sh.in
# h5repack sources
./tools/h5repack/Makefile.am
./tools/h5repack/dynlib_rpk.c
@ -2956,6 +3007,7 @@
./tools/h5copy/Makefile.in
./tools/h5diff/Makefile.in
./tools/h5dump/Makefile.in
./tools/h5format_convert/Makefile.in
./tools/h5import/Makefile.in
./tools/h5jam/Makefile.in
./tools/h5ls/Makefile.in

2
configure.ac
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@ -3544,6 +3544,8 @@ AC_CONFIG_FILES([src/libhdf5.settings
tools/misc/vds/Makefile
tools/h5stat/testh5stat.sh
tools/h5stat/Makefile
tools/h5format_convert/Makefile
tools/h5format_convert/testh5fc.sh
tools/perform/Makefile
examples/Makefile
examples/run-c-ex.sh

104
src/H5D.c
View File

@ -379,7 +379,7 @@ H5Dget_space(hid_t dset_id)
done:
FUNC_LEAVE_API(ret_value)
}
} /* end H5Dget_space() */
/*-------------------------------------------------------------------------
@ -415,7 +415,7 @@ H5Dget_space_status(hid_t dset_id, H5D_space_status_t *allocation)
done:
FUNC_LEAVE_API(ret_value)
}
} /* H5Dget_space_status() */
/*-------------------------------------------------------------------------
@ -955,3 +955,103 @@ done:
FUNC_LEAVE_API(ret_value)
} /* H5Dflush */
/*-------------------------------------------------------------------------
* Function: H5Dformat_convert (Internal)
*
* Purpose: For chunked:
* Convert the chunk indexing type to version 1 B-tree if not
* For compact/contiguous:
* Downgrade layout version to 3 if greater than 3
* For virtual: no conversion
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Vailin Choi
* Feb 2015
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dformat_convert(hid_t dset_id)
{
H5D_t *dset; /* Dataset to refresh */
herr_t ret_value = SUCCEED; /* return value */
FUNC_ENTER_API(FAIL)
H5TRACE1("e", "i", dset_id);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
switch(dset->shared->layout.type) {
case H5D_CHUNKED:
/* Convert the chunk indexing type to version 1 B-tree if not */
if(dset->shared->layout.u.chunk.idx_type != H5D_CHUNK_IDX_BTREE)
if((H5D__format_convert(dset, H5AC_ind_read_dxpl_id)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTLOAD, FAIL, "unable to downgrade chunk indexing type for dataset")
break;
case H5D_CONTIGUOUS:
case H5D_COMPACT:
/* Downgrade the layout version to 3 if greater than 3 */
if(dset->shared->layout.version > H5O_LAYOUT_VERSION_DEFAULT)
if((H5D__format_convert(dset, H5AC_ind_read_dxpl_id)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTLOAD, FAIL, "unable to downgrade layout version for dataset")
break;
case H5D_VIRTUAL:
/* Nothing to do even though layout is version 4 */
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset layout type")
default:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "unknown dataset layout type")
} /* end switch */
done:
FUNC_LEAVE_API(ret_value)
} /* H5Dformat_convert */
/*-------------------------------------------------------------------------
* Function: H5Dget_chunk_index_type (Internal)
*
* Purpose: Retrieve a dataset's chunk indexing type
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Vailin Choi
* Feb 2015
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type)
{
H5D_t *dset; /* Dataset to refresh */
herr_t ret_value = SUCCEED; /* return value */
FUNC_ENTER_API(FAIL)
H5TRACE2("e", "i*Dk", did, idx_type);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(did, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
/* Should be a chunked dataset */
if(dset->shared->layout.type != H5D_CHUNKED)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not chunked")
/* Get the chunk indexing type */
if(idx_type)
*idx_type = dset->shared->layout.u.chunk.idx_type;
done:
FUNC_LEAVE_API(ret_value)
} /* H5Dget_chunk_index_type() */

142
src/H5Dchunk.c
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@ -200,6 +200,13 @@ typedef struct H5D_chunk_it_ud4_t {
uint32_t *chunk_dim; /* Chunk dimensions */
} H5D_chunk_it_ud4_t;
/* Callback info for iteration to format convert chunks */
typedef struct H5D_chunk_it_ud5_t {
H5D_chk_idx_info_t *new_idx_info; /* Dest. chunk index info object */
unsigned dset_ndims; /* Number of dimensions in dataset */
hsize_t *dset_dims; /* Dataset dimensions */
} H5D_chunk_it_ud5_t;
/* Callback info for nonexistent readvv operation */
typedef struct H5D_chunk_readvv_ud_t {
unsigned char *rbuf; /* Read buffer to initialize */
@ -250,6 +257,9 @@ H5D__nonexistent_readvv(const H5D_io_info_t *io_info,
size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]);
/* format convert cb */
static int H5D__chunk_format_convert_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
/* Helper routines */
static herr_t H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims,
const hsize_t *curr_dims, const hsize_t *max_dims);
@ -6336,3 +6346,135 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D__chunk_file_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D__chunk_format_convert_cb
*
* Purpose: Callback routine to insert chunk address into v1 B-tree
* chunk index.
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Vailin Choi
* Feb 2015
*
*-------------------------------------------------------------------------
*/
static int
H5D__chunk_format_convert_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_it_ud5_t *udata = (H5D_chunk_it_ud5_t *)_udata; /* User data */
H5D_chk_idx_info_t *new_idx_info; /* The new chunk index information */
H5D_chunk_ud_t insert_udata; /* Chunk information to be inserted */
haddr_t chunk_addr; /* Chunk address */
size_t nbytes; /* Chunk size */
void *buf = NULL; /* Pointer to buffer of chunk data */
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_STATIC
/* Set up */
new_idx_info = udata->new_idx_info;
H5_CHECKED_ASSIGN(nbytes, size_t, chunk_rec->nbytes, uint32_t);
chunk_addr = chunk_rec->chunk_addr;
if(new_idx_info->pline->nused &&
(new_idx_info->layout->flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) &&
(H5D__chunk_is_partial_edge_chunk(udata->dset_ndims, new_idx_info->layout->dim, chunk_rec->scaled, udata->dset_dims))) {
/* This is a partial non-filtered edge chunk */
/* Convert the chunk to a filtered edge chunk for v1 B-tree chunk index */
unsigned filter_mask = chunk_rec->filter_mask;
H5Z_cb_t cb_struct; /* Filter failure callback struct */
size_t read_size = nbytes; /* Bytes to read */
HDassert(read_size == new_idx_info->layout->size);
cb_struct.func = NULL; /* no callback function when failed */
/* Allocate buffer for chunk data */
if(NULL == (buf = H5MM_malloc(read_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk")
/* Read the non-filtered edge chunk */
if(H5F_block_read(new_idx_info->f, H5FD_MEM_DRAW, chunk_addr, read_size, H5AC_rawdata_dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk")
/* Pass the chunk through the pipeline */
if(H5Z_pipeline(new_idx_info->pline, 0, &filter_mask, H5Z_NO_EDC, cb_struct, &nbytes, &read_size, &buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed")
#if H5_SIZEOF_SIZE_T > 4
/* Check for the chunk expanding too much to encode in a 32-bit value */
if(nbytes > ((size_t)0xffffffff))
HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, H5_ITER_ERROR, "chunk too large for 32-bit length")
#endif /* H5_SIZEOF_SIZE_T > 4 */
/* Allocate space for the filtered chunk */
if((chunk_addr = H5MF_alloc(new_idx_info->f, H5FD_MEM_DRAW, new_idx_info->dxpl_id, (hsize_t)nbytes)) == HADDR_UNDEF)
HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, H5_ITER_ERROR, "file allocation failed for filtered chunk")
HDassert(H5F_addr_defined(chunk_addr));
/* Write the filtered chunk to disk */
if(H5F_block_write(new_idx_info->f, H5FD_MEM_DRAW, chunk_addr, nbytes, H5AC_rawdata_dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write raw data to file")
} /* end if */
/* Set up chunk information for insertion to chunk index */
insert_udata.chunk_block.offset = chunk_addr;
insert_udata.chunk_block.length = nbytes;
insert_udata.filter_mask = chunk_rec->filter_mask;
insert_udata.common.scaled = chunk_rec->scaled;
insert_udata.common.layout = new_idx_info->layout;
insert_udata.common.storage = new_idx_info->storage;
/* Insert chunk into the v1 B-tree chunk index */
if((new_idx_info->storage->ops->insert)(new_idx_info, &insert_udata, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, H5_ITER_ERROR, "unable to insert chunk addr into index")
done:
if(buf)
H5MM_xfree(buf);
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D__chunk_format_convert_cb() */
/*-------------------------------------------------------------------------
* Function: H5D__chunk_format_convert
*
* Purpose: Iterate over the chunks for the current chunk index and insert the
* the chunk addresses into v1 B-tree chunk index via callback.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Vailin Choi
* Feb 2015
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__chunk_format_convert(H5D_t *dset, H5D_chk_idx_info_t *idx_info, H5D_chk_idx_info_t *new_idx_info)
{
H5D_chunk_it_ud5_t udata; /* User data */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Check args */
HDassert(dset);
/* Set up user data */
udata.new_idx_info = new_idx_info;
udata.dset_ndims = dset->shared->ndims;
udata.dset_dims = dset->shared->curr_dims;
/* terate over the chunks in the current index and insert the chunk addresses into version 1 B-tree index */
if((dset->shared->layout.storage.u.chunk.ops->iterate)(idx_info, H5D__chunk_format_convert_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to chunk info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__chunk_format_convert() */

120
src/H5Dint.c
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@ -2830,6 +2830,126 @@ done:
FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL)
} /* end H5D__flush_real() */
/*-------------------------------------------------------------------------
* Function: H5D__format_convert
*
* Purpose: For chunked: downgrade the chunk indexing type to version 1 B-tree
* For compact/contiguous: downgrade layout version to 3
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Vailin Choi
* Feb 2015
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__format_convert(H5D_t *dataset, hid_t dxpl_id)
{
H5O_t *oh = NULL; /* Pointer to dataset's object header */
H5D_chk_idx_info_t new_idx_info; /* Index info for the new layout */
H5D_chk_idx_info_t idx_info; /* Index info for the current layout */
H5O_layout_t newlayout; /* The new layout */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE_TAG(dxpl_id, dataset->oloc.addr, FAIL)
/* Check args */
HDassert(dataset);
switch(dataset->shared->layout.type) {
case H5D_CHUNKED:
HDassert(dataset->shared->layout.u.chunk.idx_type != H5D_CHUNK_IDX_BTREE);
/* Set up the current index info */
idx_info.f = dataset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dataset->shared->dcpl_cache.pline;
idx_info.layout = &dataset->shared->layout.u.chunk;
idx_info.storage = &dataset->shared->layout.storage.u.chunk;
/* Copy the current layout info to the new layout */
HDmemcpy(&newlayout, &dataset->shared->layout, sizeof(H5O_layout_t));
/* Set up info for version 1 B-tree in the new layout */
newlayout.version = H5O_LAYOUT_VERSION_3;
newlayout.storage.u.chunk.idx_type = H5D_CHUNK_IDX_BTREE;
newlayout.storage.u.chunk.idx_addr = HADDR_UNDEF;
newlayout.storage.u.chunk.ops = H5D_COPS_BTREE;
newlayout.storage.u.chunk.u.btree.shared = NULL;
/* Set up the index info to version 1 B-tree */
new_idx_info.f = dataset->oloc.file;
new_idx_info.dxpl_id = dxpl_id;
new_idx_info.pline = &dataset->shared->dcpl_cache.pline;
new_idx_info.layout = &newlayout.u.chunk;
new_idx_info.storage = &newlayout.storage.u.chunk;
/* Initialize version 1 B-tree */
if(newlayout.storage.u.chunk.ops->init && (newlayout.storage.u.chunk.ops->init)(&new_idx_info, dataset->shared->space, dataset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information")
/* If the current chunk index exists */
if(H5F_addr_defined(dataset->shared->layout.storage.u.chunk.idx_addr)) {
/* Create v1 B-tree chunk index */
if((newlayout.storage.u.chunk.ops->create)(&new_idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create chunk index")
/* Iterate over the chunks in the current index and insert the chunk addresses
* into the version 1 B-tree chunk index */
if(H5D__chunk_format_convert(dataset, &idx_info, &new_idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to chunk info")
} /* end if */
/* Release the old (i.e. current) chunk index */
if(dataset->shared->layout.storage.u.chunk.ops->dest && (dataset->shared->layout.storage.u.chunk.ops->dest)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
/* Delete the "layout" message */
if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, TRUE, dxpl_id) < 0)
HGOTO_ERROR(H5E_SYM, H5E_CANTDELETE, FAIL, "unable to delete layout message")
HDmemcpy(&dataset->shared->layout, &newlayout, sizeof(H5O_layout_t));
if(NULL == (oh = H5O_pin(&dataset->oloc, dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header")
/* Append the new layout message to the object header */
if(H5O_msg_append_oh(dataset->oloc.file, dxpl_id, oh, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &newlayout) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update old fill value header message")
break;
case H5D_CONTIGUOUS:
case H5D_COMPACT:
HDassert(dataset->shared->layout.version > H5O_LAYOUT_VERSION_DEFAULT);
dataset->shared->layout.version = H5O_LAYOUT_VERSION_DEFAULT;
if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), dxpl_id) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message")
break;
case H5D_VIRTUAL:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "virtual dataset layout not supported")
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset layout type")
default:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "unknown dataset layout type")
} /* end switch */
done:
/* Release pointer to object header */
if(oh != NULL)
if(H5O_unpin(oh) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header")
FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL)
} /* end H5D__format_convert() */
/*-------------------------------------------------------------------------
* Function: H5D__mark

4
src/H5Dpkg.h
View File

@ -583,6 +583,9 @@ H5_DLL herr_t H5D__mark(const H5D_t *dataset, hid_t dxpl_id, unsigned flags);
H5_DLL herr_t H5D_set_io_info_dxpls(H5D_io_info_t *io_info, hid_t dxpl_id);
#endif /* H5_DEBUG_BUILD */
/* To convert a dataset's chunk indexing type to v1 B-tree */
H5_DLL herr_t H5D__format_convert(H5D_t *dataset, hid_t dxpl_id);
/* Internal I/O routines */
H5_DLL herr_t H5D__read(H5D_t *dataset, hid_t mem_type_id,
const H5S_t *mem_space, const H5S_t *file_space, hid_t dset_xfer_plist,
@ -675,6 +678,7 @@ H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t
#ifdef H5D_CHUNK_DEBUG
H5_DLL herr_t H5D__chunk_stats(const H5D_t *dset, hbool_t headers);
#endif /* H5D_CHUNK_DEBUG */
H5_DLL herr_t H5D__chunk_format_convert(H5D_t *dset, H5D_chk_idx_info_t *idx_info, H5D_chk_idx_info_t *new_idx_info);
/* Functions that operate on compact dataset storage */
H5_DLL herr_t H5D__compact_fill(const H5D_t *dset, hid_t dxpl_id);

4
src/H5Dpublic.h
View File

@ -167,6 +167,10 @@ H5_DLL herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id,
size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data);
H5_DLL herr_t H5Ddebug(hid_t dset_id);
/* Internal API routines */
H5_DLL herr_t H5Dformat_convert(hid_t dset_id);
H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
/* Symbols defined for compatibility with previous versions of the HDF5 API.
*
* Use of these symbols is deprecated.

70
src/H5F.c
View File

@ -1442,3 +1442,73 @@ done:
FUNC_LEAVE_API(ret_value)
} /* end H5Fclear_elink_file_cache() */
/*-------------------------------------------------------------------------
* Function: H5Fformat_convert_super (Internal)
*
* Purpose: Downgrade the superblock version to v2 and
* downgrade persistent file space to non-persistent
* for 1.8 library.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Vailin Choi
* Jan 2016
*
*-------------------------------------------------------------------------
*/
herr_t
H5Fformat_convert(hid_t fid)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE1("e", "i", fid);
if(H5I_FILE == H5I_get_type(fid)) {
H5F_t *f; /* File to flush */
hbool_t mark_dirty = FALSE;
/* Get file object */
if(NULL == (f = (H5F_t *)H5I_object(fid)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid file identifier")
/* Check if the superblock should be downgraded */
if(f->shared->sblock->super_vers > HDF5_SUPERBLOCK_VERSION_V18_LATEST) {
f->shared->sblock->super_vers = HDF5_SUPERBLOCK_VERSION_V18_LATEST;
mark_dirty = TRUE;
} /* end if */
/* Check for persistent freespace manager, which needs to be downgraded */
if(!(f->shared->fs_strategy == H5F_FILE_SPACE_STRATEGY_DEF &&
f->shared->fs_threshold == H5F_FREE_SPACE_THRESHOLD_DEF)) {
/* Check to remove free-space manager info message from superblock extension */
if(H5F_addr_defined(f->shared->sblock->ext_addr))
if(H5F_super_ext_remove_msg(f, H5AC_ind_read_dxpl_id, H5O_FSINFO_ID) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTRELEASE, FAIL, "error in removing message from superblock extension")
/* Close freespace manager */
if(H5MF_try_close(f, H5AC_ind_read_dxpl_id) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTRELEASE, FAIL, "unable to free free-space address")
/* Set non-persistent freespace manager */
f->shared->fs_strategy = H5F_FILE_SPACE_STRATEGY_DEF;
f->shared->fs_threshold = H5F_FREE_SPACE_THRESHOLD_DEF;
/* Indicate that the superblock should be marked dirty */
mark_dirty = TRUE;
} /* end if */
/* Check if we should mark the superblock dirty */
if(mark_dirty)
/* Mark superblock as dirty */
if(H5F_super_dirty(f) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTMARKDIRTY, FAIL, "unable to mark superblock as dirty")
} /* end if */
else
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file or file object")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Fformat_convert() */

1
src/H5Fprivate.h
View File

@ -484,6 +484,7 @@
#define HDF5_SUPERBLOCK_VERSION_1 1 /* Version with non-default B-tree 'K' value */
#define HDF5_SUPERBLOCK_VERSION_2 2 /* Revised version with superblock extension and checksum */
#define HDF5_SUPERBLOCK_VERSION_LATEST HDF5_SUPERBLOCK_VERSION_2 /* The maximum super block format */
#define HDF5_SUPERBLOCK_VERSION_V18_LATEST HDF5_SUPERBLOCK_VERSION_2 /* The latest superblock version for v18 */
#define HDF5_FREESPACE_VERSION 0 /* of the Free-Space Info */
#define HDF5_OBJECTDIR_VERSION 0 /* of the Object Directory format */
#define HDF5_SHAREDHEADER_VERSION 0 /* of the Shared-Header Info */

1
src/H5Fpublic.h
View File

@ -219,6 +219,7 @@ H5_DLL herr_t H5Fget_info2(hid_t obj_id, H5F_info2_t *finfo);
H5_DLL ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type,
size_t nsects, H5F_sect_info_t *sect_info/*out*/);
H5_DLL herr_t H5Fclear_elink_file_cache(hid_t file_id);
H5_DLL herr_t H5Fformat_convert(hid_t fid);
#ifdef H5_HAVE_PARALLEL
H5_DLL herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag);
H5_DLL herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag);

188
src/H5MF.c
View File

@ -86,6 +86,7 @@ typedef struct {
/* Allocator routines */
static herr_t H5MF_alloc_create(H5F_t *f, hid_t dxpl_id, H5FD_mem_t type);
static herr_t H5MF_alloc_close(H5F_t *f, hid_t dxpl_id, H5FD_mem_t type);
static herr_t H5MF__close_delete(H5F_t *f, hid_t dxpl_id);
/*********************/
@ -1145,6 +1146,141 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5MF_close_shrink_eoa() */
/*-------------------------------------------------------------------------
* Function: H5MF__close_delete
*
* Purpose: Common code for closing and deleting freespace managers from
* the file.
*
* Return: SUCCEED/FAIL
*
* Programmer: Vailin Choi
* Jan 2016
*
*-------------------------------------------------------------------------
*/
static herr_t
H5MF__close_delete(H5F_t *f, hid_t dxpl_id)
{
H5FD_mem_t type; /* Memory type for iteration */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
#ifdef H5MF_ALLOC_DEBUG
HDfprintf(stderr, "%s: Entering\n", FUNC);
#endif /* H5MF_ALLOC_DEBUG */
/* check args */
HDassert(f);
HDassert(f->shared);
/* Iterate over all the free space types that have managers and get each free list's space */
for(type = H5FD_MEM_DEFAULT; type < H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t, type)) {
#ifdef H5MF_ALLOC_DEBUG_MORE
HDfprintf(stderr, "%s: Check 1.0 - f->shared->fs_man[%u] = %p, f->shared->fs_addr[%u] = %a\n", FUNC, (unsigned)type, f->shared->fs_man[type], (unsigned)type, f->shared->fs_addr[type]);
#endif /* H5MF_ALLOC_DEBUG_MORE */
/* If the free space manager for this type is open, close it */
if(f->shared->fs_man[type]) {
#ifdef H5MF_ALLOC_DEBUG_MORE
HDfprintf(stderr, "%s: Before closing free space manager\n", FUNC);
#endif /* H5MF_ALLOC_DEBUG_MORE */
if(H5FS_close(f, dxpl_id, f->shared->fs_man[type]) < 0)
HGOTO_ERROR(H5E_FSPACE, H5E_CANTRELEASE, FAIL, "can't release free space info")
f->shared->fs_man[type] = NULL;
f->shared->fs_state[type] = H5F_FS_STATE_CLOSED;
} /* end if */
#ifdef H5MF_ALLOC_DEBUG_MORE
HDfprintf(stderr, "%s: Check 2.0 - f->shared->fs_man[%u] = %p, f->shared->fs_addr[%u] = %a\n", FUNC, (unsigned)type, f->shared->fs_man[type], (unsigned)type, f->shared->fs_addr[type]);
#endif /* H5MF_ALLOC_DEBUG_MORE */
/* If there is free space manager info for this type, delete it */
if(H5F_addr_defined(f->shared->fs_addr[type])) {
haddr_t tmp_fs_addr; /* Temporary holder for free space manager address */
/* Put address into temporary variable and reset it */
/* (Avoids loopback in file space freeing routine) */
tmp_fs_addr = f->shared->fs_addr[type];
f->shared->fs_addr[type] = HADDR_UNDEF;
/* Shift to "deleting" state, to make certain we don't track any
* file space freed as a result of deleting the free space manager.
*/
f->shared->fs_state[type] = H5F_FS_STATE_DELETING;
#ifdef H5MF_ALLOC_DEBUG_MORE
HDfprintf(stderr, "%s: Before deleting free space manager\n", FUNC);
#endif /* H5MF_ALLOC_DEBUG_MORE */
/* Delete free space manager for this type */
if(H5FS_delete(f, dxpl_id, tmp_fs_addr) < 0)
HGOTO_ERROR(H5E_FSPACE, H5E_CANTFREE, FAIL, "can't delete free space manager")
/* Shift [back] to closed state */
HDassert(f->shared->fs_state[type] == H5F_FS_STATE_DELETING);
f->shared->fs_state[type] = H5F_FS_STATE_CLOSED;
/* Sanity check that the free space manager for this type wasn't started up again */
HDassert(!H5F_addr_defined(f->shared->fs_addr[type]));
} /* end if */
} /* end for */
done:
#ifdef H5MF_ALLOC_DEBUG
HDfprintf(stderr, "%s: Leaving\n", FUNC);
#endif /* H5MF_ALLOC_DEBUG */
FUNC_LEAVE_NOAPI(ret_value)
} /* H5MF__close_delete() */
/*-------------------------------------------------------------------------
* Function: H5MF_try_close
*
* Purpose: This is called by H5Fformat_convert() to close and delete
* free-space managers when downgrading persistent free-space
* to non-persistent.
*
* Return: SUCCEED/FAIL
*
* Programmer: Vailin Choi
* Jan 2016
*
*-------------------------------------------------------------------------
*/
herr_t
H5MF_try_close(H5F_t *f, hid_t dxpl_id)
{
H5P_genplist_t *dxpl = NULL; /* DXPL for setting ring */
H5AC_ring_t orig_ring = H5AC_RING_INV; /* Original ring value */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
#ifdef H5MF_ALLOC_DEBUG
HDfprintf(stderr, "%s: Entering\n", FUNC);
#endif /* H5MF_ALLOC_DEBUG */
/* check args */
HDassert(f);
/* Set the ring type in the DXPL */
if(H5AC_set_ring(dxpl_id, H5AC_RING_FSM, &dxpl, &orig_ring) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTSET, FAIL, "unable to set ring value")
/* Close and delete freespace managers from the file */
if(H5MF__close_delete(f, dxpl_id) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTSET, FAIL, "unable to close delete free-space managers")
done:
/* Reset the ring in the DXPL */
if(H5AC_reset_ring(dxpl, orig_ring) < 0)
HDONE_ERROR(H5E_RESOURCE, H5E_CANTSET, FAIL, "unable to set property value")
#ifdef H5MF_ALLOC_DEBUG
HDfprintf(stderr, "%s: Leaving\n", FUNC);
#endif /* H5MF_ALLOC_DEBUG */
FUNC_LEAVE_NOAPI(ret_value)
} /* H5MF_try_close() */
/*-------------------------------------------------------------------------
* Function: H5MF_close
@ -1287,55 +1423,9 @@ HDfprintf(stderr, "%s: Entering\n", FUNC);
} /* end for */
} /* end if */
else { /* super_vers can be 0, 1, 2 */
/* Iterate over all the free space types that have managers and get each free list's space */
for(type = H5FD_MEM_DEFAULT; type < H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t, type)) {
#ifdef H5MF_ALLOC_DEBUG_MORE
HDfprintf(stderr, "%s: Check 1.0 - f->shared->fs_man[%u] = %p, f->shared->fs_addr[%u] = %a\n", FUNC, (unsigned)type, f->shared->fs_man[type], (unsigned)type, f->shared->fs_addr[type]);
#endif /* H5MF_ALLOC_DEBUG_MORE */
/* If the free space manager for this type is open, close it */
if(f->shared->fs_man[type]) {
#ifdef H5MF_ALLOC_DEBUG_MORE
HDfprintf(stderr, "%s: Before closing free space manager\n", FUNC);
#endif /* H5MF_ALLOC_DEBUG_MORE */
if(H5FS_close(f, dxpl_id, f->shared->fs_man[type]) < 0)
HGOTO_ERROR(H5E_FSPACE, H5E_CANTRELEASE, FAIL, "can't release free space info")
f->shared->fs_man[type] = NULL;
f->shared->fs_state[type] = H5F_FS_STATE_CLOSED;
} /* end if */
#ifdef H5MF_ALLOC_DEBUG_MORE
HDfprintf(stderr, "%s: Check 2.0 - f->shared->fs_man[%u] = %p, f->shared->fs_addr[%u] = %a\n", FUNC, (unsigned)type, f->shared->fs_man[type], (unsigned)type, f->shared->fs_addr[type]);
#endif /* H5MF_ALLOC_DEBUG_MORE */
/* If there is free space manager info for this type, delete it */
if(H5F_addr_defined(f->shared->fs_addr[type])) {
haddr_t tmp_fs_addr; /* Temporary holder for free space manager address */
/* Put address into temporary variable and reset it */
/* (Avoids loopback in file space freeing routine) */
tmp_fs_addr = f->shared->fs_addr[type];
f->shared->fs_addr[type] = HADDR_UNDEF;
/* Shift to "deleting" state, to make certain we don't track any
* file space freed as a result of deleting the free space manager.
*/
f->shared->fs_state[type] = H5F_FS_STATE_DELETING;
#ifdef H5MF_ALLOC_DEBUG_MORE
HDfprintf(stderr, "%s: Before deleting free space manager\n", FUNC);
#endif /* H5MF_ALLOC_DEBUG_MORE */
/* Delete free space manager for this type */
if(H5FS_delete(f, dxpl_id, tmp_fs_addr) < 0)
HGOTO_ERROR(H5E_FSPACE, H5E_CANTFREE, FAIL, "can't delete free space manager")
/* Shift [back] to closed state */
HDassert(f->shared->fs_state[type] == H5F_FS_STATE_DELETING);
f->shared->fs_state[type] = H5F_FS_STATE_CLOSED;
/* Sanity check that the free space manager for this type wasn't started up again */
HDassert(!H5F_addr_defined(f->shared->fs_addr[type]));
} /* end if */
} /* end for */
/* Close and delete freespace managers from the file */
if(H5MF__close_delete(f, dxpl_id) < 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't initialize file free space")
} /* end else */
/* Free the space in aggregators (again) */

1
src/H5MFprivate.h
View File

@ -54,6 +54,7 @@ H5_DLL herr_t H5MF_init_merge_flags(H5F_t *f);
H5_DLL herr_t H5MF_get_freespace(H5F_t *f, hid_t dxpl_id, hsize_t *tot_space,
hsize_t *meta_size);
H5_DLL herr_t H5MF_close(H5F_t *f, hid_t dxpl_id);
H5_DLL herr_t H5MF_try_close(H5F_t *f, hid_t dxpl_id);
/* File space allocation routines */
H5_DLL haddr_t H5MF_alloc(H5F_t *f, H5FD_mem_t type, hid_t dxpl_id, hsize_t size);

2
tools/Makefile.am
View File

@ -25,6 +25,6 @@ CONFIG=ordered
# All subdirectories
SUBDIRS=lib h5diff h5ls h5dump misc h5import h5repack h5jam h5copy h5stat \
perform
h5format_convert perform
include $(top_srcdir)/config/conclude.am

49
tools/h5format_convert/Makefile.am Normal file
View File

@ -0,0 +1,49 @@
#
# 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.
##
## Makefile.am
## Run automake to generate a Makefile.in from this file.
#
# HDF5 Library Makefile(.in)
#
include $(top_srcdir)/config/commence.am
# Include src directory
AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
#test script and program
TEST_PROG=h5fc_gentest
TEST_SCRIPT=testh5fc.sh
check_PROGRAMS=$(TEST_PROG) h5fc_chk_idx
check_SCRIPTS=$(TEST_SCRIPT)
SCRIPT_DEPEND=h5format_convert$(EXEEXT)
# These are our main targets, the tools
bin_PROGRAMS=h5format_convert
# Add h5format_convert specific linker flags here
h5format_convert_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
# Tell automake to clean h5redeploy script
CHECK_CLEANFILES+=*.h5
# These were generated by configure. Remove them only when distclean.
DISTCLEANFILES=testh5fc.sh
# All programs rely on hdf5 library and h5tools library
LDADD=$(LIBH5TOOLS) $(LIBHDF5)
include $(top_srcdir)/config/conclude.am

1502
tools/h5format_convert/Makefile.in Normal file
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File diff suppressed because it is too large Load Diff

103
tools/h5format_convert/h5fc_chk_idx.c Normal file
View File

@ -0,0 +1,103 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* A program to verify that the chunk indexing type of a dataset in a file
* is version 1 B-tree.
* This is to support the testing of the tool "h5format_convert".
*/
#include "hdf5.h"
#include "H5private.h"
#include "h5tools.h"
static void usage(void);
static void
usage(void)
{
HDfprintf(stdout, "Usage: h5fc_chk_idx file_name dataset_pathname\n");
} /* usage() */
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: To check that the chunk indexing type for the dataset in
* the file is version 1 B-tree.
*
* Return: 0 -- the indexing type is version 1 B-tree
* 1 -- otherwise
*
*-------------------------------------------------------------------------
*/
int
main(int argc, char *argv[])
{
char *fname = NULL;
char *dname = NULL;
hid_t fid = -1;
hid_t did = -1;
H5D_chunk_index_t idx_type;
/* h5fc_chk_idx fname dname */
if(argc != 3) {
usage();
HDexit(EXIT_FAILURE);
} /* end if */
/* Duplicate the file name & dataset name */
fname = HDstrdup(argv[1]);
dname = HDstrdup(argv[2]);
/* Try opening the file */
if((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0) {
HDfprintf(stderr, "h5fc_chk_idx: unable to open the file\n");
HDexit(EXIT_FAILURE);
} /* end if */
/* Open the dataset */
if((did = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0) {
HDfprintf(stderr, "h5fc_chk_idx: unable to open the dataset\n");
HDexit(EXIT_FAILURE);
} /* end if */
/* Get the dataset's chunk indexing type */
if(H5Dget_chunk_index_type(did, &idx_type) < 0) {
HDfprintf(stderr, "h5fc_chk_idx: unable to get chunk index type for the dataset\n");
HDexit(EXIT_FAILURE);
} /* end if */
/* Close the dataset */
if(H5Dclose(did) < 0) {
HDfprintf(stderr, "h5fc_chk_idx: unable to close the dataset\n");
HDexit(EXIT_FAILURE);
} /* end if */
/* Close the file */
if(H5Fclose(fid) < 0) {
HDfprintf(stderr, "h5fc_chk_idx_type: cannot close the file\n");
HDexit(EXIT_FAILURE);
} /* end if */
/* Return success when the chunk indexing type is version 1 B-tree */
if(idx_type == H5D_CHUNK_IDX_BTREE)
HDexit(EXIT_SUCCESS);
else {
HDfprintf(stderr, "Error: chunk indexing type is %d\n", idx_type);
HDexit(EXIT_FAILURE);
} /* end if */
} /* main() */

661
tools/h5format_convert/h5fc_gentest.c Normal file
View File

@ -0,0 +1,661 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Generate the binary hdf5 files for the h5format_convert tests.
* Usage: just execute the program without any arguments will
* generate all the binary hdf5 files
*
* If you regenerate the test files (e.g., changing some code,
* trying it on a new platform, ...), you need to verify the correctness
* of the expected output and update the corresponding *.ddl files.
*/
#include "hdf5.h"
#include "H5private.h"
#define NON_V3_FILE "h5fc_non_v3.h5"
#define EDGE_V3_FILE "h5fc_edge_v3.h5"
const char *FILENAME[] = {
"h5fc_ext1_i.h5", /* 0 */
"h5fc_ext1_s.h5", /* 1 */
"h5fc_ext1_f.h5", /* 2 */
"h5fc_ext2_is.h5", /* 3 */
"h5fc_ext2_if.h5", /* 4 */
"h5fc_ext2_sf.h5", /* 5 */
"h5fc_ext3_isf.h5", /* 6 */
"h5fc_ext_none.h5", /* 7 */
NULL
};
#define GROUP "GROUP"
#define DSET_COMPACT "DSET_COMPACT"
#define DSET_CONTIGUOUS "DSET_CONTIGUOUS"
#define DSET_EA "DSET_EA"
#define DSET_NDATA_EA "DSET_NDATA_EA"
#define DSET_BT2 "DSET_BT2"
#define DSET_NDATA_BT2 "DSET_NDATA_BT2"
#define DSET_FA "DSET_FA"
#define DSET_NDATA_FA "DSET_NDATA_FA"
#define DSET_NONE "DSET_NONE"
#define DSET_NDATA_NONE "DSET_NDATA_NONE"
#define DSET_EDGE "DSET_EDGE"
#define ISTORE_IK 64
/*
* Function: gen_non()
*
* Create empty file with latest-format--this will result in v3 superbock
* Close and re-open file with non-latest-format--v3 superblock will result in latest version support:
* 1) 1 chunked dataset with extensible array chunk indexing type (without data)
* 2) 1 chunked dataset with version 2 B-tree chunk indexing type (with data)
* Re-open the file with write+non-latest-format and create:
* 3) 1 chunked dataset with version 2 B-tree chunk indexing type (without data)
* 4) 1 chunked dataset with extensible array indexing type (with data)
* 5) 1 compact and 1 contiguous datasets
*/
static void
gen_non(const char *fname)
{
hid_t fid = -1; /* file id */
hid_t fcpl = -1; /* file creation property list */
hid_t fapl = -1; /* file access property list */
hid_t gid = -1; /* group id */
hid_t sid = -1; /* space id */
hid_t dcpl = -1; /* dataset creation property id */
hid_t did1 = -1, did2 = -1; /* dataset id */
hsize_t dims1[1] = {10}; /* dataset dimension */
hsize_t dims2[2] = {4, 6}; /* dataset dimension */
hsize_t max_dims[2]; /* maximum dataset dimension */
hsize_t c_dims[2] = {2, 3}; /* chunk dimension */
int i; /* local index variable */
int buf[24]; /* data buffer */
if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
goto error;
if(H5Pset_shared_mesg_nindexes(fcpl, 4) < 0)
goto error;
if(H5Pset_istore_k(fcpl, 64) < 0)
goto error;
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
goto error;
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
goto error;
/* Create an empty file with latest-format */
if((fid = H5Fcreate(fname, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
goto error;
/* Create a group */
if((gid = H5Gcreate2(fid, GROUP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Create data */
for(i = 0; i < 24; i++)
buf[i] = i;
/* Set chunk */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
goto error;
if(H5Pset_chunk(dcpl, 2, c_dims) < 0)
goto error;
/*
* Create a chunked dataset with extensible array chunk indexing type (without data)
*/
/* Create dataspace */
max_dims[0] = 10;
max_dims[1] = H5S_UNLIMITED;
if((sid = H5Screate_simple(2, dims2, max_dims)) < 0)
goto error;
/* Create the dataset */
if((did1 = H5Dcreate2(fid, DSET_NDATA_EA, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Closing */
if(H5Sclose(sid) < 0)
goto error;
if(H5Dclose(did1) < 0)
goto error;
/*
* Create a chunked dataset with version 2 B-tree chunk indexing type (with data)
*/
/* Create dataspace */
max_dims[0] = 10;
max_dims[0] = H5S_UNLIMITED;
max_dims[1] = H5S_UNLIMITED;
if((sid = H5Screate_simple(2, dims2, max_dims)) < 0)
goto error;
/* Create the dataset */
if((did1 = H5Dcreate2(gid, DSET_BT2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Write to the dataset */
if(H5Dwrite(did1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/* Closing */
if(H5Sclose(sid) < 0)
goto error;
if(H5Dclose(did1) < 0)
goto error;
if(H5Pclose(dcpl) < 0)
goto error;
if(H5Gclose(gid) < 0)
goto error;
/* Open the group */
if((gid = H5Gopen2(fid, GROUP, H5P_DEFAULT)) < 0)
goto error;
/*
* Create a dataset with version 2 B-btree chunk indexing type (without data)
*/
/* Set chunk */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
goto error;
if(H5Pset_chunk(dcpl, 2, c_dims) < 0)
goto error;
/* Create dataspace */
max_dims[0] = H5S_UNLIMITED;
max_dims[1] = H5S_UNLIMITED;
if((sid = H5Screate_simple(2, dims2, max_dims)) < 0)
goto error;
/* Create the dataset */
if((did1 = H5Dcreate2(fid, DSET_NDATA_BT2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Close the dataspace */
if(H5Sclose(sid) < 0)
goto error;
/*
* Create a dataset with extensible array chunk indexing type (with data) in the group
*/
/* Create dataspace */
max_dims[0] = 10;
max_dims[1] = H5S_UNLIMITED;
if((sid = H5Screate_simple(2, dims2, max_dims)) < 0)
goto error;
/* Create the dataset */
if((did2 = H5Dcreate2(gid, DSET_EA, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Write to the dataset */
if(H5Dwrite(did2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/* Closing */
if(H5Sclose(sid) < 0)
goto error;
if(H5Pclose(dcpl) < 0)
goto error;
if(H5Dclose(did1) < 0)
goto error;
if(H5Dclose(did2) < 0)
goto error;
/*
* Create a compact dataset in the group
*/
/* Create dataspace */
if((sid = H5Screate_simple(1, dims1, NULL)) < 0)
goto error;
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
goto error;
if(H5Pset_layout(dcpl, H5D_COMPACT) < 0)
goto error;
/* Create the dataset */
if((did1 = H5Dcreate2(gid, DSET_COMPACT, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Closing */
if(H5Dclose(did1) < 0)
goto error;
if(H5Pclose(dcpl) < 0)
goto error;
if(H5Sclose(sid) < 0)
goto error;
/*
* Create a contiguous dataset with (2d with data) in the file
*/
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
goto error;
if(H5Pset_layout(dcpl, H5D_CONTIGUOUS) < 0)
goto error;
if((sid = H5Screate_simple(2, dims2, NULL)) < 0)
goto error;
/* Create the dataset */
if((did2 = H5Dcreate2(fid, DSET_CONTIGUOUS, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Write to the dataset */
if(H5Dwrite(did2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/* Closing */
if(H5Dclose(did2) < 0)
goto error;
if(H5Pclose(dcpl) < 0)
goto error;
if(H5Sclose(sid) < 0)
goto error;
if(H5Gclose(gid) < 0)
goto error;
if(H5Pclose(fcpl) < 0)
goto error;
if(H5Pclose(fapl) < 0)
goto error;
if(H5Fclose(fid) < 0)
goto error;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Sclose(sid);
H5Dclose(did1);
H5Dclose(did2);
H5Gclose(gid);
H5Fclose(fcpl);
H5Fclose(fapl);
H5Fclose(fid);
} H5E_END_TRY;
} /* gen_non() */
/*
* Function: gen_edge()
*
* Create a file with write+latest-format--this will result in v3 superblock+latest version support:
* A dataset: chunked, filtered, H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS enabled
* (i.e. the dataset does not filter partial edge chunks)
*/
static void
gen_edge(const char *fname)
{
hid_t fid = -1; /* file id */
hid_t fapl = -1; /* file access property list */
hid_t sid = -1; /* dataspace id */
hid_t dcpl = -1; /* dataset creation property id */
hid_t did = -1; /* dataset id */
hsize_t dims2[2] = {12, 6}; /* Dataset dimensions */
hsize_t c_dims[2] = {5, 5}; /* Chunk dimensions */
float buf[12][6]; /* Buffer for writing data */
int i, j; /* local index variable */
/* Create a new format file */
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
goto error;
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
goto error;
if((fid = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
goto error;
/* Set chunk, filter, no-filter-edge-chunk */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
goto error;
if(H5Pset_chunk(dcpl, 2, c_dims) < 0)
goto error;
if(H5Pset_deflate(dcpl, 9) < 0)
goto error;
if(H5Pset_chunk_opts(dcpl, H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS) < 0)
goto error;
/* Create dataspace */
if((sid = H5Screate_simple(2, dims2, NULL)) < 0)
goto error;
/* Create the dataset */
if((did = H5Dcreate2(fid, DSET_EDGE, H5T_NATIVE_FLOAT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Create data */
for (i = 0; i< 12; i++)
for (j = 0; j< 6; j++)
buf[i][j] = 100.0F;
/* Write to the dataset */
if(H5Dwrite(did, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/* Closing */
if(H5Pclose(dcpl) < 0)
goto error;
if(H5Sclose(sid) < 0)
goto error;
if(H5Dclose(did) < 0)
goto error;
if(H5Pclose(fapl) < 0)
goto error;
if(H5Fclose(fid) < 0)
goto error;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Sclose(sid);
H5Dclose(did);
H5Fclose(fid);
H5Pclose(fapl);
} H5E_END_TRY;
} /* gen_edge() */
/*
* Function: gen_ext()
*
* Create a file with/without latest format with:
* 1) 1 contiguous dataset (without data)
* 2) 2 chunked datasets with extensible array chunk indexing type (with/without data)
* 3) 2 chunked datasets with version 2 B-tree chunk indexing type (with/without data)
* 4) 2 chunked datasets with fixed array chunk indexing type (with/without data)
* 5) 2 chunked datasets with implicit array chunk indexing type (with/without data)
* It will create the file with/without messages in the superblock extension depending
* on the parameter "what".
*/
static void
gen_ext(const char *fname, unsigned latest, unsigned what)
{
hid_t fid = -1; /* file id */
hid_t fapl = -1; /* file access property list */
hid_t fcpl = -1; /* file creation property list */
hid_t gid = -1; /* group id */
hid_t sid = -1; /* space id */
hid_t dcpl = -1; /* dataset creation property id */
hid_t did1 = -1, did2 = -1; /* dataset id */
hsize_t dims1[1] = {10}; /* dataset dimension */
hsize_t dims2[2] = {4, 6}; /* dataset dimension */
hsize_t max_dims[2]; /* maximum dataset dimension */
hsize_t c_dims[2] = {2, 3}; /* chunk dimension */
int i; /* local index variable */
int buf[24]; /* data buffer */
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
goto error;
if(latest)
/* Create a new format file */
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
goto error;
/* Create a file creation property list */
fcpl = H5Pcreate(H5P_FILE_CREATE);
/* Generate messages that might be placed in superblock extension */
switch(what) {
case 0:
H5Pset_istore_k(fcpl, ISTORE_IK);
break;
case 1:
H5Pset_shared_mesg_nindexes(fcpl, 4);
break;
case 2:
H5Pset_file_space(fcpl, H5F_FILE_SPACE_ALL_PERSIST, (hsize_t)0);
break;
case 3:
H5Pset_istore_k(fcpl, ISTORE_IK);
H5Pset_shared_mesg_nindexes(fcpl, 4);
break;
case 4:
H5Pset_istore_k(fcpl, ISTORE_IK);
H5Pset_file_space(fcpl, H5F_FILE_SPACE_DEFAULT, (hsize_t)2);
break;
case 5:
H5Pset_shared_mesg_nindexes(fcpl, 4);
H5Pset_file_space(fcpl, H5F_FILE_SPACE_VFD, (hsize_t)0);
break;
case 6:
H5Pset_istore_k(fcpl, ISTORE_IK);
H5Pset_shared_mesg_nindexes(fcpl, 4);
H5Pset_file_space(fcpl, H5F_FILE_SPACE_AGGR_VFD, (hsize_t)0);
break;
default:
break;
}
/* Create the file */
if((fid = H5Fcreate(fname, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
goto error;
/* Create a group */
if((gid = H5Gcreate2(fid, GROUP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Set chunk */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
goto error;
if(H5Pset_chunk(dcpl, 2, c_dims) < 0)
goto error;
/*
* Create a contiguous dataset
*/
/* Create dataspace */
if((sid = H5Screate_simple(1, dims1, NULL)) < 0)
goto error;
/* Create the dataset */
if((did1 = H5Dcreate2(fid, DSET_CONTIGUOUS, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Closing */
if(H5Sclose(sid) < 0)
goto error;
if(H5Dclose(did1) < 0)
goto error;
/*
* Create 2 chunked datasets with extensible array chunk indexing type
* (one with data; one without data)
*/
/* Create dataspace */
max_dims[0] = 10;
max_dims[1] = H5S_UNLIMITED;
if((sid = H5Screate_simple(2, dims2, max_dims)) < 0)
goto error;
/* Create the 2 datasets */
if((did1 = H5Dcreate2(gid, DSET_NDATA_EA, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
if((did2 = H5Dcreate2(fid, DSET_EA, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Create data */
for(i = 0; i < 24; i++)
buf[i] = i;
/* Write to one dataset */
if(H5Dwrite(did2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/* Closing */
if(H5Sclose(sid) < 0)
goto error;
if(H5Dclose(did1) < 0)
goto error;
if(H5Dclose(did2) < 0)
goto error;
/*
* Create 2 chunked datasets with version 2 B-tree chunk indexing type
* (one with data; one without data)
*/
/* Create dataspace */
max_dims[0] = 10;
max_dims[0] = H5S_UNLIMITED;
max_dims[1] = H5S_UNLIMITED;
if((sid = H5Screate_simple(2, dims2, max_dims)) < 0)
goto error;
/* Create the 2 datasets */
if((did1 = H5Dcreate2(fid, DSET_NDATA_BT2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
if((did2 = H5Dcreate2(gid, DSET_BT2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Write to one dataset */
if(H5Dwrite(did2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/* Closing */
if(H5Sclose(sid) < 0)
goto error;
if(H5Dclose(did1) < 0)
goto error;
if(H5Dclose(did2) < 0)
goto error;
/*
* Create 2 chunked datasets with fixed array chunk indexing type
* (one with data; one without data)
*/
/* Create dataspace */
max_dims[0] = 20;
max_dims[1] = 10;
if((sid = H5Screate_simple(2, dims2, max_dims)) < 0)
goto error;
/* Create the datasets */
if((did1 = H5Dcreate2(fid, DSET_FA, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
if((did2 = H5Dcreate2(gid, DSET_NDATA_FA, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Write to the dataset */
if(H5Dwrite(did1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/* Closing */
if(H5Sclose(sid) < 0)
goto error;
if(H5Dclose(did1) < 0)
goto error;
if(H5Dclose(did2) < 0)
goto error;
/*
* Create 2 chunked datasets with implicit chunk indexing type
* (one with data; one without data)
*/
/* Create dataspace */
if((sid = H5Screate_simple(2, dims2, NULL)) < 0)
goto error;
/* Set early allocation */
if(H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_EARLY) < 0)
goto error;
/* Create the 2 datasets */
if((did1 = H5Dcreate2(fid, DSET_NONE, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
if((did2 = H5Dcreate2(gid, DSET_NDATA_NONE, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Write to one dataset */
if(H5Dwrite(did1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/* Closing */
if(H5Dclose(did1) < 0)
goto error;
if(H5Dclose(did2) < 0)
goto error;
if(H5Sclose(sid) < 0)
goto error;
if(H5Pclose(dcpl) < 0)
goto error;
if(H5Gclose(gid) < 0)
goto error;
if(H5Fclose(fid) < 0)
goto error;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Sclose(sid);
H5Dclose(did1);
H5Dclose(did2);
H5Gclose(gid);
H5Fclose(fid);
H5Pclose(fapl);
H5Pclose(fcpl);
} H5E_END_TRY;
} /* gen_ext() */
int main(void)
{
unsigned i, latest;
/* Generate a non-latest-format file with v3 superblock */
gen_non(NON_V3_FILE);
/* Generate a new format file with a no-filter-edge-chunk dataset */
gen_edge(EDGE_V3_FILE);
/* Generate old/new format file with/without messages in the superblock extension */
for(latest = FALSE; latest <= TRUE; latest++) {
for(i = 0; i < 8; i++) {
char filename[50];
HDmemset(filename, 0, sizeof(filename));
if(!latest)
HDstrcat(filename, "old_");
HDstrcat(filename, FILENAME[i]);
gen_ext(filename, latest, i);
}
} /* end for latest */
return 0;
}

474
tools/h5format_convert/h5format_convert.c Normal file
View File

@ -0,0 +1,474 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Vailin Choi; Feb 2015
*/
/*
* We include the private header file so we can get to the uniform
* programming environment it declares.
* HDF5 API functions (except for H5G_basename())
*/
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5trav.h"
/* Name of tool */
#define PROGRAMNAME "h5format_convert"
static char *fname_g = NULL;
static char *dname_g = NULL;
static int dset_g = FALSE;
static int noop_g = FALSE;
static int verbose_g = 0;
/*
* Command-line options: The user can specify short or long-named
* parameters.
*/
static const char *s_opts = "hVvd:n";
static struct long_options l_opts[] = {
{ "help", no_arg, 'h' },
{ "hel", no_arg, 'h'},
{ "he", no_arg, 'h'},
{ "version", no_arg, 'V' },
{ "version", no_arg, 'V' },
{ "versio", no_arg, 'V' },
{ "versi", no_arg, 'V' },
{ "vers", no_arg, 'V' },
{ "verbose", no_arg, 'v' },
{ "verbos", no_arg, 'v' },
{ "verbo", no_arg, 'v' },
{ "verb", no_arg, 'v' },
{ "dname", require_arg, 'd' },
{ "dnam", require_arg, 'd' },
{ "dna", require_arg, 'd' },
{ "dn", require_arg, 'd' },
{ "noop", no_arg, 'n' },
{ "noo", no_arg, 'n' },
{ "no", no_arg, 'n' },
{ NULL, 0, '\0' }
};
/*-------------------------------------------------------------------------
* Function: usage
*
* Purpose: print usage
*
* Return: void
*
*-------------------------------------------------------------------------
*/
static void usage(const char *prog)
{
HDfprintf(stdout, "usage: %s [OPTIONS] file_name\n", prog);
HDfprintf(stdout, " OPTIONS\n");
HDfprintf(stdout, " -h, --help Print a usage message and exit\n");
HDfprintf(stdout, " -V, --version Print version number and exit\n");
HDfprintf(stdout, " -v, --verbose Turn on verbose mode\n");
HDfprintf(stdout, " -d dname, --dname=dataset_name Pathname for the dataset\n");
HDfprintf(stdout, " -n, --noop Perform all the steps except the actual conversion\n");
HDfprintf(stdout, "\n");
HDfprintf(stdout, "Examples of use:\n");
HDfprintf(stdout, "\n");
HDfprintf(stdout, "h5format_convert -d /group/dataset file_name\n");
HDfprintf(stdout, " Convert the dataset </group/dataset> in the HDF5 file <file_name>:\n");
HDfprintf(stdout, " a. chunked dataset: convert the chunk indexing type to version 1 B-tree\n");
HDfprintf(stdout, " b. compact/contiguous dataset: downgrade the layout version to 3\n");
HDfprintf(stdout, " c. virtual dataset: no action\n");
HDfprintf(stdout, "\n");
HDfprintf(stdout, "h5format_convert file_name\n");
HDfprintf(stdout, " Convert all datasets in the HDF5 file <file_name>:\n");
HDfprintf(stdout, " a. chunked dataset: convert the chunk indexing type to version 1 B-tree\n");
HDfprintf(stdout, " b. compact/contiguous dataset: downgrade the layout version to 3\n");
HDfprintf(stdout, " c. virtual dataset: no action\n");
HDfprintf(stdout, "\n");
HDfprintf(stdout, "h5format_convert -n -d /group/dataset file_name\n");
HDfprintf(stdout, " Go through all the steps except the actual conversion when \n");
HDfprintf(stdout, " converting the dataset </group/dataset> in the HDF5 file <file_name>.\n");
} /* usage() */
/*-------------------------------------------------------------------------
* Function: parse_command_line
*
* Purpose: parse command line input
*
* Return: Success: 0
* Failure: 1
*
*-------------------------------------------------------------------------
*/
static int
parse_command_line(int argc, const char **argv)
{
int opt;
/* no arguments */
if (argc == 1) {
usage(h5tools_getprogname());
h5tools_setstatus(EXIT_FAILURE);
goto error;
}
/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch((char) opt) {
case 'h':
usage(h5tools_getprogname());
h5tools_setstatus(EXIT_SUCCESS);
goto error;
case 'V':
print_version(h5tools_getprogname());
h5tools_setstatus(EXIT_SUCCESS);
goto error;
case 'v':
verbose_g = TRUE;
break;
case 'd': /* -d dname */
if(opt_arg != NULL && *opt_arg)
dname_g = HDstrdup(opt_arg);
if(dname_g == NULL) {
h5tools_setstatus(EXIT_FAILURE);
error_msg("No dataset name\n", opt_arg);
usage(h5tools_getprogname());
goto error;
}
dset_g = TRUE;
break;
case 'n': /* -n */
noop_g = TRUE;
break;
default:
h5tools_setstatus(EXIT_FAILURE);
usage(h5tools_getprogname());
goto error;
break;
} /* switch */
} /* while */
if (argc <= opt_ind) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
h5tools_setstatus(EXIT_FAILURE);
goto error;
}
fname_g = HDstrdup(argv[opt_ind]);
return(0);
error:
return(-1); ;
} /* parse_command_line() */
/*-------------------------------------------------------------------------
* Function: leave
*
* Purpose: Close HDF5
*
* Return: Does not return
*
*-------------------------------------------------------------------------
*/
static void
leave(int ret)
{
h5tools_close();
HDexit(ret);
} /* leave() */
/*-------------------------------------------------------------------------
* Function: convert()
*
* Purpose: To downgrade a dataset's indexing type or layout version:
* For chunked:
* Downgrade the chunk indexing type to version 1 B-tree
* If type is already version 1 B-tree, no further action
* For compact/contiguous:
* Downgrade the layout version from 4 to 3
* If version is already <= 3, no further action
* For virtual:
* No further action
*
* Return: Success: 0
* Failure: 1
*
*-------------------------------------------------------------------------
*/
static int
convert(hid_t fid, const char *dname)
{
hid_t dcpl = -1;
hid_t did = -1;
H5D_layout_t layout_type;
H5D_chunk_index_t idx_type;
/* Open the dataset */
if((did = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0) {
error_msg("unable to open dataset \"%s\"\n", dname);
h5tools_setstatus(EXIT_FAILURE);
goto error;
} else if(verbose_g)
HDfprintf(stdout, "Open the dataset\n");
/* Get the dataset's creation property list */
if((dcpl = H5Dget_create_plist(did)) < 0) {
error_msg("unable to get the dataset creation property list\n");
h5tools_setstatus(EXIT_FAILURE);
goto error;
}
/* Get the dataset's layout */
if((layout_type = H5Pget_layout(dcpl)) < 0) {
error_msg("unable to get the dataset layout type\n");
h5tools_setstatus(EXIT_FAILURE);
goto error;
} else if(verbose_g)
HDfprintf(stdout, "Retrieve the dataset's layout\n");
switch(layout_type) {
case H5D_CHUNKED:
if(verbose_g)
HDfprintf(stdout, "Dataset is a chunked dataset\n");
/* Get the dataset's chunk indexing type */
if(H5Dget_chunk_index_type(did, &idx_type) < 0) {
error_msg("unable to get the chunk indexing type for \"%s\"\n", dname);
h5tools_setstatus(EXIT_FAILURE);
goto error;
} else if(verbose_g)
HDfprintf(stdout, "Retrieve the dataset's chunk indexing type\n");
if(idx_type == H5D_CHUNK_IDX_BTREE) {
if(verbose_g)
HDfprintf(stdout, "Dataset's chunk indexing type is already version 1 B-tree: no further action\n");
h5tools_setstatus(EXIT_SUCCESS);
goto done;
} else if (verbose_g)
HDfprintf(stdout, "Dataset's chunk indexing type is not version 1 B-tree\n");
break;
case H5D_CONTIGUOUS:
if(verbose_g)
HDfprintf(stdout, "Dataset is a contiguous dataset: downgrade layout version as needed\n");
break;
case H5D_COMPACT:
if(verbose_g)
HDfprintf(stdout, "Dataset is a compact dataset: downgrade layout version as needed\n");
break;
case H5D_VIRTUAL:
if(verbose_g)
HDfprintf(stdout, "No further action for virtual dataset\n");
goto done;
case H5D_NLAYOUTS:
case H5D_LAYOUT_ERROR:
default:
error_msg("unknown layout type for \"%s\"\n", dname);
h5tools_setstatus(EXIT_FAILURE);
goto error;
} /* end switch */
/* No further action if it is a noop */
if(noop_g) {
if(verbose_g)
HDfprintf(stdout, "Not converting the dataset\n");
h5tools_setstatus(EXIT_SUCCESS);
goto done;
}
if(verbose_g)
HDfprintf(stdout, "Converting the dataset...\n");
/* Downgrade the dataset */
if(H5Dformat_convert(did) < 0) {
error_msg("unable to downgrade dataset for \"%s\"\n", dname);
h5tools_setstatus(EXIT_FAILURE);
goto error;
} else if(verbose_g)
HDfprintf(stdout, "Done\n");
done:
/* Close the dataset */
if(H5Dclose(did) < 0) {
error_msg("unable to close dataset \"%s\"\n", dname);
h5tools_setstatus(EXIT_FAILURE);
goto error;
} else if(verbose_g)
HDfprintf(stdout, "Close the dataset\n");
/* Close the dataset creation property list */
if(H5Pclose(dcpl) < 0) {
error_msg("unable to close dataset creation property list\n");
h5tools_setstatus(EXIT_FAILURE);
goto error;
} else if(verbose_g)
printf("Close the dataset creation property list\n");
return(0);
error:
if(verbose_g)
HDfprintf(stdout, "Error encountered\n");
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Dclose(did);
} H5E_END_TRY;
return(-1);
} /* convert() */
/*-------------------------------------------------------------------------
* Function: convert_dsets_cb()
*
* Purpose: The callback routine from the traversal to convert the
* chunk indexing type of the dataset object.
*
* Return: Success: 0
* Failure: 1
*-------------------------------------------------------------------------
*/
static int
convert_dsets_cb(const char *path, const H5O_info_t *oi, const char *already_visited, void *_fid)
{
hid_t fid = *(hid_t *)_fid;
/* If the object has already been seen then just return */
if(NULL == already_visited) {
if(oi->type == H5O_TYPE_DATASET) {
if(verbose_g)
HDfprintf(stdout, "Going to process dataset:%s...\n", path);
if(convert(fid, path) < 0)
goto error;
} /* end if */
} /* end if */
return 0;
error:
return -1;
} /* end convert_dsets_cb() */
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: To convert the chunk indexing type of a dataset in a file to
* version 1 B-tree.
*
* Return: Success: 0
* Failure: 1
*
*-------------------------------------------------------------------------
*/
int
main(int argc, const char *argv[])
{
H5E_auto2_t func;
void *edata;
hid_t fid = -1;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Disable error reporting */
H5Eget_auto2(H5E_DEFAULT, &func, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
/* Parse command line options */
if(parse_command_line(argc, argv) < 0)
goto done;
else if(verbose_g)
HDfprintf(stdout, "Process command line options\n");
if(noop_g && verbose_g)
HDfprintf(stdout, "It is noop...\n");
/* Open the HDF5 file */
if((fid = h5tools_fopen(fname_g, H5F_ACC_RDWR, H5P_DEFAULT, NULL, NULL, 0)) < 0) {
error_msg("unable to open file \"%s\"\n", fname_g);
h5tools_setstatus(EXIT_FAILURE);
goto done;
} else if(verbose_g)
HDfprintf(stdout, "Open the file %s\n", fname_g);
if(dset_g) { /* Convert a specified dataset in the file */
if(verbose_g)
HDfprintf(stdout, "Going to process dataset: %s...\n", dname_g);
if(convert(fid, dname_g) < 0)
goto done;
} else { /* Convert all datasets in the file */
if(verbose_g)
HDfprintf(stdout, "Processing all datasets in the file...\n");
if(h5trav_visit(fid, "/", TRUE, TRUE, convert_dsets_cb, NULL, &fid) < 0)
goto done;
} /* end else */
if(verbose_g) {
if(noop_g) {
HDfprintf(stdout, "Not processing the file's superblock...\n");
h5tools_setstatus(EXIT_SUCCESS);
goto done;
} /* end if */
HDfprintf(stdout, "Processing the file's superblock...\n");
} /* end if */
/* Process superblock */
if(H5Fformat_convert(fid) < 0) {
error_msg("unable to convert file's superblock\"%s\"\n", fname_g);
h5tools_setstatus(EXIT_FAILURE);
goto done;
} /* end if */
done:
/* Close the file */
if(fid >= 0) {
if(H5Fclose(fid) < 0) {
error_msg("unable to close file \"%s\"\n", fname_g);
h5tools_setstatus(EXIT_FAILURE);
} else if(verbose_g)
HDfprintf(stdout, "Close the file\n");
} /* end if */
if(fname_g)
HDfree(fname_g);
if(dname_g)
HDfree(dname_g);
H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(h5tools_getstatus());
} /* end main() */

26
tools/h5format_convert/testfiles/h5fc_d_file.ddl Normal file
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@ -0,0 +1,26 @@
usage: h5format_convert [OPTIONS] file_name
OPTIONS
-h, --help Print a usage message and exit
-V, --version Print version number and exit
-v, --verbose Turn on verbose mode
-d dname, --dname=dataset_name Pathname for the dataset
-n, --noop Perform all the steps except the actual conversion
Examples of use:
h5format_convert -d /group/dataset file_name
Convert the dataset </group/dataset> in the HDF5 file <file_name>:
a. chunked dataset: convert the chunk indexing type to version 1 B-tree
b. compact/contiguous dataset: downgrade the layout version to 3
c. virtual dataset: no action
h5format_convert file_name
Convert all datasets in the HDF5 file <file_name>:
a. chunked dataset: convert the chunk indexing type to version 1 B-tree
b. compact/contiguous dataset: downgrade the layout version to 3
c. virtual dataset: no action
h5format_convert -n -d /group/dataset file_name
Go through all the steps except the actual conversion when
converting the dataset </group/dataset> in the HDF5 file <file_name>.
h5format_convert error: missing file name

26
tools/h5format_convert/testfiles/h5fc_dname.ddl Normal file
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usage: h5format_convert [OPTIONS] file_name
OPTIONS
-h, --help Print a usage message and exit
-V, --version Print version number and exit
-v, --verbose Turn on verbose mode
-d dname, --dname=dataset_name Pathname for the dataset
-n, --noop Perform all the steps except the actual conversion
Examples of use:
h5format_convert -d /group/dataset file_name
Convert the dataset </group/dataset> in the HDF5 file <file_name>:
a. chunked dataset: convert the chunk indexing type to version 1 B-tree
b. compact/contiguous dataset: downgrade the layout version to 3
c. virtual dataset: no action
h5format_convert file_name
Convert all datasets in the HDF5 file <file_name>:
a. chunked dataset: convert the chunk indexing type to version 1 B-tree
b. compact/contiguous dataset: downgrade the layout version to 3
c. virtual dataset: no action
h5format_convert -n -d /group/dataset file_name
Go through all the steps except the actual conversion when
converting the dataset </group/dataset> in the HDF5 file <file_name>.
h5format_convert error: No dataset name

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tools/h5format_convert/testfiles/h5fc_edge_v3.h5 Normal file
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58
tools/h5format_convert/testfiles/h5fc_ext1_f.ddl Normal file
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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 32
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/h5fc_ext1_f.h5 Normal file
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58
tools/h5format_convert/testfiles/h5fc_ext1_i.ddl Normal file
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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 64
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/h5fc_ext1_i.h5 Normal file
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58
tools/h5format_convert/testfiles/h5fc_ext1_s.ddl Normal file
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@ -0,0 +1,58 @@
HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 32
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/h5fc_ext1_s.h5 Normal file
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58
tools/h5format_convert/testfiles/h5fc_ext2_if.ddl Normal file
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@ -0,0 +1,58 @@
HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 64
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/h5fc_ext2_if.h5 Normal file
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58
tools/h5format_convert/testfiles/h5fc_ext2_is.ddl Normal file
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@ -0,0 +1,58 @@
HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 64
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/h5fc_ext2_is.h5 Normal file
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58
tools/h5format_convert/testfiles/h5fc_ext2_sf.ddl Normal file
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@ -0,0 +1,58 @@
HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 32
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/h5fc_ext2_sf.h5 Normal file
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58
tools/h5format_convert/testfiles/h5fc_ext3_isf.ddl Normal file
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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 64
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/h5fc_help.ddl Normal file
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usage: h5format_convert [OPTIONS] file_name
OPTIONS
-h, --help Print a usage message and exit
-V, --version Print version number and exit
-v, --verbose Turn on verbose mode
-d dname, --dname=dataset_name Pathname for the dataset
-n, --noop Perform all the steps except the actual conversion
Examples of use:
h5format_convert -d /group/dataset file_name
Convert the dataset </group/dataset> in the HDF5 file <file_name>:
a. chunked dataset: convert the chunk indexing type to version 1 B-tree
b. compact/contiguous dataset: downgrade the layout version to 3
c. virtual dataset: no action
h5format_convert file_name
Convert all datasets in the HDF5 file <file_name>:
a. chunked dataset: convert the chunk indexing type to version 1 B-tree
b. compact/contiguous dataset: downgrade the layout version to 3
c. virtual dataset: no action
h5format_convert -n -d /group/dataset file_name
Go through all the steps except the actual conversion when
converting the dataset </group/dataset> in the HDF5 file <file_name>.

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h5format_convert error: unable to open dataset "nonexist"

1
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h5format_convert error: unable to open file "nonexist.h5"

25
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usage: h5format_convert [OPTIONS] file_name
OPTIONS
-h, --help Print a usage message and exit
-V, --version Print version number and exit
-v, --verbose Turn on verbose mode
-d dname, --dname=dataset_name Pathname for the dataset
-n, --noop Perform all the steps except the actual conversion
Examples of use:
h5format_convert -d /group/dataset file_name
Convert the dataset </group/dataset> in the HDF5 file <file_name>:
a. chunked dataset: convert the chunk indexing type to version 1 B-tree
b. compact/contiguous dataset: downgrade the layout version to 3
c. virtual dataset: no action
h5format_convert file_name
Convert all datasets in the HDF5 file <file_name>:
a. chunked dataset: convert the chunk indexing type to version 1 B-tree
b. compact/contiguous dataset: downgrade the layout version to 3
c. virtual dataset: no action
h5format_convert -n -d /group/dataset file_name
Go through all the steps except the actual conversion when
converting the dataset </group/dataset> in the HDF5 file <file_name>.

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Process command line options
Open the file tmp.h5
Processing all datasets in the file...
Going to process dataset:/DSET_CONTIGUOUS...
Open the dataset
Retrieve the dataset's layout
Dataset is a contiguous dataset: downgrade layout version as needed
Converting the dataset...
Done
Close the dataset
Close the dataset creation property list
Going to process dataset:/DSET_EA...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Going to process dataset:/DSET_FA...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Going to process dataset:/DSET_NDATA_BT2...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Going to process dataset:/DSET_NONE...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Going to process dataset:/GROUP/DSET_BT2...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Going to process dataset:/GROUP/DSET_NDATA_EA...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Going to process dataset:/GROUP/DSET_NDATA_FA...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Going to process dataset:/GROUP/DSET_NDATA_NONE...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Processing the file's superblock...
Close the file

12
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Process command line options
Open the file tmp.h5
Going to process dataset: /GROUP/DSET_BT2...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Processing the file's superblock...
Close the file

14
tools/h5format_convert/testfiles/h5fc_v_n_1d.ddl Normal file
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Process command line options
It is noop...
Open the file tmp.h5
Going to process dataset: /DSET_EA...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is not version 1 B-tree
Not converting the dataset
Close the dataset
Close the dataset creation property list
Not processing the file's superblock...
Close the file

56
tools/h5format_convert/testfiles/h5fc_v_n_all.ddl Normal file
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Process command line options
It is noop...
Open the file tmp.h5
Processing all datasets in the file...
Going to process dataset:/DSET_CONTIGUOUS...
Open the dataset
Retrieve the dataset's layout
Dataset is a contiguous dataset: downgrade layout version as needed
Not converting the dataset
Close the dataset
Close the dataset creation property list
Going to process dataset:/DSET_NDATA_BT2...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is not version 1 B-tree
Not converting the dataset
Close the dataset
Close the dataset creation property list
Going to process dataset:/DSET_NDATA_EA...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is not version 1 B-tree
Not converting the dataset
Close the dataset
Close the dataset creation property list
Going to process dataset:/GROUP/DSET_BT2...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is not version 1 B-tree
Not converting the dataset
Close the dataset
Close the dataset creation property list
Going to process dataset:/GROUP/DSET_COMPACT...
Open the dataset
Retrieve the dataset's layout
Dataset is a contiguous dataset: downgrade layout version as needed
Not converting the dataset
Close the dataset
Close the dataset creation property list
Going to process dataset:/GROUP/DSET_EA...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is not version 1 B-tree
Not converting the dataset
Close the dataset
Close the dataset creation property list
Not processing the file's superblock...
Close the file

13
tools/h5format_convert/testfiles/h5fc_v_ndata_bt1.ddl Normal file
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Process command line options
It is noop...
Open the file tmp.h5
Going to process dataset: /DSET_NDATA_BT2...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is already version 1 B-tree: no further action
Close the dataset
Close the dataset creation property list
Not processing the file's superblock...
Close the file

12
tools/h5format_convert/testfiles/h5fc_v_non_chunked.ddl Normal file
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Process command line options
Open the file tmp.h5
Going to process dataset: /DSET_CONTIGUOUS...
Open the dataset
Retrieve the dataset's layout
Dataset is a contiguous dataset: downgrade layout version as needed
Converting the dataset...
Done
Close the dataset
Close the dataset creation property list
Processing the file's superblock...
Close the file

58
tools/h5format_convert/testfiles/old_h5fc_ext1_f.ddl Normal file
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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 32
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 1
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 64
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/old_h5fc_ext1_s.ddl Normal file
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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 32
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/old_h5fc_ext2_if.ddl Normal file
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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 64
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/old_h5fc_ext2_is.ddl Normal file
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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 64
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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tools/h5format_convert/testfiles/old_h5fc_ext2_sf.ddl Normal file
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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 32
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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HDF5 "./testfiles/tmp.h5" {
SUPER_BLOCK {
SUPERBLOCK_VERSION 2
FREELIST_VERSION 0
SYMBOLTABLE_VERSION 0
OBJECTHEADER_VERSION 0
OFFSET_SIZE 8
LENGTH_SIZE 8
BTREE_RANK 16
BTREE_LEAF 4
ISTORE_K 64
FILE_SPACE_STRATEGY H5F_FILE_SPACE_ALL
FREE_SPACE_THRESHOLD 1
USER_BLOCK {
USERBLOCK_SIZE 0
}
}
GROUP "/" {
DATASET "DSET_CONTIGUOUS" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "DSET_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
GROUP "GROUP" {
DATASET "DSET_BT2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_EA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 10, H5S_UNLIMITED ) }
}
DATASET "DSET_NDATA_FA" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 20, 10 ) }
}
DATASET "DSET_NDATA_NONE" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
}
}
}
}

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#! /bin/sh
#
# 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.
#
# Tests for the h5format_convert tool
#
#
srcdir=@srcdir@
# Determine which filters are available
USE_FILTER_SZIP="@USE_FILTER_SZIP@"
USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@"
USE_FILTER_SHUFFLE="@USE_FILTER_SHUFFLE@"
USE_FILTER_FLETCHER32="@USE_FILTER_FLETCHER32@"
USE_FILTER_NBIT="@USE_FILTER_NBIT@"
USE_FILTER_SCALEOFFSET="@USE_FILTER_SCALEOFFSET@"
TESTNAME=h5format_convert
EXIT_SUCCESS=0
EXIT_FAILURE=1
FORMCONV=h5format_convert # The tool name
FORMCONV_BIN=`pwd`/$FORMCONV # The path of the tool binary
CHK_IDX=h5fc_chk_idx # The program name
CHK_IDX_BIN=`pwd`/$CHK_IDX # The program to verify the chunk indexing type is v1 B-tree
RM='rm -rf'
CMP='cmp -s'
DIFF='diff -c'
CP='cp'
H5DUMP=../h5dump/h5dump # The h5dump tool name
H5DUMP_BIN=`pwd`/$H5DUMP # The path of the h5dump tool binary
DIRNAME='dirname'
LS='ls'
AWK='awk'
nerrors=0
verbose=yes
# source dirs
SRC_TOOLS="$srcdir/.."
SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
# testfiles source dirs for tools
SRC_H5LS_TESTFILES="$SRC_TOOLS_TESTFILES"
SRC_H5DUMP_TESTFILES="$SRC_TOOLS_TESTFILES"
SRC_H5DIFF_TESTFILES="$SRC_TOOLS/h5diff/testfiles"
SRC_H5COPY_TESTFILES="$SRC_TOOLS/h5copy/testfiles"
SRC_H5REPACK_TESTFILES="$SRC_TOOLS/h5repack/testfiles"
SRC_H5JAM_TESTFILES="$SRC_TOOLS/h5jam/testfiles"
SRC_H5STAT_TESTFILES="$SRC_TOOLS/h5stat/testfiles"
SRC_H5IMPORT_TESTFILES="$SRC_TOOLS/h5import/testfiles"
SRC_H5FORMCONV_TESTFILES="$SRC_TOOLS/h5format_convert/testfiles"
TESTDIR=./testfiles
test -d $TESTDIR || mkdir $TESTDIR
# Copy the testfile to a temporary file for testing as h5format_convert is changing the file in place
TMPFILE=tmp.h5
######################################################################
# test files
# --------------------------------------------------------------------
# All the test files copy from source directory to test directory
# NOTE: Keep this framework to add/remove test files.
# Any test files from other tools can be used in this framework.
# This list are also used for checking exist.
# Comment '#' without space can be used.
# --------------------------------------------------------------------
LIST_HDF5_TEST_FILES="
$SRC_H5FORMCONV_TESTFILES/h5fc_non_v3.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_edge_v3.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_ext_none.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext_none.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_ext1_i.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_ext1_s.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_ext1_f.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_ext2_if.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_ext2_is.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_ext2_sf.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_ext3_isf.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext1_i.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext1_s.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext1_f.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_if.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_is.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_sf.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext3_isf.h5
"
LIST_OTHER_TEST_FILES="
$SRC_H5FORMCONV_TESTFILES/h5fc_help.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_nooption.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_nonexistfile.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_d_file.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_dname.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_nonexistdset_file.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_v_non_chunked.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_v_bt1.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_v_ndata_bt1.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_v_all.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_v_n_1d.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_v_n_all.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_ext1_i.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_ext1_s.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_ext1_f.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_ext2_if.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_ext2_is.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_ext2_sf.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_ext3_isf.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext1_i.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext1_s.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext1_f.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_if.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_is.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_sf.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext3_isf.ddl
"
#
# copy test files and expected output files from source dirs to test dir
#
COPY_TESTFILES="$LIST_HDF5_TEST_FILES $LIST_OTHER_TEST_FILES"
COPY_TESTFILES_TO_TESTDIR()
{
# copy test files. Used -f to make sure get a new copy
for tstfile in $COPY_TESTFILES
do
# ignore '#' comment
echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
RET=$?
if [ $RET -eq 1 ]; then
# skip cp if srcdir is same as destdir
# this occurs when build/test performed in source dir and
# make cp fail
SDIR=`$DIRNAME $tstfile`
INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
$CP -f $tstfile $TESTDIR
if [ $? -ne 0 ]; then
echo "Error: FAILED to copy $tstfile ."
# Comment out this to CREATE expected file
exit $EXIT_FAILURE
fi
fi
fi
done
}
CLEAN_TESTFILES_AND_TESTDIR()
{
# skip rm if srcdir is same as destdir
# this occurs when build/test performed in source dir and
# make cp fail
SDIR=`$DIRNAME $tstfile`
INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
$RM $TESTDIR
else
$RM $TESTDIR/$TMPFILE
fi
}
# Print a line-line message left justified in a field of 80 characters
# beginning with the word "Testing".
#
TESTING() {
SPACES=" "
echo "Testing $* $SPACES" | cut -c1-80 | tr -d '\012'
}
# Run a test and print PASS or *FAIL*. If a test fails then increment
# the `nerrors' global variable and (if $verbose is set) display the
# difference between the actual output and the expected output. The
# expected output is given as the first argument to this function and
# the actual output file is calculated by replacing the `.ddl' with
# `.out'. The actual output is not removed if $HDF5_NOCLEANUP has a
# non-zero value.
#
# $1: expected output
# $2: the test file name
# --fname might be empty or fname does not exist
# --fname is copied to a temporary file for testing
# $3 to at most $6--options to the tool such as:
# -d dname or --dname=dname
# -v or --verbose
# -n or --noop
TOOLTEST_OUT() {
# Prepare expected and actual output
expect="$TESTDIR/$1"
actual="$TESTDIR/`basename $1 .ddl`.out"
actual_err="$TESTDIR/`basename $1 .ddl`.err"
actual_sav=${actual}-sav
actual_err_sav=${actual_err}-sav
# Prepare the test file
$RM $TESTDIR/$TMPFILE
TFILE=$2
if [ ! -z "$2" ] && [ -e $TESTDIR/$2 ] ; then
$CP $TESTDIR/$2 $TESTDIR/$TMPFILE
TFILE=$TMPFILE
fi
# Run test.
TESTING $FORMCONV $3 $4 $5 $6 $2
(
cd $TESTDIR
$RUNSERIAL $FORMCONV_BIN $3 $4 $5 $6 $TFILE
) >$actual 2>$actual_err
cp $actual $actual_sav
cp $actual_err $actual_err_sav
cat $actual_err >> $actual
# Compare output
COMPARE_OUT $expect $actual
# Clean up output file
if test -z "$HDF5_NOCLEANUP"; then
$RM $actual $actual_err
$RM $actual $actual_err $actual_sav $actual_err_sav
fi
}
# To check that the tool exits success, no output
# Assume all short options
# $1 is the test file name
# --fname exists
# --fname is copied to a temporary file for testing
# $2 to at most $4--options to the tool such as:
# -d dname
# -n
TOOLTEST() {
TESTING $FORMCONV $2 $3 $4 $1
$RM $TESTDIR/$TMPFILE
$CP $TESTDIR/$1 $TESTDIR/$TMPFILE
$RUNSERIAL $FORMCONV_BIN $2 $3 $4 $TESTDIR/$TMPFILE
exitcode=$?
if [ $exitcode -ne 0 ]; then
echo "*FAILED*"
echo " The tool exits failure"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
fi
}
CHECKING() {
SPACES=" "
echo "Verifying $* $SPACES" | cut -c1-80 | tr -d '\012'
}
# Assume $TESTDIR/$TMPFILE is the converted test file
# $1 dataset name
IDX_CHECK() {
CHECKING $1
$RUNSERIAL $CHK_IDX_BIN $TESTDIR/$TMPFILE $1
ret=$?
if [ $ret -eq 0 ]; then
echo " PASSED"
else
echo "*FAILED*"
echo " The chunk indexing type is not correct"
nerrors="`expr $nerrors + 1`"
fi
}
# $1 is the expected output
# $2 is the output from testing
COMPARE_OUT() {
if $CMP $1 $2; then
echo " PASSED"
else
echo "*FAILED*"
echo " Expected result (*.ddl) differs from actual result (*.out)"
nerrors="`expr $nerrors + 1`"
test yes = "$verbose" && $DIFF $expect $actual |sed 's/^/ /'
fi
}
# Assume $TESTDIR/$TMPFILE is the converted test file
# $1 is the test file for verifying h5dump output
# $2 is the expected output from h5dump
H5DUMP_CHECK() {
CHECKING h5dump output for $1
expect="$TESTDIR/$2"
actual="$TESTDIR/`basename $2 .ddl`.out"
actual_err="$TESTDIR/`basename $2 .ddl`.err"
$RUNSERIAL $H5DUMP_BIN -BH $TESTDIR/$TMPFILE > $actual 2>$actual_err
cat $actual_err >> $actual
# Compare output
COMPARE_OUT $expect $actual
# Clean up output file
if test -z "$HDF5_NOCLEANUP"; then
$RM $actual $actual_err
fi
}
# Print a "SKIP" message
SKIP() {
TESTING $STAT $@
echo " -SKIP-"
}
##############################################################################
##############################################################################
### T H E T E S T S ###
##############################################################################
##############################################################################
# prepare for test
COPY_TESTFILES_TO_TESTDIR
#
#
#
# h5format_convert --help
# h5format_convert (no options)
# h5format_convert nonexist.h5 (no options, file does not exist)
TOOLTEST_OUT h5fc_help.ddl '' --help
TOOLTEST_OUT h5fc_nooption.ddl ''
TOOLTEST_OUT h5fc_nonexistfile.ddl nonexist.h5
#
#
# h5format_convert -d old_h5fc_ext_none.h5 (just -d option, file exists)
# h5format_convert --dname old_h5fc_ext_none.h5 (just --dname option, file exists)
# h5format_convert --dname (just --dname option)
# h5format_convert --dname=nonexist old_h5fc_ext_none.h5 (dataset does not exist, file exists)
TOOLTEST_OUT h5fc_d_file.ddl old_h5fc_ext_none.h5 -d
TOOLTEST_OUT h5fc_d_file.ddl old_h5fc_ext_none.h5 --dname
TOOLTEST_OUT h5fc_dname.ddl '' --dname
TOOLTEST_OUT h5fc_nonexistdset_file.ddl old_h5fc_ext_none.h5 --dname=nonexist
#
#
#
# h5format_convert -d /DSET_CONTIGUOUS -v old_h5fc_ext_none.h5 (verbose, contiguous dataset)
# h5format_convert -d /GROUP/DSET_BT2 --verbose old_h5fc_ext_none.h5 (verbose, bt1 dataset)
# h5format_convert -d /DSET_NDATA_BT2 -v -n old_h5fc_ext_none.h5 (verbose, noop, bt1+nodata dataset)
# h5format_convert -v old_h5fc_ext_none.h5 (verbose, all datasets)
TOOLTEST_OUT h5fc_v_non_chunked.ddl old_h5fc_ext_none.h5 -d /DSET_CONTIGUOUS -v
TOOLTEST_OUT h5fc_v_bt1.ddl old_h5fc_ext_none.h5 -d /GROUP/DSET_BT2 --verbose
TOOLTEST_OUT h5fc_v_ndata_bt1.ddl old_h5fc_ext_none.h5 -d /DSET_NDATA_BT2 -v -n
TOOLTEST_OUT h5fc_v_all.ddl old_h5fc_ext_none.h5 -v
#
#
#
# h5format_convert -d /DSET_EA -v -n h5fc_ext_none.h5 (verbose, noop, one ea dataset)
# h5format_convert -v -n h5fc_non_v3.h5 (verbose, noop, all datasets)
TOOLTEST_OUT h5fc_v_n_1d.ddl h5fc_ext_none.h5 -d /DSET_EA -v -n
TOOLTEST_OUT h5fc_v_n_all.ddl h5fc_non_v3.h5 -v -n
#
#
#
# No output from tests
# 1) Use the tool to convert the dataset
# 2) Verify the chunk indexing type is correct
# h5format_convert -d /DSET_EA h5fc_ext_none.h5
# h5format_convert -d /GROUP/DSET_NDATA_EA h5fc_ext_none.h5
# h5format_convert -d /GROUP/DSET_BT2 h5fc_ext_none.h5
# h5format_convert -d /DSET_NDATA_BT2 h5fc_ext_none.h5
# h5format_convert -d /DSET_FA h5fc_ext_none.h5
# h5format_convert -d /GROUP/DSET_FA h5fc_ext_none.h5
# h5format_convert -d /DSET_NONE h5fc_ext_none.h5
# h5format_convert -d /GROUP/DSET_NDATA_NONE h5fc_ext_none.h5
TOOLTEST h5fc_ext_none.h5 -d /DSET_EA
IDX_CHECK /DSET_EA
#
TOOLTEST h5fc_ext_none.h5 -d /GROUP/DSET_NDATA_EA
IDX_CHECK /GROUP/DSET_NDATA_EA
#
TOOLTEST h5fc_ext_none.h5 -d /GROUP/DSET_BT2
IDX_CHECK /GROUP/DSET_BT2
#
TOOLTEST h5fc_ext_none.h5 -d /DSET_NDATA_BT2
IDX_CHECK /DSET_NDATA_BT2
#
TOOLTEST h5fc_ext_none.h5 -d /DSET_FA
IDX_CHECK /DSET_FA
#
TOOLTEST h5fc_ext_none.h5 -d /GROUP/DSET_NDATA_FA
IDX_CHECK /GROUP/DSET_NDATA_FA
#
TOOLTEST h5fc_ext_none.h5 -d /DSET_NONE
IDX_CHECK /DSET_NONE
#
TOOLTEST h5fc_ext_none.h5 -d /GROUP/DSET_NDATA_NONE
IDX_CHECK /GROUP/DSET_NDATA_NONE
#
#
#
# No output from tests: just check exit code
# h5format_convert -d /DSET_NDATA_BT2 old_h5fc_ext_none.h5 (v1-btree dataset)
# h5format_convert -d /DSET_CONTIGUOUS h5fc_non_v3.h5 (non-chunked dataset)
TOOLTEST old_h5fc_ext_none.h5 -d /DSET_NDATA_BT2
TOOLTEST h5fc_non_v3.h5 -d /DSET_CONTIGUOUS
#
#
#
# No output from tests: just check exit code
# h5format_convert -d /GROUP/DSET_BT2 -n h5fc_non_v3.h5 (noop, one dataset)
# h5format_convert -n h5fc_non_v3.h5 (noop, all datasets)
TOOLTEST h5fc_non_v3.h5 -d /GROUP/DSET_BT2 -n
TOOLTEST h5fc_non_v3.h5 -n
#
#
#
# No output from tests: just check exit code
# h5format_convert h5fc_non_v3.h5
# 1) convert all datasets
# 2) verify indexing types
TOOLTEST h5fc_non_v3.h5
IDX_CHECK /DSET_NDATA_EA
IDX_CHECK /DSET_NDATA_BT2
IDX_CHECK /GROUP/DSET_BT2
IDX_CHECK /GROUP/DSET_EA
#
#
#
# No output from test: just check exit code
# h5format_convert h5fc_edge_v3.h5
# 1) convert the chunked dataset (filter, no-filter-edge-chunk)
# 2) verify the indexing type
TOOLTEST h5fc_edge_v3.h5
IDX_CHECK /DSET_EDGE
#
#
# The following test files have messages in the superblock extension.
# Verify h5dump output for correctness after conversion
TOOLTEST h5fc_ext1_i.h5
H5DUMP_CHECK h5fc_ext1_i.h5 h5fc_ext1_i.ddl
TOOLTEST h5fc_ext1_s.h5
H5DUMP_CHECK h5fc_ext1_s.h5 h5fc_ext1_s.ddl
TOOLTEST h5fc_ext1_f.h5
H5DUMP_CHECK h5fc_ext1_f.h5 h5fc_ext1_f.ddl
#
TOOLTEST h5fc_ext2_if.h5
H5DUMP_CHECK h5fc_ext2_if.h5 h5fc_ext2_if.ddl
TOOLTEST h5fc_ext2_is.h5
H5DUMP_CHECK h5fc_ext2_is.h5 h5fc_ext2_is.ddl
TOOLTEST h5fc_ext2_sf.h5
H5DUMP_CHECK h5fc_ext2_sf.h5 h5fc_ext2_sf.ddl
#
TOOLTEST h5fc_ext3_isf.h5
H5DUMP_CHECK h5fc_ext3_isf.h5 h5fc_ext3_isf.ddl
#
#
#
TOOLTEST old_h5fc_ext1_i.h5
H5DUMP_CHECK old_h5fc_ext1_i.h5 old_h5fc_ext1_i.ddl
TOOLTEST old_h5fc_ext1_s.h5
H5DUMP_CHECK old_h5fc_ext1_s.h5 old_h5fc_ext1_s.ddl
TOOLTEST old_h5fc_ext1_f.h5
H5DUMP_CHECK old_h5fc_ext1_f.h5 old_h5fc_ext1_f.ddl
#
TOOLTEST old_h5fc_ext2_if.h5
H5DUMP_CHECK old_h5fc_ext2_if.h5 old_h5fc_ext2_if.ddl
TOOLTEST old_h5fc_ext2_is.h5
H5DUMP_CHECK old_h5fc_ext2_is.h5 old_h5fc_ext2_is.ddl
TOOLTEST old_h5fc_ext2_sf.h5
H5DUMP_CHECK old_h5fc_ext2_sf.h5 old_h5fc_ext2_sf.ddl
#
TOOLTEST old_h5fc_ext3_isf.h5
H5DUMP_CHECK old_h5fc_ext3_isf.h5 old_h5fc_ext3_isf.ddl
#
# Clean up temporary files/directories
CLEAN_TESTFILES_AND_TESTDIR
if test $nerrors -eq 0 ; then
echo "All $TESTNAME tests passed."
exit $EXIT_SUCCESS
else
echo "$TESTNAME tests failed with $nerrors errors."
exit $EXIT_FAILURE
fi