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Take user block into account when returning chunk addresses
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Both H5Dchunk_iter() and H5Dget_chunk_info(_by_coord)() did not take
the size of the user block into account when reporting addresses. Since
the HDFGroup#1 use of these functions is to root around in the file for the raw
data, this is kind of a problem.

This is just the library changes. Tests will be in a future commit.
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@derobins
derobins committed Mar 15, 2024
1 parent c7c8b93 commit 866c712
Showing 1 changed file with 46 additions and 45 deletions.
91 changes: 46 additions & 45 deletions src/H5Dchunk.c
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Original file line number Diff line number Diff line change
Expand Up @@ -249,9 +249,10 @@ typedef struct H5D_chunk_coll_fill_info_t {
#endif /* H5_HAVE_PARALLEL */

typedef struct H5D_chunk_iter_ud_t {
H5D_chunk_iter_op_t op; /* User defined callback */
void *op_data; /* User data for user defined callback */
H5O_layout_chunk_t *chunk; /* Chunk layout */
H5D_chunk_iter_op_t op; /* User defined callback */
void *op_data; /* User data for user defined callback */
H5O_layout_chunk_t *chunk; /* Chunk layout */
haddr_t base_addr; /* Base address of the file, taking user block into account */
} H5D_chunk_iter_ud_t;

/********************/
Expand Down Expand Up @@ -7866,7 +7867,7 @@ H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
/*-------------------------------------------------------------------------
* Function: H5D__get_chunk_info_cb
*
* Purpose: Get the chunk info of the queried chunk, given by its index.
* Purpose: Get the chunk info of the queried chunk, given by its index
*
* Return: Success: H5_ITER_CONT or H5_ITER_STOP
* H5_ITER_STOP indicates the queried chunk is found
Expand Down Expand Up @@ -7917,21 +7918,18 @@ H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
* Note: Currently, the domain of the index in this function is of all
* the written chunks, regardless the dataspace.
*
* Return: Success: SUCCEED
* Failure: FAIL
*
* Return: SUCCEED/FAIL
*-------------------------------------------------------------------------
*/
herr_t
H5D__get_chunk_info(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_t chk_index, hsize_t *offset,
unsigned *filter_mask, haddr_t *addr, hsize_t *size)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_chunk_info_iter_ud_t udata; /* User data for callback */
const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
H5D_rdcc_ent_t *ent; /* Cache entry index */
hsize_t ii = 0; /* Dimension index */
herr_t ret_value = SUCCEED; /* Return value */
H5D_chk_idx_info_t idx_info; /* Chunked index info */
const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
H5D_rdcc_ent_t *ent; /* Cache entry index */
hsize_t ii = 0; /* Dimension index */
herr_t ret_value = SUCCEED; /* Return value */

FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)

Expand Down Expand Up @@ -7963,6 +7961,9 @@ H5D__get_chunk_info(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_

/* If the chunk is written, get its info, otherwise, return without error */
if (H5_addr_defined(idx_info.storage->idx_addr)) {

H5D_chunk_info_iter_ud_t udata;

/* Initialize before iteration */
udata.chunk_idx = chk_index;
udata.curr_idx = 0;
Expand All @@ -7983,14 +7984,14 @@ H5D__get_chunk_info(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
if (filter_mask)
*filter_mask = udata.filter_mask;
if (addr)
*addr = udata.chunk_addr;
*addr = udata.chunk_addr + H5F_BASE_ADDR(dset->oloc.file);
if (size)
*size = udata.nbytes;
if (offset)
for (ii = 0; ii < udata.ndims; ii++)
offset[ii] = udata.scaled[ii] * dset->shared->layout.u.chunk.dim[ii];
} /* end if */
} /* end if H5_addr_defined */
}
}

done:
FUNC_LEAVE_NOAPI_TAG(ret_value)
Expand Down Expand Up @@ -8055,12 +8056,11 @@ herr_t
H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned *filter_mask, haddr_t *addr,
hsize_t *size)
{
const H5O_layout_t *layout = NULL; /* Dataset layout */
const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
H5D_rdcc_ent_t *ent; /* Cache entry index */
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_chunk_info_iter_ud_t udata; /* User data for callback */
herr_t ret_value = SUCCEED; /* Return value */
const H5O_layout_t *layout = NULL; /* Dataset layout */
const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
H5D_rdcc_ent_t *ent; /* Cache entry index */
H5D_chk_idx_info_t idx_info; /* Chunked index info */
herr_t ret_value = SUCCEED; /* Return value */

FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)

Expand Down Expand Up @@ -8096,6 +8096,9 @@ H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned

/* If the dataset is not written, return without errors */
if (H5_addr_defined(idx_info.storage->idx_addr)) {

H5D_chunk_info_iter_ud_t udata;

/* Calculate the scaled of this chunk */
H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, udata.scaled);
udata.scaled[dset->shared->ndims] = 0;
Expand All @@ -8118,11 +8121,11 @@ H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned
if (filter_mask)
*filter_mask = udata.filter_mask;
if (addr)
*addr = udata.chunk_addr;
*addr = udata.chunk_addr + H5F_BASE_ADDR(dset->oloc.file);
if (size)
*size = udata.nbytes;
} /* end if */
} /* end if H5_addr_defined */
}
}

done:
FUNC_LEAVE_NOAPI_TAG(ret_value)
Expand All @@ -8131,33 +8134,32 @@ H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned
/*-------------------------------------------------------------------------
* Function: H5D__chunk_iter_cb
*
* Purpose: Call the user-defined function with the chunk data. The iterator continues if
* the user-defined function returns H5_ITER_CONT, and stops if H5_ITER_STOP is
* returned.
* Purpose: Call the user-defined function with the chunk data. The
* iterator continues if the user-defined function returns
* H5_ITER_CONT, and stops if H5_ITER_STOP is returned.
*
* Return: Success: H5_ITER_CONT or H5_ITER_STOP
* Failure: Negative (H5_ITER_ERROR)
*
*-------------------------------------------------------------------------
*/
static int
H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata)
{
const H5D_chunk_iter_ud_t *data = (H5D_chunk_iter_ud_t *)udata;
const H5O_layout_chunk_t *chunk = data->chunk;
int ret_value = H5_ITER_CONT;
const H5D_chunk_iter_ud_t *data = (H5D_chunk_iter_ud_t *)udata;
const H5O_layout_chunk_t *chunk = data->chunk;
hsize_t offset[H5O_LAYOUT_NDIMS];
unsigned ii; /* Match H5O_layout_chunk_t.ndims */
int ret_value = H5_ITER_CONT;

/* Similar to H5D__get_chunk_info */
for (ii = 0; ii < chunk->ndims; ii++)
offset[ii] = chunk_rec->scaled[ii] * chunk->dim[ii];
for (unsigned i = 0; i < chunk->ndims; i++)
offset[i] = chunk_rec->scaled[i] * chunk->dim[i];

FUNC_ENTER_PACKAGE_NOERR

/* Check for callback failure and pass along return value */
if ((ret_value = (data->op)(offset, (unsigned)chunk_rec->filter_mask, chunk_rec->chunk_addr,
(hsize_t)chunk_rec->nbytes, data->op_data)) < 0)
if ((ret_value =
(data->op)(offset, (unsigned)chunk_rec->filter_mask, data->base_addr + chunk_rec->chunk_addr,
(hsize_t)chunk_rec->nbytes, data->op_data)) < 0)
HERROR(H5E_DATASET, H5E_CANTNEXT, "iteration operator failed");

FUNC_LEAVE_NOAPI(ret_value)
Expand All @@ -8166,11 +8168,9 @@ H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata)
/*-------------------------------------------------------------------------
* Function: H5D__chunk_iter
*
* Purpose: Iterate over all the chunks in the dataset with given callback.
*
* Return: Success: Non-negative
* Failure: Negative
* Purpose: Iterate over all the chunks in the dataset with given callback
*
* Return: SUCCEED/FAIL
*-------------------------------------------------------------------------
*/
herr_t
Expand Down Expand Up @@ -8212,14 +8212,15 @@ H5D__chunk_iter(H5D_t *dset, H5D_chunk_iter_op_t op, void *op_data)
H5D_chunk_iter_ud_t ud;

/* Set up info for iteration callback */
ud.op = op;
ud.op_data = op_data;
ud.chunk = &dset->shared->layout.u.chunk;
ud.op = op;
ud.op_data = op_data;
ud.chunk = &dset->shared->layout.u.chunk;
ud.base_addr = H5F_BASE_ADDR(dset->oloc.file);

/* Iterate over the allocated chunks calling the iterator callback */
if ((ret_value = (layout->storage.u.chunk.ops->iterate)(&idx_info, H5D__chunk_iter_cb, &ud)) < 0)
HERROR(H5E_DATASET, H5E_CANTNEXT, "chunk iteration failed");
} /* end if H5_addr_defined */
}

done:
FUNC_LEAVE_NOAPI_TAG(ret_value)
Expand Down

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