diff options
63 files changed, 5022 insertions, 52 deletions
@@ -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 diff --git a/configure.ac b/configure.ac index 94e508b..b6bb44c 100644 --- a/configure.ac +++ b/configure.ac @@ -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 @@ -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() */ + diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index da6a717..f4f9104 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -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() */ + diff --git a/src/H5Dint.c b/src/H5Dint.c index ae25d17..322776b 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -2832,6 +2832,126 @@ done: /*------------------------------------------------------------------------- + * 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 * * Purpose: Mark some aspect of a dataset as dirty diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index c0b8b28..3b2727f 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -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); diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h index e1555b9..831e811 100644 --- a/src/H5Dpublic.h +++ b/src/H5Dpublic.h @@ -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. @@ -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() */ + diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index 93965e0..7d45ed9 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -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 */ diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h index 6fa18e1..fcccf07 100644 --- a/src/H5Fpublic.h +++ b/src/H5Fpublic.h @@ -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); @@ -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); /*********************/ @@ -1147,6 +1148,141 @@ done: /*------------------------------------------------------------------------- + * 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 * * Purpose: Close the free space tracker(s) for a file @@ -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) */ diff --git a/src/H5MFprivate.h b/src/H5MFprivate.h index 766834d..22ed308 100644 --- a/src/H5MFprivate.h +++ b/src/H5MFprivate.h @@ -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); diff --git a/tools/Makefile.am b/tools/Makefile.am index 38e853d..887c0f0 100644 --- a/tools/Makefile.am +++ b/tools/Makefile.am @@ -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 diff --git a/tools/h5format_convert/Makefile.am b/tools/h5format_convert/Makefile.am new file mode 100644 index 0000000..d3aef7d --- /dev/null +++ b/tools/h5format_convert/Makefile.am @@ -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 $(top_srcdir)/config/conclude.am diff --git a/tools/h5format_convert/Makefile.in b/tools/h5format_convert/Makefile.in new file mode 100644 index 0000000..de362a4 --- /dev/null +++ b/tools/h5format_convert/Makefile.in @@ -0,0 +1,1502 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +@SET_MAKE@ + +# +# Copyright by The HDF Group. +# Copyright by the Board of Trustees of the University of Illinois. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the files COPYING and Copyright.html. COPYING can be found at the root +# of the source code distribution tree; Copyright.html can be found at the +# root level of an installed copy of the electronic HDF5 document set and +# is linked from the top-level documents page. It can also be found at +# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have +# access to either file, you may request a copy from help@hdfgroup.org. +# +# HDF5 Library Makefile(.in) +# + +VPATH = @srcdir@ +am__is_gnu_make = { \ + if test -z '$(MAKELEVEL)'; then \ + false; \ + elif test -n '$(MAKE_HOST)'; then \ + true; \ + elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \ + true; \ + else \ + false; \ + fi; \ +} +am__make_running_with_option = \ + case $${target_option-} in \ + ?) ;; \ + *) echo "am__make_running_with_option: internal error: invalid" \ + "target option '$${target_option-}' specified" >&2; \ + exit 1;; \ + esac; \ + has_opt=no; \ + sane_makeflags=$$MAKEFLAGS; \ + if $(am__is_gnu_make); then \ + sane_makeflags=$$MFLAGS; \ + else \ + case $$MAKEFLAGS in \ + *\\[\ \ ]*) \ + bs=\\; \ + sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \ + | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \ + esac; \ + fi; \ + skip_next=no; \ + strip_trailopt () \ + { \ + flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \ + }; \ + for flg in $$sane_makeflags; 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E.g.,"; \ + echo " HDF5_PARAPREFIX=/PFS/user/me"; \ + echo " export HDF5_PARAPREFIX"; \ + echo " make check"; \ + echo "**** end of Hint ****"; \ + fi + @for test in $(TEST_PROG_PARA) dummy; do \ + if test $$test != dummy; then \ + $(MAKE) $(AM_MAKEFLAGS) $$test.chkexe_ \ + RUNEXEC="$(RUNPARALLEL)" || exit 1; \ + fi; \ + done + @for test in $(TEST_SCRIPT_PARA) dummy; do \ + if test $$test != dummy; then \ + $(MAKE) $(AM_MAKEFLAGS) $$test.chkexe_ || exit 1; \ + fi; \ + done + @if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then \ + echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` ended `date`===";\ + fi + +# Run test with different Virtual File Driver +check-vfd: $(LIB) $(PROGS) $(chk_TESTS) + @for vfd in $(VFD_LIST) dummy; do \ + if test $$vfd != dummy; then \ + echo "============================"; \ + echo "Testing Virtual File Driver $$vfd"; \ + echo "============================"; \ + $(MAKE) $(AM_MAKEFLAGS) check-clean || exit 1; \ + HDF5_DRIVER=$$vfd $(MAKE) $(AM_MAKEFLAGS) check || exit 1; \ + fi; \ + done + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/tools/h5format_convert/h5fc_chk_idx.c b/tools/h5format_convert/h5fc_chk_idx.c new file mode 100644 index 0000000..3a87594 --- /dev/null +++ b/tools/h5format_convert/h5fc_chk_idx.c @@ -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() */ + diff --git a/tools/h5format_convert/h5fc_gentest.c b/tools/h5format_convert/h5fc_gentest.c new file mode 100644 index 0000000..dae57fb --- /dev/null +++ b/tools/h5format_convert/h5fc_gentest.c @@ -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; +} + diff --git a/tools/h5format_convert/h5format_convert.c b/tools/h5format_convert/h5format_convert.c new file mode 100644 index 0000000..1098d35 --- /dev/null +++ b/tools/h5format_convert/h5format_convert.c @@ -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() */ + diff --git a/tools/h5format_convert/testfiles/h5fc_d_file.ddl b/tools/h5format_convert/testfiles/h5fc_d_file.ddl new file mode 100644 index 0000000..ad7a2f4 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_d_file.ddl @@ -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 diff --git a/tools/h5format_convert/testfiles/h5fc_dname.ddl b/tools/h5format_convert/testfiles/h5fc_dname.ddl new file mode 100644 index 0000000..0de42cb --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_dname.ddl @@ -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: No dataset name diff --git a/tools/h5format_convert/testfiles/h5fc_edge_v3.h5 b/tools/h5format_convert/testfiles/h5fc_edge_v3.h5 Binary files differnew file mode 100644 index 0000000..ac7dbd3 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_edge_v3.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_ext1_f.ddl b/tools/h5format_convert/testfiles/h5fc_ext1_f.ddl new file mode 100644 index 0000000..fb5192d --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext1_f.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/h5fc_ext1_f.h5 b/tools/h5format_convert/testfiles/h5fc_ext1_f.h5 Binary files differnew file mode 100644 index 0000000..68ba2ac --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext1_f.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_ext1_i.ddl b/tools/h5format_convert/testfiles/h5fc_ext1_i.ddl new file mode 100644 index 0000000..2fff4ac --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext1_i.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/h5fc_ext1_i.h5 b/tools/h5format_convert/testfiles/h5fc_ext1_i.h5 Binary files differnew file mode 100644 index 0000000..1a58089 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext1_i.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_ext1_s.ddl b/tools/h5format_convert/testfiles/h5fc_ext1_s.ddl new file mode 100644 index 0000000..fb5192d --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext1_s.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/h5fc_ext1_s.h5 b/tools/h5format_convert/testfiles/h5fc_ext1_s.h5 Binary files differnew file mode 100644 index 0000000..26e9b25 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext1_s.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_ext2_if.ddl b/tools/h5format_convert/testfiles/h5fc_ext2_if.ddl new file mode 100644 index 0000000..2fff4ac --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext2_if.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/h5fc_ext2_if.h5 b/tools/h5format_convert/testfiles/h5fc_ext2_if.h5 Binary files differnew file mode 100644 index 0000000..e5c5e25 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext2_if.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_ext2_is.ddl b/tools/h5format_convert/testfiles/h5fc_ext2_is.ddl new file mode 100644 index 0000000..2fff4ac --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext2_is.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/h5fc_ext2_is.h5 b/tools/h5format_convert/testfiles/h5fc_ext2_is.h5 Binary files differnew file mode 100644 index 0000000..0e3eca7 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext2_is.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_ext2_sf.ddl b/tools/h5format_convert/testfiles/h5fc_ext2_sf.ddl new file mode 100644 index 0000000..fb5192d --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext2_sf.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/h5fc_ext2_sf.h5 b/tools/h5format_convert/testfiles/h5fc_ext2_sf.h5 Binary files differnew file mode 100644 index 0000000..cb15f03 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext2_sf.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_ext3_isf.ddl b/tools/h5format_convert/testfiles/h5fc_ext3_isf.ddl new file mode 100644 index 0000000..2fff4ac --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext3_isf.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/h5fc_ext3_isf.h5 b/tools/h5format_convert/testfiles/h5fc_ext3_isf.h5 Binary files differnew file mode 100644 index 0000000..d46cef4 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext3_isf.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_ext_none.h5 b/tools/h5format_convert/testfiles/h5fc_ext_none.h5 Binary files differnew file mode 100644 index 0000000..defbcb3 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_ext_none.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_help.ddl b/tools/h5format_convert/testfiles/h5fc_help.ddl new file mode 100644 index 0000000..aef8c63 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_help.ddl @@ -0,0 +1,25 @@ +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>. diff --git a/tools/h5format_convert/testfiles/h5fc_non_v3.h5 b/tools/h5format_convert/testfiles/h5fc_non_v3.h5 Binary files differnew file mode 100644 index 0000000..58a340d --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_non_v3.h5 diff --git a/tools/h5format_convert/testfiles/h5fc_nonexistdset_file.ddl b/tools/h5format_convert/testfiles/h5fc_nonexistdset_file.ddl new file mode 100644 index 0000000..39450c0 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_nonexistdset_file.ddl @@ -0,0 +1 @@ +h5format_convert error: unable to open dataset "nonexist" diff --git a/tools/h5format_convert/testfiles/h5fc_nonexistfile.ddl b/tools/h5format_convert/testfiles/h5fc_nonexistfile.ddl new file mode 100644 index 0000000..706ea9d --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_nonexistfile.ddl @@ -0,0 +1 @@ +h5format_convert error: unable to open file "nonexist.h5" diff --git a/tools/h5format_convert/testfiles/h5fc_nooption.ddl b/tools/h5format_convert/testfiles/h5fc_nooption.ddl new file mode 100644 index 0000000..aef8c63 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_nooption.ddl @@ -0,0 +1,25 @@ +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>. diff --git a/tools/h5format_convert/testfiles/h5fc_v_all.ddl b/tools/h5format_convert/testfiles/h5fc_v_all.ddl new file mode 100644 index 0000000..5e7365d --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_v_all.ddl @@ -0,0 +1,77 @@ +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 diff --git a/tools/h5format_convert/testfiles/h5fc_v_bt1.ddl b/tools/h5format_convert/testfiles/h5fc_v_bt1.ddl new file mode 100644 index 0000000..c501eb0 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_v_bt1.ddl @@ -0,0 +1,12 @@ +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 diff --git a/tools/h5format_convert/testfiles/h5fc_v_n_1d.ddl b/tools/h5format_convert/testfiles/h5fc_v_n_1d.ddl new file mode 100644 index 0000000..ff5da4a --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_v_n_1d.ddl @@ -0,0 +1,14 @@ +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 diff --git a/tools/h5format_convert/testfiles/h5fc_v_n_all.ddl b/tools/h5format_convert/testfiles/h5fc_v_n_all.ddl new file mode 100644 index 0000000..d2ffbbf --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_v_n_all.ddl @@ -0,0 +1,56 @@ +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 diff --git a/tools/h5format_convert/testfiles/h5fc_v_ndata_bt1.ddl b/tools/h5format_convert/testfiles/h5fc_v_ndata_bt1.ddl new file mode 100644 index 0000000..ba794a7 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_v_ndata_bt1.ddl @@ -0,0 +1,13 @@ +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 diff --git a/tools/h5format_convert/testfiles/h5fc_v_non_chunked.ddl b/tools/h5format_convert/testfiles/h5fc_v_non_chunked.ddl new file mode 100644 index 0000000..aba0740 --- /dev/null +++ b/tools/h5format_convert/testfiles/h5fc_v_non_chunked.ddl @@ -0,0 +1,12 @@ +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 diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext1_f.ddl b/tools/h5format_convert/testfiles/old_h5fc_ext1_f.ddl new file mode 100644 index 0000000..fb5192d --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext1_f.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext1_f.h5 b/tools/h5format_convert/testfiles/old_h5fc_ext1_f.h5 Binary files differnew file mode 100644 index 0000000..3cbc7f4 --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext1_f.h5 diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext1_i.ddl b/tools/h5format_convert/testfiles/old_h5fc_ext1_i.ddl new file mode 100644 index 0000000..c906082 --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext1_i.ddl @@ -0,0 +1,58 @@ +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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext1_i.h5 b/tools/h5format_convert/testfiles/old_h5fc_ext1_i.h5 Binary files differnew file mode 100644 index 0000000..a2c9187 --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext1_i.h5 diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext1_s.ddl b/tools/h5format_convert/testfiles/old_h5fc_ext1_s.ddl new file mode 100644 index 0000000..fb5192d --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext1_s.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext1_s.h5 b/tools/h5format_convert/testfiles/old_h5fc_ext1_s.h5 Binary files differnew file mode 100644 index 0000000..fdf4f33 --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext1_s.h5 diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext2_if.ddl b/tools/h5format_convert/testfiles/old_h5fc_ext2_if.ddl new file mode 100644 index 0000000..2fff4ac --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext2_if.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext2_if.h5 b/tools/h5format_convert/testfiles/old_h5fc_ext2_if.h5 Binary files differnew file mode 100644 index 0000000..6bf0a2f --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext2_if.h5 diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext2_is.ddl b/tools/h5format_convert/testfiles/old_h5fc_ext2_is.ddl new file mode 100644 index 0000000..2fff4ac --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext2_is.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext2_is.h5 b/tools/h5format_convert/testfiles/old_h5fc_ext2_is.h5 Binary files differnew file mode 100644 index 0000000..c0c7ecc --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext2_is.h5 diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext2_sf.ddl b/tools/h5format_convert/testfiles/old_h5fc_ext2_sf.ddl new file mode 100644 index 0000000..fb5192d --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext2_sf.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext2_sf.h5 b/tools/h5format_convert/testfiles/old_h5fc_ext2_sf.h5 Binary files differnew file mode 100644 index 0000000..055cabf --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext2_sf.h5 diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext3_isf.ddl b/tools/h5format_convert/testfiles/old_h5fc_ext3_isf.ddl new file mode 100644 index 0000000..2fff4ac --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext3_isf.ddl @@ -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 ) } + } + } +} +} diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext3_isf.h5 b/tools/h5format_convert/testfiles/old_h5fc_ext3_isf.h5 Binary files differnew file mode 100644 index 0000000..f4caaf4 --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext3_isf.h5 diff --git a/tools/h5format_convert/testfiles/old_h5fc_ext_none.h5 b/tools/h5format_convert/testfiles/old_h5fc_ext_none.h5 Binary files differnew file mode 100644 index 0000000..d0bf344 --- /dev/null +++ b/tools/h5format_convert/testfiles/old_h5fc_ext_none.h5 diff --git a/tools/h5format_convert/testh5fc.sh.in b/tools/h5format_convert/testh5fc.sh.in new file mode 100644 index 0000000..f712434 --- /dev/null +++ b/tools/h5format_convert/testh5fc.sh.in @@ -0,0 +1,494 @@ +#! /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 + |