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HDFFV-10919 merge synching

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This commit is contained in:
Allen Byrne 2019-10-02 15:13:37 -05:00
parent 98720d6511
commit bc61159318
8 changed files with 189 additions and 301 deletions

32
tools/lib/h5tools.c

@ -1241,10 +1241,10 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
H5T_class_t type_class;
if((size = H5Tget_size(tid)) == 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
if((type_class = H5Tget_class(tid)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_class failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_class failed");
switch (type_class) {
case H5T_INTEGER:
@ -1264,7 +1264,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
bytes_wrote = HDfwrite(mem, 1, bytes_in, stream);
if(bytes_wrote != bytes_in || (0 == bytes_wrote && HDferror(stream)))
H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
block_index -= (hsize_t)bytes_wrote;
mem = mem + bytes_wrote;
@ -1287,7 +1287,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
if (s != NULL)
size = HDstrlen(s);
else
H5E_THROW(FAIL, H5E_tools_min_id_g, "NULL string")
H5E_THROW(FAIL, H5E_tools_min_id_g, "NULL string");
}
else {
s = (char *) mem;
@ -1295,7 +1295,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) {
HDmemcpy(&tempuchar, &s[i], sizeof(unsigned char));
if (1 != HDfwrite(&tempuchar, sizeof(unsigned char), 1, stream))
H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
} /* i */
} /* for (block_index = 0; block_index < block_nelmts; block_index++) */
}
@ -1306,7 +1306,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
unsigned nmembs;
if((snmembs = H5Tget_nmembers(tid)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers of compound failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers of compound failed");
nmembs = (unsigned)snmembs;
for (block_index = 0; block_index < block_nelmts; block_index++) {
@ -1322,7 +1322,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
if (render_bin_output(stream, container, memb, mem + offset, 1) < 0) {
H5Tclose(memb);
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output of compound member failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output of compound member failed");
}
H5Tclose(memb);
@ -1350,7 +1350,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
}
else {
H5Tclose(memb);
H5E_THROW(FAIL, H5E_tools_min_id_g, "calculate the number of array elements failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "calculate the number of array elements failed");
}
for (block_index = 0; block_index < block_nelmts; block_index++) {
@ -1358,7 +1358,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
/* dump the array element */
if (render_bin_output(stream, container, memb, mem, nelmts) < 0) {
H5Tclose(memb);
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed");
}
}
H5Tclose(memb);
@ -1380,7 +1380,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
/* dump the array element */
if (render_bin_output(stream, container, memb, ((char *) (((hvl_t *)((void *)mem))->p)), nelmts) < 0) {
H5Tclose(memb);
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed");
}
}
H5Tclose(memb);
@ -1426,7 +1426,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
if (size != HDfwrite(mem, sizeof(char), size, stream))
H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
} /* end for */
break;
@ -1434,7 +1434,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
case H5T_NCLASSES:
default:
/* Badness */
H5E_THROW(FAIL, H5E_tools_min_id_g, "bad type class")
H5E_THROW(FAIL, H5E_tools_min_id_g, "bad type class");
break;
} /* end switch */
@ -1562,12 +1562,12 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
hid_t type_id = -1;
if((snblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed")
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed");
nblocks = (hsize_t)snblocks;
/* Print block information */
if((sndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed")
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
ndims = (unsigned)sndims;
alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]);
@ -1683,12 +1683,12 @@ render_bin_output_region_points(hid_t region_space, hid_t region_id,
hid_t type_id = -1;
if((snpoints = H5Sget_select_elem_npoints(region_space)) <= 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed")
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed");
npoints = (hsize_t)snpoints;
/* Allocate space for the dimension array */
if((sndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed")
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
ndims = (unsigned)sndims;
if((dtype = H5Dget_type(region_id)) < 0)

92
tools/lib/h5tools_dump.c

@ -618,12 +618,12 @@ h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id,
HDassert(buffer);
if((snblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed")
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed");
nblocks = (hsize_t)snblocks;
/* Print block information */
if((sndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed")
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
ndims = (unsigned)sndims;
/* Render the region { element begin */
@ -944,12 +944,12 @@ h5tools_dump_region_data_points(hid_t region_space, hid_t region_id,
HDassert(buffer);
if((snpoints = H5Sget_select_elem_npoints(region_space)) <= 0)
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed")
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed");
npoints = (hsize_t)snpoints;
/* Allocate space for the dimension array */
if((sndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed")
H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
ndims = (unsigned)sndims;
/* Render the region { element begin */
@ -1156,7 +1156,7 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c
unsigned int vl_data = 0; /* contains VL datatypes */
if ((size_t) ctx->ndims > NELMTS(sm_size))
H5E_THROW(FAIL, H5E_tools_min_id_g, "ndims and sm_size comparision failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "ndims and sm_size comparision failed");
if (ctx->ndims > 0)
init_acc_pos(ctx, total_size);
@ -1184,10 +1184,10 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c
/* calculate the potential number of elements we're going to print */
if(H5Sselect_hyperslab(f_space, H5S_SELECT_SET, temp_start, temp_stride, temp_count, temp_block) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
if((ssm_nelmts = H5Sget_select_npoints(f_space)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_select_npoints failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_select_npoints failed");
sm_nelmts = (hsize_t)ssm_nelmts;
if (sm_nelmts > 0) {
@ -1196,7 +1196,7 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c
* a hyperslab whose size is manageable.
*/
if((sm_nbytes = p_type_nbytes = H5Tget_size(p_type)) == 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
if (ctx->ndims > 0)
for (i = ctx->ndims; i > 0; --i) {
@ -1210,17 +1210,17 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c
HDassert(sm_nbytes == (hsize_t) ((size_t) sm_nbytes)); /*check for overflow*/
if(NULL == (sm_buf = (unsigned char *)HDmalloc((size_t) sm_nelmts * p_type_nbytes)))
H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for strip-mine")
H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for strip-mine");
if((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed");
if(H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &sm_nelmts, NULL) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
/* read the data */
if(H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dread failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dread failed");
/* print the data */
flags = START_OF_DATA;
@ -1234,7 +1234,7 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c
/* print array indices. get the lower bound of the hyperslab and calulate
the element position at the start of hyperslab */
if(H5Sget_select_bounds(f_space, low, high) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_select_bounds failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_select_bounds failed");
elmtno = 0;
for (i = 0; i < (size_t) ctx->ndims - 1; i++) {
@ -1259,13 +1259,13 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c
H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf);
if(H5Sclose(sm_space) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if(sm_buf)
HDfree(sm_buf);
sm_buf = NULL;
}
else
H5E_THROW(SUCCEED, H5E_tools_min_id_g, "nothing to print")
H5E_THROW(SUCCEED, H5E_tools_min_id_g, "nothing to print");
ctx->continuation++;
@ -1462,10 +1462,10 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_co
hsize_t total_size[H5S_MAX_RANK];/* total size of dataset*/
if((f_space = H5Dget_space(dset)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_space failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
if((sndims = H5Sget_simple_extent_ndims(f_space)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
ctx->ndims = (unsigned)sndims;
/* assume entire data space to be printed */
@ -1474,7 +1474,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_co
ctx->p_min_idx[i] = 0;
if(H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
ctx->size_last_dim = total_size[ctx->ndims - 1];
/* Set the compound datatype field list for display */
@ -1484,7 +1484,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_co
CATCH
if(f_space >= 0 && H5Sclose(f_space) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
return ret_value;
}
@ -1540,15 +1540,15 @@ h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, h5tools_cont
f_space = H5Dget_space(dset);
if (f_space == FAIL)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_space failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
sndims = H5Sget_simple_extent_ndims(f_space);
if(sndims < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_simple_extent_ndims failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_simple_extent_ndims failed");
ctx->ndims = (unsigned)sndims;
if ((size_t)ctx->ndims > NELMTS(sm_size))
H5E_THROW(FAIL, H5E_tools_min_id_g, "ctx->ndims > NELMTS(sm_size) failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "ctx->ndims > NELMTS(sm_size) failed");
/* Assume entire data space to be printed */
if (ctx->ndims > 0)
@ -1629,7 +1629,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, h5tools_cont
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) {
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dread failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dread failed");
}
/* Print the data */
@ -1667,9 +1667,9 @@ CATCH
done:
if(sm_space >= 0 && H5Sclose(sm_space) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if(f_space >= 0 && H5Sclose(f_space) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
return ret_value;
}
@ -1696,11 +1696,11 @@ h5tools_dump_simple_mem(FILE *stream, const h5tool_format_t *info, h5tools_conte
sndims = H5Sget_simple_extent_ndims(space);
if(sndims < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_simple_extent_ndims failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_simple_extent_ndims failed");
ctx->ndims = (unsigned)sndims;
if ((size_t) ctx->ndims > NELMTS(ctx->p_min_idx))
H5E_THROW(FAIL, H5E_tools_min_id_g, "ctx->ndims > NELMTS(ctx->p_min_idx) failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "ctx->ndims > NELMTS(ctx->p_min_idx) failed");
/* Assume entire data space to be printed */
for (i = 0; i < ctx->ndims; i++)
@ -1900,7 +1900,7 @@ h5tools_print_datatype(FILE *stream, h5tools_str_t *buffer, const h5tool_format_
const char *order_s = NULL; /* byte order string */
if((type_class = H5Tget_class(type)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_class failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_class failed");
if (object_search && H5Tcommitted(type) > 0) {
H5O_info_t oinfo;
obj_t *obj = NULL; /* Found object */
@ -2280,9 +2280,9 @@ h5tools_print_datatype(FILE *stream, h5tools_str_t *buffer, const h5tool_format_
char *ttag;
if(NULL == (ttag = H5Tget_tag(type)))
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_tag failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_tag failed");
ctx->need_prefix = TRUE;
ctx->need_prefix = TRUE;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "OPAQUE_TAG \"%s\";", ttag);
@ -2308,7 +2308,7 @@ h5tools_print_datatype(FILE *stream, h5tools_str_t *buffer, const h5tool_format_
case H5T_COMPOUND:
if((snmembers = H5Tget_nmembers(type)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed");
nmembers = (unsigned)snmembers;
h5tools_str_append(buffer, "H5T_COMPOUND %s", h5tools_dump_header_format->structblockbegin);
@ -2352,7 +2352,7 @@ h5tools_print_datatype(FILE *stream, h5tools_str_t *buffer, const h5tool_format_
case H5T_ENUM:
if((super = H5Tget_super(type)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_super failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_super failed");
h5tools_str_append(buffer, "H5T_ENUM %s", h5tools_dump_header_format->enumblockbegin);
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
@ -2382,14 +2382,14 @@ h5tools_print_datatype(FILE *stream, h5tools_str_t *buffer, const h5tool_format_
case H5T_VLEN:
if((super = H5Tget_super(type)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_super failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_super failed");
h5tools_str_append(buffer, "H5T_VLEN %s ", h5tools_dump_header_format->vlenblockbegin);
h5tools_print_datatype(stream, buffer, info, ctx, super, TRUE);
if(H5Tclose(super) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed")
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->vlenblockend);
@ -2464,10 +2464,10 @@ h5tools_print_dataspace(h5tools_str_t *buffer, hid_t space)
int i;
if((ndims = H5Sget_simple_extent_dims(space, size, maxsize)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
if((space_type = H5Sget_simple_extent_type(space)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_type failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_type failed");
switch(space_type) {
case H5S_SCALAR:
@ -2552,15 +2552,15 @@ h5tools_print_enum(FILE *stream, h5tools_str_t *buffer, const h5tool_format_t *i
ncols = info->line_ncols;
if((snmembs = H5Tget_nmembers(type)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed");
nmembs = (unsigned)snmembs;
HDassert(nmembs > 0);
if((super = H5Tget_super(type)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_super failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_super failed");
if((type_size = H5Tget_size(type)) <= 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size(type) failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size(type) failed");
/*
* Determine what datatype to use for the native values. To simplify
@ -2573,7 +2573,7 @@ h5tools_print_enum(FILE *stream, h5tools_str_t *buffer, const h5tool_format_t *i
dst_size = sizeof(long long);
if((sign_type = H5Tget_sign(type))<0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_sign failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_sign failed");
if(H5T_SGN_NONE == sign_type)
native = H5T_NATIVE_ULLONG;
else
@ -2584,20 +2584,20 @@ h5tools_print_enum(FILE *stream, h5tools_str_t *buffer, const h5tool_format_t *i
/* Get the names and raw values of all members */
if(NULL == (name = (char **)HDcalloc((size_t)nmembs, sizeof(char *))))
H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for member name")
H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for member name");
if(NULL == (value = (unsigned char *)HDcalloc((size_t)nmembs, MAX(type_size, dst_size))))
H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for member value")
H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for member value");
for (i = 0; i < nmembs; i++) {
name[i] = H5Tget_member_name(type, i);
if(H5Tget_member_value(type, i, value + i * type_size) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_member_value failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_member_value failed");
}
/* Convert values to native datatype */
if (native > 0)
if(H5Tconvert(super, native, (size_t)nmembs, value, NULL, H5P_DEFAULT) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tconvert failed")
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tconvert failed");
/*
* Sort members by increasing value
@ -2654,7 +2654,7 @@ CATCH
HDfree(value);
if(super >= 0 && H5Tclose(super) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not close datatype's super class")
H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not close datatype's super class");
if(0 == nmembs)
h5tools_str_append(buffer, "\n<empty>");
@ -3223,7 +3223,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
*-------------------------------------------------------------------------
*/
if (H5D_VIRTUAL != stl) {
ctx->need_prefix = TRUE;
ctx->need_prefix = TRUE;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", FILTERS, BEGIN);

3
tools/src/h5dump/h5dump.c

@ -1641,8 +1641,7 @@ main(int argc, const char *argv[])
fid = H5Fopen(fname, H5F_ACC_RDONLY, fapl_id);
}
else {
fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT,
driver, NULL, 0);
fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, driver, NULL, 0);
}
if (fid < 0) {

89
tools/src/h5repack/h5repack.c

@ -220,11 +220,7 @@ h5repack_addlayout(const char *str, pack_opt_t *options)
*-------------------------------------------------------------------------
*/
hid_t
copy_named_datatype(hid_t type_in,
hid_t fidout,
named_dt_t **named_dt_head_p,
trav_table_t *travt,
pack_opt_t *options)
copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
{
named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
named_dt_t *dt_ret = NULL; /* Datatype to return */
@ -248,8 +244,7 @@ copy_named_datatype(hid_t type_in,
if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
/* Push onto the stack */
if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"buffer allocation failed failed");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "buffer allocation failed failed");
dt->next = *named_dt_head_p;
*named_dt_head_p = dt;
@ -289,8 +284,7 @@ copy_named_datatype(hid_t type_in,
else
dt_ret->id_out = H5Tcopy(type_in);
if (dt_ret->id_out < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"H5Tget_native_type-H5Tcopy failed");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type-H5Tcopy failed");
if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommit_anon failed");
} /* end if named datatype not yet in output file */
@ -347,12 +341,7 @@ done:
*-------------------------------------------------------------------------
*/
int
copy_attr(
hid_t loc_in,
hid_t loc_out,
named_dt_t **named_dt_head_p,
trav_table_t *travt,
pack_opt_t *options)
copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
{
int ret_value = 0;
hid_t attr_id = -1; /* attr ID */
@ -382,13 +371,13 @@ copy_attr(
*/
for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
/* open attribute */
attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT);
if (attr_id < 0)
if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
/* get the file datatype */
if ((ftype_id = H5Aget_type(attr_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed");
@ -405,8 +394,7 @@ copy_attr(
/* Copy named dt */
if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) {
H5Fclose(fidout);
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"copy_named_datatype failed");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
}
if (H5Fclose(fidout) < 0)
@ -425,8 +413,7 @@ copy_attr(
/* get dimensions */
if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"H5Sget_simple_extent_dims failed");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
nelmts = 1;
for (j = 0; j < rank; j++)
@ -622,8 +609,7 @@ check_options(pack_opt_t *options)
} /* end for each object in options */
if (options->all_layout == 1 && has_ck)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"invalid chunking input: 'all' option is present with other objects");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid chunking input: 'all' option is present with other objects");
/*-------------------------------------------------------------------------
* Objects to filter
@ -669,14 +655,10 @@ check_options(pack_opt_t *options)
if (options->verbose) {
if (pack.filter[j].filtn >= 0) {
if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) {
HDprintf(" <%s> with %s filter %d\n", name,
get_sfilter(pack.filter[j].filtn),
pack.filter[j].filtn);
HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn);
}
else {
HDprintf(" <%s> with %s filter\n",
name,
get_sfilter(pack.filter[j].filtn));
HDprintf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn));
}
}
}
@ -685,9 +667,7 @@ check_options(pack_opt_t *options)
} /* end for each object in options table */
if (options->all_filter == 1 && has_cp)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"invalid compression input: 'all' option is present with " \
"other objects");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid compression input: 'all' option is present with other objects");
/*-------------------------------------------------------------------------
* Check options for the latest format
@ -695,18 +675,14 @@ check_options(pack_opt_t *options)
*/
if (options->grp_compact < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"invalid maximum number of links to store as header messages");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid maximum number of links to store as header messages");
if (options->grp_indexed < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"invalid minimum number of links to store in indexed format");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid minimum number of links to store in the indexed format");
if (options->grp_indexed > options->grp_compact)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"minimum indexed size is greater than maximum compact size");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "minimum indexed size is greater than the maximum compact size");
for (i = 0; i < 8; i++)
if (options->msg_size[i] < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"invalid shared message size");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid shared message size");
/*------------------------------------------------------------------------
* Verify new user userblock options; file name must be present
@ -720,8 +696,7 @@ check_options(pack_opt_t *options)
}
if (options->ublock_filename == NULL && options->ublock_size != 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"file name missing for user block", options->ublock_filename);
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file name missing for user block", options->ublock_filename);
/*------------------------------------------------------------------------
* Verify alignment options; threshold is zero default but alignment not
@ -729,8 +704,7 @@ check_options(pack_opt_t *options)
*/
if (options->alignment == 0 && options->threshold != 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"alignment for H5Pset_alignment missing");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "alignment for H5Pset_alignment missing");
done:
return ret_value;
@ -765,8 +739,7 @@ check_objects(const char* fname, pack_opt_t *options)
*-------------------------------------------------------------------------
*/
if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR);
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR);
/*-------------------------------------------------------------------------
* get the list of objects in the file
@ -775,6 +748,7 @@ check_objects(const char* fname, pack_opt_t *options)
/* Initialize indexing options */
h5trav_set_index(sort_by, sort_order);
/* init table */
trav_table_init(&travt);
/* get the list of objects in the file */
@ -798,8 +772,7 @@ check_objects(const char* fname, pack_opt_t *options)
/* the input object names are present in the file and are valid */
if (h5trav_getindext(name, travt) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"%s Could not find <%s> in file <%s>. Exiting...\n",
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%s Could not find <%s> in file <%s>. Exiting...\n",
(options->verbose ? "\n" : ""), name, fname);
if (options->verbose)
HDprintf("...Found\n");
@ -825,27 +798,21 @@ check_objects(const char* fname, pack_opt_t *options)
}
else {
if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"H5Dopen2 failed");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
if ((sid = H5Dget_space(did)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"H5Dget_space failed");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"H5Sget_simple_extent_ndims failed");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
HDmemset(dims, 0, sizeof dims);
if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"H5Sget_simple_extent_dims failed");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
for (j = 0; j < rank; j++)
csize *= dims[j];
if (H5Sclose(sid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"H5Sclose failed");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if (H5Dclose(did) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
"H5Dclose failed");
} /* end else (chunk rank is 0) */
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
}
if (csize < ppb) {
HDprintf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");

138
tools/src/h5repack/h5repack_copy.c

@ -37,7 +37,7 @@
* local functions
*-------------------------------------------------------------------------
*/
static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
static int get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr);
static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
@ -145,8 +145,7 @@ copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
/* Adjust group creation parameters for root group */
/* (So that it is created in "dense storage" form) */
if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
(unsigned) options->grp_indexed) < 0)
if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed to adjust group creation parameters for root group");
for (i = 0; i < 5; i++) {
@ -368,7 +367,7 @@ done:
} /* end copy_objects() */
/*-------------------------------------------------------------------------
* Function: Get_hyperslab
* Function: get_hyperslab
*
* Purpose: Calulate a hyperslab from a dataset for higher performance.
* The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
@ -400,7 +399,7 @@ done:
*-----------------------------------------*/
int
Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
{
int ret_value = 0;
@ -521,7 +520,7 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
done:
return ret_value;
} /* end Get_hyperslab() */
} /* end get_hyperslab() */
/*-------------------------------------------------------------------------
* Function: do_copy_objects
@ -569,7 +568,7 @@ done:
* in (2) is that, when using the strip mine size, it assures that the "remaining" part
* of the dataset that does not fill an entire strip mine is processed.
*
* 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()).
* 1. figure out a hyperslab (dimentions) and size (refer to get_hyperslab()).
* 2. Calculate the hyperslab selections as the selection is moving forward.
* Selection would be same as the hyperslab except for the remaining edge portion
* of the dataset. The code take care of the remaining portion if exist.
@ -678,11 +677,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
}
else {
if (options->grp_compact > 0 || options->grp_indexed > 0)
if (H5Pset_link_phase_change(
gcpl_out,
(unsigned) options->grp_compact,
(unsigned) options->grp_indexed)
< 0)
if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed");
if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
@ -799,8 +794,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
}
else
if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) {
else if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) {
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
}
@ -847,25 +841,14 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
* changing to COMPACT. For the reference, COMPACT is limited
* by size 64K by library.
*/
if (options->layout_g != H5D_COMPACT) {
if (size_dset < options->min_comp) {
if (options->layout_g != H5D_COMPACT)
if (size_dset < options->min_comp)
apply_s = 0;
}
}
/* apply the filter */
if (apply_s) {
if (apply_filters(
travt->objs[i].name,
rank,
dims,
msize,
dcpl_out,
options,
&has_filter)
< 0)
if (apply_s)
if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, options, &has_filter) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed");
}
/* only if layout change requested for entire file or
* individual obj */
@ -904,36 +887,13 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
* modified dcpl; in that case use the original instead
*-------------------------------------------------------------------------
*/
dset_out = H5Dcreate2(fidout,
travt->objs[i].name,
wtype_id,
f_space_id,
H5P_DEFAULT,
dcpl_out,
H5P_DEFAULT);
/* if unable to create, retry with original DCPL */
if (dset_out < 0) {
H5Epush2(H5tools_ERR_STACK_g,
__FILE__,
FUNC,
__LINE__,
H5tools_ERR_CLS_g,
H5E_tools_g,
H5E_tools_min_id_g,
"H5Dcreate2 failed");
if (options->verbose) {
HDprintf(" warning: could not create dataset <%s>. Applying original settings\n",
travt->objs[i].name);
}
dset_out = H5Dcreate2(
fidout,
travt->objs[i].name,
wtype_id,
f_space_id,
H5P_DEFAULT,
dcpl_in,
H5P_DEFAULT);
if (dset_out < 0)
dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
if (dset_out == FAIL) {
H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
if (options->verbose)
HDprintf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name);
if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
apply_f = 0;
} /* end if retry dataset create */
@ -1003,15 +963,9 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
dcpl_tmp = dcpl_in; /* reading dataset */
}
if (Get_hyperslab(
dcpl_tmp,
rank,
dims,
p_type_nbytes,
hslab_dims,
&hslab_nbytes)
< 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed");
/* get hyperslab dims and size in byte */
if (get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "get_hyperslab failed");
hslab_buf = HDmalloc((size_t)hslab_nbytes);
if (hslab_buf == NULL)
@ -1033,30 +987,14 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*/
for (k = 0, hs_select_nelmts = 1; k < rank; k++) {
/* MIN() is used to get the remaining edge portion if exist.
* "dims[k] - hs_sel_offset[k]" is remaining edge portion that is
* smaller then the hyperslab.
*/
* "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
hs_select_nelmts *= hs_sel_count[k];
}
if (H5Sselect_hyperslab(
f_space_id,
H5S_SELECT_SET,
hs_sel_offset,
NULL,
hs_sel_count,
NULL)
< 0)
if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
if (H5Sselect_hyperslab(
hslab_space,
H5S_SELECT_SET,
zero,
NULL,
&hs_select_nelmts,
NULL)
< 0)
if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
} /* end if rank > 0 */
else {
@ -1065,25 +1003,12 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
hs_select_nelmts = 1;
} /* end (else) rank == 0 */
if (H5Dread(
dset_in,
wtype_id,
hslab_space,
f_space_id,
H5P_DEFAULT,
hslab_buf)
< 0)
if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
if (H5Dwrite(
dset_out,
wtype_id,
hslab_space,
f_space_id,
H5P_DEFAULT,
hslab_buf)
< 0)
if(H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
/* reclaim any VL memory, if necessary */
if (vl_data)
H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
@ -1129,11 +1054,8 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
/* print a message that the filter was not applied
* (in case there was a filter)
*/
if (has_filter && apply_s == 0) {
HDprintf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
travt->objs[i].name,
(int) options->min_comp);
}
if (has_filter && apply_s == 0)
HDprintf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp);
if (has_filter && apply_f == 0)
HDprintf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name);

10
tools/src/h5repack/h5repack_main.c

@ -237,11 +237,6 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, " Using latest file format with maximum compact group size of 10 and\n");
PRINTVALSTREAM(rawoutstream, " minimum shared datatype size of 20\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, "5) h5repack --low=0 --high=1 file1 file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via\n");
PRINTVALSTREAM(rawoutstream, " H5Pset_libver_bounds() when creating the repacked file, file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, "5) h5repack -f SHUF -f GZIP=1 file1 file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Add both filters SHUF and GZIP in this order to all datasets\n");
@ -250,6 +245,11 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Add bzip2 filter to all datasets\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, "7) h5repack --low=0 --high=1 file1 file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via\n");
PRINTVALSTREAM(rawoutstream, " H5Pset_libver_bounds() when creating the repacked file, file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
}
/*-------------------------------------------------------------------------

116
tools/src/misc/h5debug.c

@ -254,7 +254,7 @@ main(int argc, char *argv[])
uint8_t sig[H5F_SIGNATURE_LEN];
size_t u;
H5E_auto2_t func;
void *edata;
void *edata;
hbool_t api_ctx_pushed = FALSE; /* Whether API context pushed */
herr_t status = SUCCEED;
@ -274,8 +274,8 @@ main(int argc, char *argv[])
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/*
* Open the file and get the file descriptor.
*/
* Open the file and get the file descriptor.
*/
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
HDfprintf(stderr, "cannot create file access property list\n");
HDexit(1);
@ -309,8 +309,8 @@ main(int argc, char *argv[])
}
/*
* Parse command arguments.
*/
* Parse command arguments.
*/
if(argc > 2)
addr = (haddr_t)HDstrtoll(argv[2], NULL, 0);
if(argc > 3)
@ -323,8 +323,8 @@ main(int argc, char *argv[])
extra4 = (haddr_t)HDstrtoll(argv[6], NULL, 0);
/*
* Read the signature at the specified file position.
*/
* Read the signature at the specified file position.
*/
HDfprintf(stdout, "Reading signature at address %a (rel)\n", addr);
if(H5F_block_read(f, H5FD_MEM_SUPER, addr, sizeof(sig), sig) < 0) {
HDfprintf(stderr, "cannot read signature\n");
@ -332,28 +332,28 @@ main(int argc, char *argv[])
}
if(!HDmemcmp(sig, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN)) {
/*
* Debug the file's super block.
*/
* Debug the file's super block.
*/
status = H5F_debug(f, stdout, 0, VCOL);
} else if(!HDmemcmp(sig, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a local heap.
*/
* Debug a local heap.
*/
status = H5HL_debug(f, addr, stdout, 0, VCOL);
}
else if(!HDmemcmp (sig, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a global heap collection.
*/
* Debug a global heap collection.
*/
status = H5HG_debug(f, addr, stdout, 0, VCOL);
}
else if(!HDmemcmp(sig, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a symbol table node.
*/
* Debug a symbol table node.
*/
/* Check for extra parameters */
if(extra == 0) {
@ -367,10 +367,10 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a B-tree. B-trees are debugged through the B-tree
* subclass. The subclass identifier is the byte immediately
* after the B-tree signature.
*/
* Debug a B-tree. B-trees are debugged through the B-tree
* subclass. The subclass identifier is the byte immediately
* after the B-tree signature.
*/
H5B_subid_t subtype = (H5B_subid_t)sig[H5_SIZEOF_MAGIC];
unsigned ndims;
uint32_t dim[H5O_LAYOUT_NDIMS];
@ -435,8 +435,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a v2 B-tree header.
*/
* Debug a v2 B-tree header.
*/
const H5B2_class_t *cls = get_H5B2_class(sig);
HDassert(cls);
@ -452,8 +452,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a v2 B-tree internal node.
*/
* Debug a v2 B-tree internal node.
*/
const H5B2_class_t *cls = get_H5B2_class(sig);
HDassert(cls);
@ -479,8 +479,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a v2 B-tree leaf node.
*/
* Debug a v2 B-tree leaf node.
*/
const H5B2_class_t *cls = get_H5B2_class(sig);
HDassert(cls);
@ -505,15 +505,15 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a fractal heap header.
*/
* Debug a fractal heap header.
*/
status = H5HF_hdr_debug(f, addr, stdout, 0, VCOL);
}
else if(!HDmemcmp(sig, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a fractal heap direct block.
*/
* Debug a fractal heap direct block.
*/
/* Check for enough valid parameters */
if(extra == 0 || extra2 == 0) {
@ -528,8 +528,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a fractal heap indirect block.
*/
* Debug a fractal heap indirect block.
*/
/* Check for enough valid parameters */
if(extra == 0 || extra2 == 0) {
@ -544,16 +544,16 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a free space header.
*/
* Debug a free space header.
*/
status = H5FS_debug(f, addr, stdout, 0, VCOL);
}
else if(!HDmemcmp(sig, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug free space serialized sections.
*/
* Debug free space serialized sections.
*/
/* Check for enough valid parameters */
if(extra == 0 || extra2 == 0) {
@ -568,16 +568,16 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5SM_TABLE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug shared message master table.
*/
* Debug shared message master table.
*/
status = H5SM_table_debug(f, addr, stdout, 0, VCOL, (unsigned) UFAIL, (unsigned) UFAIL);
}
else if(!HDmemcmp(sig, H5SM_LIST_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug shared message list index.
*/
* Debug shared message list index.
*/
/* Check for enough valid parameters */
if(extra == 0) {
@ -592,8 +592,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug an extensible aray header.
*/
* Debug an extensible aray header.
*/
const H5EA_class_t *cls = get_H5EA_class(sig);
HDassert(cls);
@ -610,8 +610,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug an extensible aray index block.
*/
* Debug an extensible aray index block.
*/
const H5EA_class_t *cls = get_H5EA_class(sig);
HDassert(cls);
@ -628,8 +628,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug an extensible aray super block.
*/
* Debug an extensible aray super block.
*/
const H5EA_class_t *cls = get_H5EA_class(sig);
HDassert(cls);
@ -646,8 +646,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug an extensible aray data block.
*/
* Debug an extensible aray data block.
*/
const H5EA_class_t *cls = get_H5EA_class(sig);
HDassert(cls);
@ -664,8 +664,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a fixed array header.
*/
* Debug a fixed array header.
*/
const H5FA_class_t *cls = get_H5FA_class(sig);
HDassert(cls);
@ -682,8 +682,8 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug a fixed array data block.
*/
* Debug a fixed array data block.
*/
const H5FA_class_t *cls = get_H5FA_class(sig);
HDassert(cls);
@ -700,24 +700,24 @@ main(int argc, char *argv[])
}
else if(!HDmemcmp(sig, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
* Debug v2 object header (which have signatures).
*/
* Debug v2 object header (which have signatures).
*/
status = H5O_debug(f, addr, stdout, 0, VCOL);
}
else if(sig[0] == H5O_VERSION_1) {
/*
* This could be a v1 object header. Since they don't have a signature
* it's a somewhat "ify" detection.
*/
* This could be a v1 object header. Since they don't have a signature
* it's a somewhat "ify" detection.
*/
status = H5O_debug(f, addr, stdout, 0, VCOL);
}
else {
/*
* Got some other unrecognized signature.
*/
* Got some other unrecognized signature.
*/
HDprintf("%-*s ", VCOL, "Signature:");
for (u = 0; u < sizeof(sig); u++) {
if (sig[u] > ' ' && sig[u] <= '~' && '\\' != sig[u])

10
tools/test/h5repack/testfiles/h5repack-help.txt

@ -159,11 +159,6 @@ Examples of use:
Using latest file format with maximum compact group size of 10 and
minimum shared datatype size of 20
5) h5repack --low=0 --high=1 file1 file2
Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via
H5Pset_libver_bounds() when creating the repacked file, file2
5) h5repack -f SHUF -f GZIP=1 file1 file2
Add both filters SHUF and GZIP in this order to all datasets
@ -172,3 +167,8 @@ Examples of use:
Add bzip2 filter to all datasets
7) h5repack --low=0 --high=1 file1 file2
Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via
H5Pset_libver_bounds() when creating the repacked file, file2